Clinical Focus

  • Anatomic Pathology
  • Sarcoma

Academic Appointments

Professional Education

  • Residency:Stanford University School of Medicine Registrar (1994) CA
  • Fellowship:Stanford Hospital and Clinics (1994) CA
  • Board Certification: Anatomic Pathology, American Board of Pathology (1993)
  • Medical Education:Universiteit Van Amsterdam (1986) Netherlands

Research & Scholarship

Current Research and Scholarly Interests

Our research focuses on gene microarray analysis of human soft tissue tumors (sarcomas). In addition we work with tissue microarrays to characterize large numbers of novel antisera raised against peptides derived from genes found to be of interest during gene array analysis. These genes are not only identified in sarcomas but, through collaborations with other laboratories, also in a large number of other human neoplasms, including breast, kidney, prostate, lung, and liver tumors.


2018-19 Courses

Stanford Advisees


All Publications

  • Tissue-specific expression of the low-affinity IgG receptor, Fc gamma RIIb, on human Mast cells FRONTIERS IN IMMUNOLOGY Burton, O. T., Epp, A., Fanny, M. E., Miller, S. J., Stranks, A. J., Teague, J. E., Clark, R. A., van de Rijn, M., Oettgen, H. C. 2018; 9: 1244


    Immediate hypersensitivity reactions are induced by the interaction of allergens with specific IgE antibodies bound via FcεRI to mast cells and basophils. While these specific IgE antibodies are needed to trigger such reactions, not all individuals harboring IgE exhibit symptoms of allergy. The lack of responsiveness seen in some subjects correlates with the presence of IgG antibodies of the same specificity. In cell culture studies and in vivo animal models of food allergy and anaphylaxis such IgG antibodies have been shown to exert suppression via FcγRIIb. However, the reported absence of this inhibitory receptor on primary mast cells derived from human skin has raised questions about the role of IgG-mediated inhibition of immediate hypersensitivity in human subjects. Here, we tested the hypothesis that mast cell FcγRIIb expression might be tissue specific. Utilizing a combination of flow cytometry, quantitative PCR, and immunofluorescence staining of mast cells derived from the tissues of humanized mice, human skin, or in fixed paraffin-embedded sections of human tissues, we confirm that FcγRIIb is absent from dermal mast cells but is expressed by mast cells throughout the gastrointestinal tract. IgE-induced systemic anaphylaxis in humanized mice is strongly inhibited by antigen-specific IgG. These findings support the concept that IgG, signaling via FcγRIIb, plays a physiological role in suppressing hypersensitivity reactions.

    View details for DOI 10.3389/fimmu.2018.01244

    View details for Web of Science ID 000434282600001

    View details for PubMedID 29928276

    View details for PubMedCentralID PMC5997819

  • GFPT2-expressing cancer-associated fibroblasts mediate metabolic reprogramming in human lung adenocarcinoma. Cancer research Zhang, W., Bouchard, G., Yu, A., Shafiq, M., Jamali, M., Shrager, J. B., Ayers, K., Bakr, S., Gentles, A. J., Diehn, M., Quon, A., West, R. B., Nair, V., van de Rijn, M., Napel, S., Plevritis, S. K. 2018


    Metabolic reprogramming of the tumor microenvironment is recognized as a cancer hallmark. To identify new molecular processes associated with tumor metabolism, we analyzed the transcriptome of bulk and flow-sorted human primary non-small cell lung cancer (NSCLC) together with 18FDG-positron emission tomography scans, which provide a clinical measure of glucose uptake. Tumors with higher glucose uptake were functionally enriched for molecular processes associated with invasion in adenocarcinoma (AD) and cell growth in squamous cell carcinoma (SCC). Next, we identified genes correlated to glucose uptake that were predominately overexpressed in a single cell-type comprising the tumor microenvironment. For SCC, most of these genes were expressed by malignant cells, whereas in AD they were predominately expressed by stromal cells, particularly cancer-associated fibroblasts (CAFs). Among these AD genes correlated to glucose uptake, we focused on Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2), which codes for the Glutamine-Fructose-6-Phosphate Aminotransferase 2 (GFAT2), a rate-limiting enzyme of the hexosamine biosynthesis pathway (HBP), which is responsible for glycosylation. GFPT2 was predictive of glucose uptake independent of GLUT1, the primary glucose transporter, and was prognostically significant at both gene and protein level. We confirmed that normal fibroblasts transformed to CAF-like cells, following TGF-beta treatment, upregulated HBP genes, including GFPT2, with less change in genes driving glycolysis, pentose phosphate pathway and TCA cycle. Our work provides new evidence of histology-specific tumor-stromal properties associated with glucose uptake in NSCLC and identifies GFPT2 as a critical regulator of tumor metabolic reprogramming in AD.

    View details for DOI 10.1158/0008-5472.CAN-17-2928

    View details for PubMedID 29760045

  • Gene expression profiling of low-grade endometrial stromal sarcoma indicates fusion protein-mediated activation of the Wnt signaling pathway GYNECOLOGIC ONCOLOGY Przybyl, J., Kidzinski, L., Hastie, T., Debiec-Rychter, M., Nusse, R., van de Rijn, M. 2018; 149 (2): 388–93


    Low-grade endometrial stromal sarcomas (LGESS) harbor chromosomal translocations that affect proteins associated with chromatin remodeling Polycomb Repressive Complex 2 (PRC2), including SUZ12, PHF1 and EPC1. Roughly half of LGESS also demonstrate nuclear accumulation of β-catenin, which is a hallmark of Wnt signaling activation. However, the targets affected by the fusion proteins and the role of Wnt signaling in the pathogenesis of these tumors remain largely unknown.Here we report the results of a meta-analysis of three independent gene expression profiling studies on LGESS and immunohistochemical evaluation of nuclear expression of β-catenin and Lef1 in 112 uterine sarcoma specimens obtained from 20 LGESS and 89 LMS patients.Our results demonstrate that 143 out of 310 genes overexpressed in LGESS are known to be directly regulated by SUZ12. In addition, our gene expression meta-analysis shows activation of multiple genes implicated in Wnt signaling. We further emphasize the role of the Wnt signaling pathway by demonstrating concordant nuclear expression of β-catenin and Lef1 in 7/16 LGESS.Based on our findings, we suggest that LGESS-specific fusion proteins disrupt the repressive function of the PRC2 complex similar to the mechanism seen in synovial sarcoma, where the SS18-SSX fusion proteins disrupt the mSWI/SNF (BAF) chromatin remodeling complex. We propose that these fusion proteins in LGESS contribute to overexpression of Wnt ligands with subsequent activation of Wnt signaling pathway and formation of an active β-catenin/Lef1 transcriptional complex. These observations could lead to novel therapeutic approaches that focus on the Wnt pathway in LGESS.

    View details for DOI 10.1016/j.ygyno.2018.03.007

    View details for Web of Science ID 000432645000025

    View details for PubMedID 29544705

  • Vangl2/RhoA Signaling Pathway Regulates Stem Cell Self-Renewal Programs and Growth in Rhabdomyosarcoma CELL STEM CELL Hayes, M. N., McCarthy, K., Jin, A., Oliveira, M. L., Iyer, S., Garcia, S. P., Sindiri, S., Gryder, B., Motala, Z., Nielsen, G., Borg, J., De Rijn, M., Malkin, D., Khan, J., Ignatius, M. S., Langenau, D. M. 2018; 22 (3): 414-+


    Tumor growth and relapse are driven by tumor propagating cells (TPCs). However, mechanisms regulating TPC fate choices, maintenance, and self-renewal are not fully understood. Here, we show that Van Gogh-like 2 (Vangl2), a core regulator of the non-canonical Wnt/planar cell polarity (Wnt/PCP) pathway, affects TPC self-renewal in rhabdomyosarcoma (RMS)-a pediatric cancer of muscle. VANGL2 is expressed in a majority of human RMS and within early mononuclear progenitor cells. VANGL2 depletion inhibited cell proliferation, reduced TPC numbers, and induced differentiation of human RMS in vitro and in mouse xenografts. Using a zebrafish model of embryonal rhabdomyosarcoma (ERMS), we determined that Vangl2 expression enriches for TPCs and promotes their self-renewal. Expression of constitutively active and dominant-negative isoforms of RHOA revealed that it acts downstream of VANGL2 to regulate proliferation and maintenance of TPCs in human RMS. Our studies offer insights into pathways that control TPCs and identify new potential therapeutic targets.

    View details for DOI 10.1016/j.stem.2018.02.002

    View details for Web of Science ID 000426471000019

    View details for PubMedID 29499154

  • Circulating tumor DNA levels correlate with response to treatment in LMS patients Przybyl, J., Chabon, J. J., Spans, L., Ganjoo, K., Vennam, S., Newman, A. M., Forgo, E., Varma, S., Zhu, S., Debiec-Rychter, M., Alizadeh, A., Diehn, M., van de Rijn, M. AMER ASSOC CANCER RESEARCH. 2018: 38–39
  • Immunohistochemistry for PAX7 is a useful confirmatory marker for Ewing sarcoma in decalcified bone marrow core biopsy specimens. Virchows Archiv : an international journal of pathology Fernandez-Pol, S., van de Rijn, M., Natkunam, Y., Charville, G. W. 2018


    PAX7 has been recently demonstrated to be a highly sensitive marker for Ewing sarcoma, and thus far has only been shown to label a relatively small set of other mesenchymal neoplasms. Because the processing of bone marrow core biopsies can often hinder the performance of immunohistochemical stains, we set out to determine if our laboratory's PAX7 staining protocol effectively detects Ewing sarcoma in Bouin's fixed, decalcified bone marrow core biopsies. We stained ten core biopsies involved by Ewing sarcoma, nine non-involved core biopsies, and 13 core biopsies involved by histologic mimics of Ewing sarcoma. Only the ten biopsies involved by Ewing sarcoma and four biopsies with rhabdomyosarcoma showed strong nuclear PAX7 staining. None of the other tumors demonstrated PAX7 expression. This study demonstrates that the PAX7 staining protocol used in our laboratory is a useful marker for Ewing sarcoma and other PAX7-positive tumors in decalcified bone marrow core biopsies.

    View details for DOI 10.1007/s00428-018-2410-5

    View details for PubMedID 30014288

  • PAX7 expression in sarcomas bearing the EWSR1-NFATC2 translocation. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc Charville, G. W., Wang, W. L., Ingram, D. R., Roy, A., Thomas, D., Patel, R. M., Hornick, J. L., van de Rijn, M., Lazar, A. J. 2018

    View details for DOI 10.1038/s41379-018-0095-6

    View details for PubMedID 29985454

  • Combination approach for detecting different types of alterations in circulating tumor DNA in leiomyosarcoma. Clinical cancer research : an official journal of the American Association for Cancer Research Przybyl, J., Chabon, J. J., Spans, L., Ganjoo, K., Vennam, S., Newman, A. M., Forgó, E., Varma, S., Zhu, S., Debiec-Rychter, M., Alizadeh, A. A., Diehn, M., van de Rijn, M. 2018


    The clinical utility of circulating tumor DNA (ctDNA) monitoring has been shown in tumors that harbor highly recurrent mutations. Leiomyosarcoma (LMS) represents a type of tumor with a wide spectrum of heterogeneous genomic abnormalities; thus, targeting hotspot mutations or a narrow genomic region for ctDNA detection may not be practical. Here we demonstrate a combinatorial approach that integrates different sequencing protocols for the orthogonal detection of single nucleotide variants (SNVs), small indels and copy number alterations (CNAs) in ctDNA.We employed Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) for the analysis of SNVs and indels, together with a genome-wide interrogation of CNAs by Genome Representation Profiling (GRP). We profiled 28 longitudinal plasma samples and 25 tumor specimens from 7 patients with LMS.We detected ctDNA in 6 of 7 of these patients with >98% specificity for mutant allele fractions down to a level of 0.01%. We show that results from CAPP-Seq and GRP are highly concordant, and the combination of these methods allows for more comprehensive monitoring of ctDNA by profiling a wide spectrum of tumor-specific markers. By analyzing multiple tumor specimens in individual patients obtained from different sites and at different times during treatment, we observed clonal evolution of these tumors that was reflected by ctDNA profiles.Our strategy allows for a comprehensive monitoring of a broad spectrum of tumor-specific markers in plasma. Our approach may be clinically useful not only in LMS but also in other tumor types that lack recurrent genomic alterations.

    View details for DOI 10.1158/1078-0432.CCR-17-3704

    View details for PubMedID 29463554

  • Dystrophin is a tumor suppressor in peripheral nerve sheath tumors. Schaefer, I., Dufresne, A., Bahri, N., de Rooij, M. J., Yanofsky, S. M., Wang, Y., Raut, C. P., Baker, L. H., Marino-Enriquez, A., van de Rijn, M., Fletcher, J. A. AMER ASSOC CANCER RESEARCH. 2018: 62–63
  • Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas CELL Lazar, A. J., McLellan, M. D., Bailey, M. H., Miller, C. A., Appelbaum, E. L., Cordes, M. G., Fronick, C. C., Fulton, L. A., Fulton, R. S., Mardis, E. R., Schmidt, H. K., Wong, W., Wilson, R. K., Yellapantula, V., Radenbaugh, A. J., Hoadley, K. A., Hayes, D., Parker, J. S., Wilkerson, M. D., Auman, J., Balu, S., Bodenheimer, T., Hoyle, A. P., Jefferys, S. R., Jones, C. D., Lehmann, K., Meng, S., Mieczkowski, P. A., Mose, L. E., Perou, C. M., Roach, J., Senbabaoglu, Y., Shi, Y., Simons, J. V., Skelly, T., Soloway, M. G., Tan, D., Veluvolu, U., Davis, I. J., Hepperla, A. J., Brohl, A. S., Kasaian, K., Mungall, K., Sadeghi, S., Barthel, F. P., Verhaak, R., Hu, X., Chibon, F., Cherniack, A. D., Shih, J., Beroukhim, R., Meyerson, M., Cibulskis, C., Gabriel, S. B., Saksena, G., Schumacher, S. E., Bailey, M. H., Gao, Q., Wong, W., Wyczalkowski, M., Bowlby, R., Robertson, A., Ally, A., Balasundaram, M., Brooks, D., Carlsen, R., Chuah, E., Dhalla, N., Holt, R. A., Jones, S. M., Lee, D., Li, I., Ma, Y., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Parker, J. S., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Wong, T., Danilova, L., Cope, L., Baylin, S. B., Bootwalla, M. S., Lai, P. H., Laird, P. W., Maglinte, D. T., Van Den Berg, D. J., Weisenberger, D. J., Wrangle, J., Drill, E., Shen, R., Iype, L., Reynolds, S. M., Shmulevich, I., Yau, C., Armenia, J., Liu, E., Benz, C., Pastore, A., Sanchez-Vega, F., Schultz, N., Akbani, R., Hegde, A. M., Liu, W., Lu, Y., Mills, G. B., Weinstein, J. N., Roszik, J., Anur, P., Spellman, P., Abeshouse, A., Chen, H., Gao, J., Heins, Z., Kundra, R., Larsson, E., Ochoa, A., Sanchez-Vega, F., Sander, C., Schultz, N., Socci, N., Zhang, H., Noble, M. S., Heiman, D. I., Kim, J., Chin, L., Getz, G., Cho, J., Defreitas, T., Frazer, S., Gehlenborg, N., Lawrence, M. S., Lin, P., Meier, S., Voet, D., Zhang, H., Byers, L., Diao, L., Gay, C. M., Wang, J., Newton, Y., Cooper, L. D., Gutman, D. A., Lazar, A. J., Lee, S., Nalisnik, M., Bowen, J., Gastier-Foster, J. M., Gerken, M., Helsel, C., Hobensack, S., Leraas, K. M., Lichtenberg, T. M., Ramirez, N. C., Wise, L., Zmuda, E., Anderson, M. L., Castro, P., Ittmann, M., Gordienko, E., Paklina, O., Setdikova, G., Raut, C. P., Karlan, B. Y., Lester, J., Belyaev, D., Fulidou, V., Potapova, O., Voronina, O., Demetri, G. D., Ramalingam, S. S., Behera, M., Delman, K., Owonikoko, T. K., Sica, G. L., Boyd, J., Magliocco, A., Salner, A., Bennett, J., Iacocca, M., Swanson, P., Dottino, P., Kalir, T., Pereira, E., Akeredolu, T., Crain, D., Curley, E., Gardner, J., Mallery, D., Morris, S., Paulauskis, J., Penny, R., Shelton, C., Shelton, T., Thompson, E., Hoon, D. B., Parfitt, J., Birrer, M., Karseladze, A., Mariamidze, A., Dao, F., Levine, D. A., Olvera, N., Maki, R. G., Bartlett, J., Eschbacher, J., Dubina, M., Mozgovoy, E., Fedosenko, K., Manikhas, G., Sekhon, H., Ramirez, N., Lazar, A. J., Ingram, D. R., Torres, K. E., DiSaia, P., Godwin, A. K., Godwin, E. M., Kuo, H., Madan, R., Reilly, C., Adebamowo, C., Adebamowo, S. N., Bocklage, T., Higgins, K., Martinez, C., Auman, J., Boice, L., Grilley-Olson, J. E., Huang, M., Perou, A. H., Thorne, L. B., Rathmell, W., Gutmann, D. H., Singer, S., Chudamani, S., Liu, J., Lolla, L., Naresh, R., Pihl, T., Sun, Q., Wan, Y., Wu, Y., Felau, I., Zenklusen, J. C., Demchok, J. A., Ferguson, M. L., Hutter, C. M., Sofia, H. J., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Demicco, E. G., Doyle, L. A., Hornick, J. L., Lazar, A. J., Rubin, B. P., de Rijn, M., Demetri, G. D., Baker, L., Grilley-Olson, J. E., Iype, L., Lazar, A. J., Lichtenberg, T. M., Raut, C. P., Riedel, R. F., Demicco, E. G., Ding, L., Ladanyi, M., Lazar, A. J., Novak, J. E., Sanchez-Vega, F., Singer, S., Van Tine, B. A., Byers, L., Cope, L., Cherniack, A. D., Cooper, L. D., Davis, I. J., Davis, L. E., Demetri, G. D., Doyle, L. A., Drill, E., Godwin, A. K., Grilley-Olsen, J. E., Gutmann, D. H., Hayes, D., Hepperla, A. J., Hoadley, K. A., Hoon, D. B., Hornick, J. L., Iype, L., Kim, J., Maki, R. G., Pollock, R. E., Raut, C. P., Riedel, R. F., Robertson, A., Rubin, B. P., Shih, J., Weinstein, J. N., Wong, W., Akbani, R., Anderson, M. L., Anur, P., Bailey, M. H., Benz, C., Bowen, J., Bowlby, R., Brohl, A. S., Cherniack, A. D., Cooper, L. D., Cope, L., Danilova, L., Davis, L. E., Demetri, G. D., Gay, C. M., Godwin, A. K., Grilley-Olson, J. E., Gutman, D. A., Hegde, A. M., Jones, K. B., Kasaian, K., Ladanyi, M., Lazar, A. J., Lee, S., Leraas, K. M., Lichtenberg, T. M., Martignetti, J. A., McLellan, M. D., Miller, C. A., Mungall, K., Nalisnik, M., Noble, M. S., Raut, C. P., Riedel, R. F., Robertson, A., Roszik, J., Sadeghi, S., Sanchez-Vega, F., Shen, R., Shih, J., Tong, P., Torres, K. E., Yau, C., Zenklusen, J. C., Canc Genome Atlas Res Network 2017; 171 (4): 950-+


    Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types.

    View details for DOI 10.1016/j.cell.2017.10.014

    View details for Web of Science ID 000414250900021

    View details for PubMedID 29100075

    View details for PubMedCentralID PMC5693358

  • CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer NEW ENGLAND JOURNAL OF MEDICINE Dalerba, P., Sahoo, D., Paik, S., Guo, X., Yothers, G., Song, N., Wilcox-Fogel, N., Forgo, E., Rajendran, P. S., Miranda, S. P., Hisamori, S., Hutchison, J., Kalisky, T., Qian, D., Wolmark, N., Fisher, G. A., van de Rijn, M., Clarke, M. F. 2016; 374 (3): 211-222
  • KIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and Is Up-Regulated in a Subset of Human Colon Cancers. Gastroenterology Chen, E. C., Karl, T. A., Kalisky, T., Gupta, S. K., O'Brien, C. A., Longacre, T. A., van de Rijn, M., Quake, S. R., Clarke, M. F., Rothenberg, M. E. 2015; 149 (3): 705-17 e2


    Receptor tyrosine kinase (RTK) inhibitors have advanced colon cancer treatment. We investigated the role of the RTK KIT in development of human colon cancer.An array of 137 patient-derived colon tumors and their associated xenografts were analyzed by immunohistochemistry to measure levels of KIT and its ligand KITLG. KIT and/or KITLG was stably knocked down by expression of small hairpin RNAs from lentiviral vectors in DLD1, HT29, LS174T, and COLO320 DM colon cancer cell lines, and in UM-COLON#8 and POP77 xenografts; cells transduced with only vector were used as controls. Cells were analyzed by real-time quantitative reverse transcription polymerase chain reaction, single-cell gene expression analysis, flow cytometry, and immunohistochemical, immunoblot, and functional assays. Xenograft tumors were grown from control and KIT-knockdown DLD1 and UM-COLON#8 cells in immunocompromised mice and compared. Some mice were given the RTK inhibitor imatinib after injection of cancer cells; tumor growth was measured based on bioluminescence. We assessed tumorigenicity using limiting dilution analysis.KIT and KITLG were expressed heterogeneously by a subset of human colon tumors. Knockdown of KIT decreased proliferation of colon cancer cell lines and growth of xenograft tumors in mice compared with control cells. KIT knockdown cells had increased expression of enterocyte markers, decreased expression of cycling genes, and, unexpectedly, increased expression of LGR5 associated genes. No activating mutations in KIT were detected in DLD1, POP77, or UM-COLON#8 cells. However, KITLG-knockdown DLD1 cells formed smaller xenograft tumors than control cells. Gene expression analysis of single CD44(+) cells indicated that KIT can promote growth via KITLG autocrine and/or paracrine signaling. Imatinib inhibited growth of KIT(+) colon cancer organoids in culture and growth of xenograft tumors in mice. Cancer cells with endogenous KIT expression were more tumorigenic in mice.KIT and KITLG are expressed by a subset of human colon tumors. KIT signaling promotes growth of colon cancer cells and organoids in culture and xenograft tumors in mice via its ligand, KITLG, in an autocrine or paracrine manner. Patients with KIT-expressing colon tumors can benefit from KIT RTK inhibitors.

    View details for DOI 10.1053/j.gastro.2015.05.042

    View details for PubMedID 26026391

    View details for PubMedCentralID PMC4550533

  • Molecular subtyping of leiomyosarcoma with 3' end RNA sequencing. Genomics data Guo, X., Forgó, E., van de Rijn, M. 2015; 5: 366-367


    Leiomyosarcoma (LMS) is a malignant neoplasm with smooth muscle differentiation. Little is known about its molecular heterogeneity and no targeted therapy currently exists for LMS. We performed expression profiling on 99 cases of LMS with 3'end RNA sequencing (3SEQ) and demonstrated the existence of 3 molecular subtypes in this cohort. We consequently showed that these molecular subtypes are reproducible using an independent cohort of 82 LMS cases from TCGA. Two new formalin-fixed, paraffin-embedded (FFPE) tissue-compatible diagnostic immunohistochemical markers were identified for two of the three subtypes: LMOD1 for subtype I LMS and ARL4C for subtype II LMS. Subtype I and subtype II LMS were associated with good and poor prognosis, respectively. Here, we describe the details of LMS diagnosis, RNA isolation, 3SEQ library construction, 3SEQ sequencing data analysis and molecular subtype determination. The 3SEQ data produced in this study was deposited into Gene Expression Omnibus (GEO) under GSE45510.

    View details for PubMedID 26240788

    View details for PubMedCentralID PMC4521214

  • Clinically Relevant Molecular Subtypes in Leiomyosarcoma. Clinical cancer research Guo, X., Jo, V. Y., Mills, A. M., Zhu, S. X., Lee, C., Espinosa, I., Nucci, M. R., Varma, S., Forgó, E., Hastie, T., Anderson, S., Ganjoo, K., Beck, A. H., West, R. B., Fletcher, C. D., van de Rijn, M. 2015; 21 (15): 3501-3511


    Leiomyosarcoma is a malignant neoplasm with smooth muscle differentiation. Little is known about its molecular heterogeneity and no targeted therapy currently exists for leiomyosarcoma. Recognition of different molecular subtypes is necessary to evaluate novel therapeutic options. In a previous study on 51 leiomyosarcomas, we identified three molecular subtypes in leiomyosarcoma. The current study was performed to determine whether the existence of these subtypes could be confirmed in independent cohorts.Ninety-nine cases of leiomyosarcoma were expression profiled with 3'end RNA-Sequencing (3SEQ). Consensus clustering was conducted to determine the optimal number of subtypes.We identified 3 leiomyosarcoma molecular subtypes and confirmed this finding by analyzing publically available data on 82 leiomyosarcoma from The Cancer Genome Atlas (TCGA). We identified two new formalin-fixed, paraffin-embedded tissue-compatible diagnostic immunohistochemical markers; LMOD1 for subtype I leiomyosarcoma and ARL4C for subtype II leiomyosarcoma. A leiomyosarcoma tissue microarray with known clinical outcome was used to show that subtype I leiomyosarcoma is associated with good outcome in extrauterine leiomyosarcoma while subtype II leiomyosarcoma is associated with poor prognosis in both uterine and extrauterine leiomyosarcoma. The leiomyosarcoma subtypes showed significant differences in expression levels for genes for which novel targeted therapies are being developed, suggesting that leiomyosarcoma subtypes may respond differentially to these targeted therapies.We confirm the existence of 3 molecular subtypes in leiomyosarcoma using two independent datasets and show that the different molecular subtypes are associated with distinct clinical outcomes. The findings offer an opportunity for treating leiomyosarcoma in a subtype-specific targeted approach. Clin Cancer Res; 21(15); 3501-11. ©2015 AACR.

    View details for DOI 10.1158/1078-0432.CCR-14-3141

    View details for PubMedID 25896974

    View details for PubMedCentralID PMC4526352

  • Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor NEW ENGLAND JOURNAL OF MEDICINE Tap, W. D., Wainberg, Z. A., Anthony, S. P., Ibrahim, P. N., Zhang, C., Healey, J. H., Chmielowski, B., Staddon, A. P., Cohn, A. L., Shapiro, G. I., Keedy, V. L., Singh, A. S., Puzanov, I., Kwak, E. L., Wagner, A. J., Von Hoff, D. D., Weiss, G. J., Ramanathan, R. K., Zhang, J., Habets, G., Zhang, Y., Burton, E. A., VISOR, G., Sanftner, L., Severson, P., Nguyen, H., Kim, M. J., Marimuthu, A., Tsang, G., Shellooe, R., Gee, C., West, B. L., Hirth, P., Nolop, K., van de Rijn, M., Hsu, H. H., Peterfy, C., Lin, P. S., Tong-Starksen, S., Bollag, G. 2015; 373 (5): 428-437


    Expression of the colony-stimulating factor 1 (CSF1) gene is elevated in most tenosynovial giant-cell tumors. This observation has led to the discovery and clinical development of therapy targeting the CSF1 receptor (CSF1R).Using x-ray co-crystallography to guide our drug-discovery research, we generated a potent, selective CSF1R inhibitor, PLX3397, that traps the kinase in the autoinhibited conformation. We then conducted a multicenter, phase 1 trial in two parts to analyze this compound. In the first part, we evaluated escalations in the dose of PLX3397 that was administered orally in patients with solid tumors (dose-escalation study). In the second part, we evaluated PLX3397 at the chosen phase 2 dose in an extension cohort of patients with tenosynovial giant-cell tumors (extension study). Pharmacokinetic and tumor responses in the enrolled patients were assessed, and CSF1 in situ hybridization was performed to confirm the mechanism of action of PLX3397 and that the pattern of CSF1 expression was consistent with the pathological features of tenosynovial giant-cell tumor.A total of 41 patients were enrolled in the dose-escalation study, and an additional 23 patients were enrolled in the extension study. The chosen phase 2 dose of PLX3397 was 1000 mg per day. In the extension study, 12 patients with tenosynovial giant-cell tumors had a partial response and 7 patients had stable disease. Responses usually occurred within the first 4 months of treatment, and the median duration of response exceeded 8 months. The most common adverse events included fatigue, change in hair color, nausea, dysgeusia, and periorbital edema; adverse events rarely led to discontinuation of treatment.Treatment of tenosynovial giant-cell tumors with PLX3397 resulted in a prolonged regression in tumor volume in most patients. (Funded by Plexxikon; number, NCT01004861.).

    View details for DOI 10.1056/NEJMoa1411366

    View details for Web of Science ID 000358662200006

  • Leiomyosarcoma: One Disease or Distinct Biologic Entities Based on Site of Origin? JOURNAL OF SURGICAL ONCOLOGY Worhunsky, D. J., Gupta, M., Gholami, S., Tran, T. B., Ganjoo, K. N., van de Rijn, M., Visser, B. C., Norton, J. A., Poultsides, G. A. 2015; 111 (7): 808-812


    Leiomyosarcoma (LMS) can originate from the retroperitoneum, uterus, extremity, and trunk. It is unclear whether tumors of different origin represent discrete entities. We compared clinicopathologic features and outcomes following surgical resection of LMS stratified by site of origin.Patients with LMS undergoing resection at a single institution were retrospectively reviewed. Clinicopathologic variables were compared across sites. Survival was calculated using the Kaplan-Meier method and compared using log-rank and Cox regression analyses.From 1983 to 2011, 138 patients underwent surgical resection for LMS. Retroperitoneal and uterine LMS were larger, higher grade, and more commonly associated with synchronous metastases. However, disease-specific survival, recurrence-free survival, and recurrence patterns were not significantly different across the four sites. Synchronous metastases (HR 3.20, P < 0.001), but not site of origin, size, grade, or margin status, were independently associated with worse DSS. A significant number of recurrences and disease-related deaths were noted beyond 5 years.Although larger and higher grade, retroperitoneal and uterine LMS share similar survival and recurrence patterns with their trunk and extremity counterparts. LMS of various anatomic sites may not represent distinct disease processes based on clinical outcomes. The presence of metastatic disease remains the most important prognostic factor for LMS.

    View details for DOI 10.1002/jso.23904

    View details for Web of Science ID 000353996400003

    View details for PubMedID 25920434

  • Progressive loss of myogenic differentiation in leiomyosarcoma has prognostic value HISTOPATHOLOGY Demicco, E. G., Boland, G. M., Savannah, K. J., Lusby, K., Young, E. D., Ingram, D., Watson, K. L., Bailey, M., Guo, X., Hornick, J. L., van de Rijn, M., Wang, W., Torres, K. E., Lev, D., Lazar, A. J. 2015; 66 (5): 627-638


    Well-differentiated leiomyosarcomas show morphologically recognizable smooth muscle differentiation, whereas poorly differentiated tumours may form a spectrum with a subset of undifferentiated pleomorphic sarcomas. The expression of certain muscle markers has been reported to have prognostic impact. We investigated the correlation between the morphological spectrum and the muscle marker expression profile of leiomyosarcoma, and the impact of these factors on patient outcomes.Tissue microarrays including 202 non-uterine and 181 uterine leiomyosarcomas with a spectrum of tumour morphologies were evaluated for expression of immunohistochemical markers of muscle differentiation. Poorly differentiated tumours frequently lost one or more conventional smooth muscle markers [smooth muscle actin, desmin, h-caldesmon, and smooth muscle myosin (P < 0.0001)], as well as the more recently described markers SLMAP, MYLK, and ACTG2 (P < 0.0001). In primary tumours, both desmin and CFL2 expression predicted improved overall survival in multivariate analyses (P = 0.0111 and P = 0.043, respectively). Patients with muscle marker-enriched tumours (expressing all four conventional markers or any three of ACTG2, CFL2, CASQ2, MYLK, and SLMAP) had improved overall survival (P < 0.05) in univariate analyses.Morphologically and immunohistochemically, poorly differentiated leiomyosarcomas can masquerade as undifferentiated pleomorphic sarcomas with progressive loss of muscle markers. The expression of muscle markers has prognostic significance in primary leiomyosarcomas independently of tumour morphology.

    View details for DOI 10.1111/his.12466

    View details for Web of Science ID 000351378200002

    View details for PubMedID 24889065

  • A Role for Versican in the Development of Leiomyosarcoma JOURNAL OF BIOLOGICAL CHEMISTRY Keire, P. A., Bressler, S. L., Lemire, J. M., Edris, B., Rubin, B. P., Rahmani, M., McManus, B. M., van de Rijn, M., Wight, T. N. 2014; 289 (49): 34089-34103


    Leiomyosarcoma (LMS) is a mesenchymal cancer that occurs throughout the body. Although LMS is easily recognized histopathologically, the cause of the disease remains unknown. Versican, an extracellular matrix proteoglycan, increases in LMS. Microarray analyses of 80 LMSs and 24 leiomyomas showed a significant elevated expression of versican in human LMS versus benign leiomyomas. To explore the importance of versican in this smooth muscle cell tumor, we used versican-directed siRNA to knock down versican expression in a LMS human cell line, SK-LMS-1. Decreased versican expression was accompanied by slower rates of LMS cell proliferation and migration, increased adhesion, and decreased accumulation of the extracellular matrix macromolecule hyaluronan. Addition of purified versican to cells expressing versican siRNA restored cell proliferation to the level of LMS controls, increased the pericellular coat and the retention of hyaluronan, and decreased cell adhesion in a dose-dependent manner. The presence of versican was not only synergistic with hyaluronan in increasing cell proliferation, but the depletion of versican decreased hyaluronan synthase expression and decreased the retention of hyaluronan. When LMS cells stably expressing versican siRNA were injected into nude mice, the resulting tumors displayed significantly less versican and hyaluronan staining, had lower volumes, and had reduced levels of mitosis as compared with controls. Collectively, these results suggest a role for using versican as a point of control in the management and treatment of LMS.

    View details for DOI 10.1074/jbc.M114.607168

    View details for Web of Science ID 000346077600034

    View details for PubMedID 25320080

  • A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis. Nature cell biology Scheeren, F. A., Kuo, A. H., van Weele, L. J., Cai, S., Glykofridis, I., Sikandar, S. S., Zabala, M., Qian, D., Lam, J. S., Johnston, D., Volkmer, J. P., Sahoo, D., van de Rijn, M., Dirbas, F. M., Somlo, G., Kalisky, T., Rothenberg, M. E., Quake, S. R., Clarke, M. F. 2014; 16 (12): 1238-1248


    It has been postulated that there is a link between inflammation and cancer. Here we describe a role for cell-intrinsic toll-like receptor-2 (TLR2; which is involved in inflammatory response) signalling in normal intestinal and mammary epithelial cells and oncogenesis. The downstream effectors of TLR2 are expressed by normal intestinal and mammary epithelia, including the stem/progenitor cells. Deletion of MYD88 or TLR2 in the intestinal epithelium markedly reduces DSS-induced colitis regeneration and spontaneous tumour development in mice. Limiting dilution transplantations of breast epithelial cells devoid of TLR2 or MYD88 revealed a significant decrease in mammary repopulating unit frequency compared with the control. Inhibition of TLR2, its co-receptor CD14, or its downstream targets MYD88 and IRAK1 inhibits growth of human breast cancers in vitro and in vivo. These results suggest that inhibitors of the TLR2 pathway merit investigation as possible therapeutic and chemoprevention agents.

    View details for DOI 10.1038/ncb3058

    View details for PubMedID 25362351

  • A cell-intrinsic role for TLR2 MYD88 in intestinal and breast epithelia and oncogenesis NATURE CELL BIOLOGY Scheeren, F. A., Kuo, A. H., van Weele, L. J., Cai, S., Glykofridis, I., Sikandar, S. S., Zabala, M., Qian, D., Lam, J. S., Johnston, D., Volkmer, J. P., Sahoo, D., van de Rijn, M., Dirbas, F. M., Somlo, G., Kalisky, T., Rothenberg, M. E., Quake, S. R., Clarke, M. F. 2014; 16 (12): 1238-U245


    It has been postulated that there is a link between inflammation and cancer. Here we describe a role for cell-intrinsic toll-like receptor-2 (TLR2; which is involved in inflammatory response) signalling in normal intestinal and mammary epithelial cells and oncogenesis. The downstream effectors of TLR2 are expressed by normal intestinal and mammary epithelia, including the stem/progenitor cells. Deletion of MYD88 or TLR2 in the intestinal epithelium markedly reduces DSS-induced colitis regeneration and spontaneous tumour development in mice. Limiting dilution transplantations of breast epithelial cells devoid of TLR2 or MYD88 revealed a significant decrease in mammary repopulating unit frequency compared with the control. Inhibition of TLR2, its co-receptor CD14, or its downstream targets MYD88 and IRAK1 inhibits growth of human breast cancers in vitro and in vivo. These results suggest that inhibitors of the TLR2 pathway merit investigation as possible therapeutic and chemoprevention agents.

    View details for DOI 10.1038/ncb3058

    View details for Web of Science ID 000345777300014

    View details for PubMedID 25362351

  • Endoscopic molecular imaging of human bladder cancer using a CD47 antibody SCIENCE TRANSLATIONAL MEDICINE Pan, Y., Volkmer, J., Mach, K. E., Rouse, R. V., Liu, J., Sahoo, D., Chang, T. C., Metzner, T. J., Kang, L., van de Rijn, M., Skinner, E. C., Gambhir, S. S., Weissman, I. L., Liao, J. C. 2014; 6 (260)


    A combination of optical imaging technologies with cancer-specific molecular imaging agents is a potentially powerful strategy to improve cancer detection and enable image-guided surgery. Bladder cancer is primarily managed endoscopically by white light cystoscopy with suboptimal diagnostic accuracy. Emerging optical imaging technologies hold great potential for improved diagnostic accuracy but lack imaging agents for molecular specificity. Using fluorescently labeled CD47 antibody (anti-CD47) as molecular imaging agent, we demonstrated consistent identification of bladder cancer with clinical grade fluorescence imaging systems, confocal endomicroscopy, and blue light cystoscopy in fresh surgically removed human bladders. With blue light cystoscopy, the sensitivity and specificity for CD47-targeted imaging were 82.9 and 90.5%, respectively. We detected variants of bladder cancers, which are diagnostic challenges, including carcinoma in situ, residual carcinoma in tumor resection bed, recurrent carcinoma following prior intravesical immunotherapy with Bacillus Calmette-Guérin (BCG), and excluded cancer from benign but suspicious-appearing mucosa. CD47-targeted molecular imaging could improve diagnosis and resection thoroughness for bladder cancer.

    View details for DOI 10.1126/scitranslmed.3009457

    View details for Web of Science ID 000343920500006

  • Endoscopic molecular imaging of human bladder cancer using a CD47 antibody. Science translational medicine Pan, Y., Volkmer, J., Mach, K. E., Rouse, R. V., Liu, J., Sahoo, D., Chang, T. C., Metzner, T. J., Kang, L., van de Rijn, M., Skinner, E. C., Gambhir, S. S., Weissman, I. L., Liao, J. C. 2014; 6 (260): 260ra148-?


    A combination of optical imaging technologies with cancer-specific molecular imaging agents is a potentially powerful strategy to improve cancer detection and enable image-guided surgery. Bladder cancer is primarily managed endoscopically by white light cystoscopy with suboptimal diagnostic accuracy. Emerging optical imaging technologies hold great potential for improved diagnostic accuracy but lack imaging agents for molecular specificity. Using fluorescently labeled CD47 antibody (anti-CD47) as molecular imaging agent, we demonstrated consistent identification of bladder cancer with clinical grade fluorescence imaging systems, confocal endomicroscopy, and blue light cystoscopy in fresh surgically removed human bladders. With blue light cystoscopy, the sensitivity and specificity for CD47-targeted imaging were 82.9 and 90.5%, respectively. We detected variants of bladder cancers, which are diagnostic challenges, including carcinoma in situ, residual carcinoma in tumor resection bed, recurrent carcinoma following prior intravesical immunotherapy with Bacillus Calmette-Guérin (BCG), and excluded cancer from benign but suspicious-appearing mucosa. CD47-targeted molecular imaging could improve diagnosis and resection thoroughness for bladder cancer.

    View details for DOI 10.1126/scitranslmed.3009457

    View details for PubMedID 25355698

  • Geographic differences in the distribution of molecular subtypes of breast cancer in Brazil BMC WOMENS HEALTH Carvalho, F. M., Bacchi, L. M., Pincerato, K. M., van de Rijn, M., Bacchi, C. E. 2014; 14


    To compare the distribution of the intrinsic molecular subtypes of breast cancer based on immunohistochemical profile in the five major geographic regions of Brazil, a country of continental dimension, with a wide racial variation of people.The study was retrospective observational. We classified 5,687 invasive breast cancers by molecular subtype based on immunohistochemical expression of estrogen-receptor (ER), progesterone-receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki-67 proliferation index. Cases were classified as luminal A (ER and/or PR positive and HER2 negative, Ki-67 < 14%), luminal B (ER and/or PR positive, HER2 negative, and Ki-67 > 14%), triple-positive (ER and/or PR positive and HER2 positive), HER2-enriched (ER and PR negative, and HER2- positive), and triple-negative (TN) (ER negative, PR negative, and HER2- negative). Comparisons of the ages of patients and molecular subtypes between different geographic regions were performed.South and Southeast regions with a higher percentage of European ancestry and higher socioeconomic status presented with the highest proportion of luminal tumors. The North region presented with more aggressive subtypes (HER2-enriched and triple-negative), while the Central-West region predominated triple-positive carcinomas. The Northeast--a region with a high African influence--presented intermediate frequency of the different molecular subtypes. The differences persisted in subgroups of patients under and over 50 years.The geographic regions differ according to the distribution of molecular subtypes of breast cancer. However, other differences, beside those related to African ancestry, such as socioeconomic, climatic, nutritional, and geographic, have to be considered to explain our results. The knowledge of the differences in breast cancer characteristics among the geographic regions may help to organize healthcare programs in large countries like Brazil with diverse economic and race composition among different geographic regions.

    View details for DOI 10.1186/1472-6874-14-102

    View details for Web of Science ID 000341209200001

    View details for PubMedID 25174527

  • Dystrophin is a tumor suppressor in human cancers with myogenic programs. Nature genetics Wang, Y., Marino-Enriquez, A., Bennett, R. R., Zhu, M., Shen, Y., Eilers, G., Lee, J., Henze, J., Fletcher, B. S., Gu, Z., Fox, E. A., Antonescu, C. R., Fletcher, C. D., Guo, X., Raut, C. P., Demetri, G. D., van de Rijn, M., Ordog, T., Kunkel, L. M., Fletcher, J. A. 2014; 46 (6): 601-606


    Many common human mesenchymal tumors, including gastrointestinal stromal tumor (GIST), rhabdomyosarcoma (RMS) and leiomyosarcoma (LMS), feature myogenic differentiation. Here we report that intragenic deletion of the dystrophin-encoding and muscular dystrophy-associated DMD gene is a frequent mechanism by which myogenic tumors progress to high-grade, lethal sarcomas. Dystrophin is expressed in the non-neoplastic and benign counterparts of GIST, RMS and LMS tumors, and DMD deletions inactivate larger dystrophin isoforms, including 427-kDa dystrophin, while preserving the expression of an essential 71-kDa isoform. Dystrophin inhibits myogenic sarcoma cell migration, invasion, anchorage independence and invadopodia formation, and dystrophin inactivation was found in 96%, 100% and 62% of metastatic GIST, embryonal RMS and LMS samples, respectively. These findings validate dystrophin as a tumor suppressor and likely anti-metastatic factor, suggesting that therapies in development for muscular dystrophies may also have relevance in the treatment of cancer.

    View details for DOI 10.1038/ng.2974

    View details for PubMedID 24793134

  • Stromal signatures in endometrioid endometrial carcinomas MODERN PATHOLOGY Espinosa, I., Catasus, L., D'angelo, E., Mozos, A., Pedrola, N., Bertolo, C., Ferrer, I., Zannoni, G. F., West, R. B., van de Rijn, M., Matias-Guiu, X., Prat, J. 2014; 27 (4): 631-639


    The pattern of myometrial invasion in endometrioid endometrial carcinomas varies considerably; ie, from widely scattered glands and cell nests, often associated with a fibromyxoid stromal reaction (desmoplasia) and/or a lymphocytic infiltrate, to invasive glands with little or no stromal response. Recently, two distinct stromal signatures derived from a macrophage response (colony-stimulating factor 1, CSF1) and a fibroblastic response (desmoid-type fibromatosis, DTF) were identified in breast carcinomas and correlated with clinicopathologic features including outcome. In this study, we explored whether these stromal signatures also apply to endometrioid carcinomas and how their expression patterns correlated with morphologic changes. We studied the stromal signatures both by immunohistochemistry and in situ hybridization in 98 primary endometrioid carcinomas with (87 cases) and without (11 cases) myometrial invasion as well as in the corresponding regional lymph nodes metatases of 9 myoinvasive tumors. Desmoplasia correlated positively with the DTF expression signature. Likewise, mononuclear infiltrates were found in the stroma of tumors expressing CSF1. Twenty-four out of eighty-seven (27%) myoinvasive endometrioid carcinomas were positive for the macrophage signature and thirteen out of eighty-seven (15%) expressed the fibroblast signature. Eleven additional cases were positive for both DTF and CSF1 signatures (11/87; 13%). However, over half of the cases (39/87; 45%) and the majority of the non-myoinvasive tumors (8/11; 73%) failed to express any of the two stromal signatures. The macrophage response (CSF1) was associated with higher tumor grade, lymphovascular invasion, and PIK3CA mutations (P<0.05). There was a concordance in the expression of the CSF1 signature in the primary tumors and their corresponding lymph node metastases. This study is the first characterization of stromal signatures in endometrioid carcinomas. Our findings shed new light on the relationship between genetically different endometrioid carcinomas and various stromal responses. Preservation of the CSF1 macrophage stromal response in the metastases leds support to targeting the CSF1 pathway in endometrioid endometrial carcinomas.

    View details for DOI 10.1038/modpathol.2013.131

    View details for Web of Science ID 000334014200016

    View details for PubMedID 24263966

  • Stromal responses among carcinomas--response. Clinical cancer research West, R. B., van de Rijn, M., Chen, J. L. 2014; 20 (5): 1397-?

    View details for DOI 10.1158/1078-0432.CCR-13-3238

    View details for PubMedID 24590889

  • Molecular pathological analysis of sarcomas using paraffin-embedded tissue: current limitations and future possibilities HISTOPATHOLOGY van de Rijn, M., Guo, X., Sweeney, R. T., Beck, A. H., West, R. B. 2014; 64 (1): 163-170


    Sarcomas of soft tissue and bone are rare neoplasms that can be separated into a large number of different diagnostic entities. Over the years, a number of diagnostic markers have been developed that aid pathologists in reaching the appropriate diagnoses. Many of these markers are sarcoma-specific proteins that can be detected by immunohistochemistry in formalin-fixed, paraffin-embedded (FFPE) sections. In addition, a wide range of molecular studies have been developed that can detect gene mutations, gene amplifications or chromosomal translocations in FFPE material. Until recently, most sequencing-based approaches relied on the availability of fresh frozen tissue. However, with the advent of next-generation sequencing technologies, FFPE material is increasingly being used as a tool to identify novel immunohistochemistry markers, gene mutations, and chromosomal translocations, and to develop diagnostic tests.

    View details for DOI 10.1111/his.12290

    View details for Web of Science ID 000328219100013

    View details for PubMedID 24107169

  • Stromal Responses among Common Carcinomas Correlated with Clinicopathologic Features. Clinical cancer research Chen, J. L., Espinosa, I., Lin, A. Y., Liao, O. Y., van de Rijn, M., West, R. B. 2013; 19 (18): 5127-5135


    We have previously characterized a tumor stroma expression signature in a subset of breast tumors that correlates with better clinical outcome. The purpose of this study is to determine whether this stromal signature, termed the DTF fibroblast signature, is specific to breast cancer or is a common stromal response found in different types of cancer. Experimental Designs: The DTF fibroblast signature was applied to gene expression profiles from five ovarian, five lung, two colon and three prostate cancer expression microarray datasets. Additionally, two different tissue microarrays of 204 ovarian tumors and 140 colon tumors were examined for the expression of previously characterized protein markers of DTF fibroblast signature. The DTF fibroblast stromal response was then correlated with clinicopathologic features.The DTF fibroblast signature is robustly present in ovarian, lung, and colon carcinomas. Both expression microarray data and immunohistochemistry show the subset of ovarian tumors with strong DTF fibroblast signature expression has statistically significant worse survival outcomes. No reproducible survival differences were found in either the lung or the colon cancers. The prostate cancers failed to demonstrate a DTF fibroblast signature. Multi-variant analysis showed that DTF fibroblast signature was significantly more prognostic than the proliferation status in ovarian carcinomas.Our results suggest that the DTF fibroblast signature is a common tumor stroma signature in different types of cancer including ovarian, lung and colon carcinomas. Our findings provide further insight into the DTF fibroblast stromal responses across different types of carcinomas and their potential as prognostic and therapeutic targets.

    View details for DOI 10.1158/1078-0432.CCR-12-3127

    View details for PubMedID 23804424

  • Engineered SIRPa variants as immunotherapeutic adjuvants to anticancer antibodies. Science Weiskopf, K., Ring, A. M., Ho, C. C., Volkmer, J., Levin, A. M., Volkmer, A. K., Ozkan, E., Fernhoff, N. B., van de Rijn, M., Weissman, I. L., Garcia, K. C. 2013; 341 (6141): 88-91


    CD47 is an antiphagocytic signal that cancer cells employ to inhibit macrophage-mediated destruction. Here, we modified the binding domain of human SIRPα, the receptor for CD47, for use as a CD47 antagonist. We engineered high-affinity SIRPα variants with approximately 50,000-fold increased affinity for human CD47 relative to wild-type SIRPα. As high-affinity SIRPα monomers, they potently antagonized CD47 on cancer cells but did not induce macrophage phagocytosis on their own. Instead, they exhibited remarkable synergy with all tumor-specific monoclonal antibodies tested by increasing phagocytosis in vitro and enhancing antitumor responses in vivo. This "one-two punch" directs immune responses against tumor cells while lowering the threshold for macrophage activation, thereby providing a universal method for augmenting the efficacy of therapeutic anticancer antibodies.

    View details for DOI 10.1126/science.1238856

    View details for PubMedID 23722425

  • Engineered SIRP alpha Variants as Immunotherapeutic Adjuvants to Anticancer Antibodies SCIENCE Weiskopf, K., Ring, A. M., Ho, C. C., Volkmer, J., Levin, A. M., Volkmer, A. K., Oezkan, E., Fernhoff, N. B., van de Rijn, M., Weissman, I. L., Garcia, K. C. 2013; 341 (6141): 88-91
  • Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations. American journal of surgical pathology Sweeney, R. T., Zhang, B., Zhu, S. X., Varma, S., Smith, K. S., Montgomery, S. B., van de Rijn, M., Zehnder, J., West, R. B. 2013; 37 (6): 796-803


    Somatic mutations, often translocations or single nucleotide variations, are pathognomonic for certain types of cancers and are increasingly of clinical importance for diagnosis and prediction of response to therapy. Conventional clinical assays only evaluate 1 mutation at a time, and targeted tests are often constrained to identify only the most common mutations. Genome-wide or transcriptome-wide high-throughput sequencing (HTS) of clinical samples offers an opportunity to evaluate for all clinically significant mutations with a single test. Recently a "desktop version" of HTS has become available, but most of the experience to date is based on data obtained from high-quality DNA from frozen specimens. In this study, we demonstrate, as a proof of principle, that translocations in sarcomas can be diagnosed from formalin-fixed paraffin-embedded (FFPE) tissue with desktop HTS. Using the first generation MiSeq platform, full transcriptome sequencing was performed on FFPE material from archival blocks of 3 synovial sarcomas, 3 myxoid liposarcomas, 2 Ewing sarcomas, and 1 clear cell sarcoma. Mapping the reads to the "sarcomatome" (all known 83 genes involved in translocations and mutations in sarcoma) and using a novel algorithm for ranking fusion candidates, the pathognomonic fusions and the exact breakpoints were identified in all cases of synovial sarcoma, myxoid liposarcoma, and clear cell sarcoma. The Ewing sarcoma fusion gene was detectable in FFPE material only with a sequencing platform that generates greater sequencing depth. The results show that a single transcriptome HTS assay, from FFPE, has the potential to replace conventional molecular diagnostic techniques for the evaluation of clinically relevant mutations in cancer.

    View details for DOI 10.1097/PAS.0b013e31827ad9b2

    View details for PubMedID 23598961

  • Use of a KIT-specific monoclonal antibody to bypass imatinib resistance in gastrointestinal stromal tumors ONCOIMMUNOLOGY Edris, B., Willingham, S., Weiskopf, K., Volkmer, A. K., Volkmer, J., Muehlenberg, T., Weissman, I. L., van de Rijn, M. 2013; 2 (6)

    View details for DOI 10.4161/onci.24452

    View details for Web of Science ID 000322060900007

  • Post-Transcriptional Dysregulation by miRNAs Is Implicated in the Pathogenesis of Gastrointestinal Stromal Tumor [GIST] PLOS ONE Kelly, L., Bryan, K., Kim, S. Y., Janeway, K. A., Killian, J. K., Schildhaus, H., Miettinen, M., Helman, L., Meltzer, P. S., van de Rijn, M., Debiec-Rychter, M., O'Sullivan, M. 2013; 8 (5)


    In contrast to adult mutant gastrointestinal stromal tumors [GISTs], pediatric/wild-type GISTs remain poorly understood overall, given their lack of oncogenic activating tyrosine kinase mutations. These GISTs, with a predilection for gastric origin in female patients, show limited response to therapy with tyrosine kinase inhibitors and generally pursue a more indolent course, but still may prove fatal. Defective cellular respiration appears to underpin tumor development in these wild-type cases, which as a group lack expression of succinate dehydrogenase [SDH] B, a surrogate marker for respiratory chain metabolism. Yet, only a small subset of the wild-type tumors show mutations in the genes coding for the SDH subunits [SDHx]. To explore additional pathogenetic mechanisms in these wild-type GISTs, we elected to investigate post-transcriptional regulation of these tumors by conducting microRNA (miRNA) profiling of a mixed cohort of 73 cases including 18 gastric pediatric wild-type, 25 (20 gastric, 4 small bowel and 1 retroperitoneal) adult wild-type GISTs and 30 gastric adult mutant GISTs. By this approach we have identified distinct signatures for GIST subtypes which correlate tightly with clinico-pathological parameters. A cluster of miRNAs on 14q32 show strikingly different expression patterns amongst GISTs, a finding which appears to be explained at least in part by differential allelic methylation of this imprinted region. Small bowel and retroperitoneal wild-type GISTs segregate with adult mutant GISTs and express SDHB, while adult wild-type gastric GISTs are dispersed amongst adult mutant and pediatric wild-type cases, clustering in this situation on the basis of SDHB expression. Interestingly, global methylation analysis has recently similarly demonstrated that these wild-type, SDHB-immunonegative tumors show a distinct pattern compared with KIT and PDGFRA mutant tumors, which as a rule do express SDHB. All cases with Carney triad within our cohort cluster together tightly.

    View details for DOI 10.1371/journal.pone.0064102

    View details for Web of Science ID 000319385300026

    View details for PubMedID 23717541

  • Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS genetics Giacomini, C. P., Sun, S., Varma, S., Shain, A. H., Giacomini, M. M., Balagtas, J., Sweeney, R. T., Lai, E., Del Vecchio, C. A., Forster, A. D., Clarke, N., Montgomery, K. D., Zhu, S., Wong, A. J., van de Rijn, M., West, R. B., Pollack, J. R. 2013; 9 (4)


    Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a "breakpoint analysis" pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis.

    View details for DOI 10.1371/journal.pgen.1003464

    View details for PubMedID 23637631

    View details for PubMedCentralID PMC3636093

  • Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS genetics Giacomini, C. P., Sun, S., Varma, S., Shain, A. H., Giacomini, M. M., Balagtas, J., Sweeney, R. T., Lai, E., Del Vecchio, C. A., Forster, A. D., Clarke, N., Montgomery, K. D., Zhu, S., Wong, A. J., van de Rijn, M., West, R. B., Pollack, J. R. 2013; 9 (4)

    View details for DOI 10.1371/journal.pgen.1003464

    View details for PubMedID 23637631

  • Anti-KIT monoclonal antibody inhibits imatinib-resistant gastrointestinal stromal tumor growth PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Edris, B., Willingham, S. B., Weiskopf, K., Volkmer, A. K., Volkmer, J., Muehlenberg, T., Montgomery, K. D., Contreras-Trujillo, H., Czechowicz, A., Fletcher, J. A., West, R. B., Weissman, I. L., van de Rijn, M. 2013; 110 (9): 3501-3506


    Gastrointestinal stromal tumor (GIST) is the most common sarcoma of the gastrointestinal tract and arises from the interstitial cells of Cajal. It is characterized by expression of the receptor tyrosine kinase CD117 (KIT). In 70-80% of GIST cases, oncogenic mutations in KIT are present, leading to constitutive activation of the receptor, which drives the proliferation of these tumors. Treatment of GIST with imatinib, a small-molecule tyrosine kinase inhibitor, inhibits KIT-mediated signaling and initially results in disease control in 70-85% of patients with KIT-positive GIST. However, the vast majority of patients eventually develop resistance to imatinib treatment, leading to disease progression and posing a significant challenge in the clinical management of these tumors. Here, we show that an anti-KIT monoclonal antibody (mAb), SR1, is able to slow the growth of three human GIST cell lines in vitro. Importantly, these reductions in cell growth were equivalent between imatinib-resistant and imatinib-sensitive GIST cell lines. Treatment of GIST cell lines with SR1 reduces cell-surface KIT expression, suggesting that mAb-induced KIT down-regulation may be a mechanism by which SR1 inhibits GIST growth. Furthermore, we also show that SR1 treatment enhances phagocytosis of GIST cells by macrophages, indicating that treatment with SR1 may enhance immune cell-mediated tumor clearance. Finally, using two xenotransplantation models of imatinib-sensitive and imatinib-resistant GIST, we demonstrate that SR1 is able to strongly inhibit tumor growth in vivo. These results suggest that treatment with mAbs targeting KIT may represent an alternative, or complementary, approach for treating GIST.

    View details for DOI 10.1073/pnas.1222893110

    View details for Web of Science ID 000315841900062

    View details for PubMedID 23382202

    View details for PubMedCentralID PMC3587280

  • Modeling Clear Cell Sarcomagenesis in the Mouse: Cell of Origin Differentiation State Impacts Tumor Characteristics CANCER CELL Straessler, K. M., Jones, K. B., Hu, H., Jin, H., van de Rijn, M., Capecchi, M. R. 2013; 23 (2): 215-227


    Clear cell sarcoma (CCS) of tendons and aponeuroses is a deadly soft-tissue malignancy resembling melanoma, with a predilection for young adults. EWS-ATF1, the fusion product of a balanced chromosomal translocation between chromosomes 22 and 12, is considered the definitional feature of the tumor. Conditional expression of the EWS-ATF1 human cDNA in the mouse generates CCS-like tumors with 100% penetrance. Tumors, developed through varied means of initiating expression of the fusion oncogene, model human CCS morphologically, immunohistochemically, and by genome-wide expression profiling. We also demonstrate that although fusion oncogene expression in later stages of differentiation can transform mesenchymal progenitor cells and generate tumors resembling CCS generally, expression in cells retaining stem cell markers permits the full melanoma-related phenotype.

    View details for DOI 10.1016/j.ccr.2012.12.019

    View details for Web of Science ID 000315067700011

    View details for PubMedID 23410975

    View details for PubMedCentralID PMC3640275

  • Two New Stromal Signatures Stratify Breast Cancers with Different Prognosis 102nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP) Guo, X., Zhu, S. X., Montgomery, K., van de Rijn, M., West, R. B. NATURE PUBLISHING GROUP. 2013: 434A–435A
  • Desktop Transcriptome Sequencing from Archival Tissue To Identify Clinically Relevant Translocations 102nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP) SWEENEY, R. T., Zhang, B., Zhu, S. X., Varma, S., Smith, K., Montgomery, S. B., van de Rijn, M., Zehnder, J., West, R. B. NATURE PUBLISHING GROUP. 2013: 438A–438A
  • ROR2 Expression in Breast Cancer 102nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP) Guo, X., Sweeny, P., Varma, S., Montgomery, K., West, R. B., van de Rijn, M. NATURE PUBLISHING GROUP. 2013: 45A–45A
  • Next generation sequencing-based expression profiling identifies signatures from benign stromal proliferations that define stromal components of breast cancer BREAST CANCER RESEARCH Guo, X., Zhu, S. X., Brunner, A. L., van de Rijn, M., West, R. B. 2013; 15 (6)


    Multiple studies have shown that the tumor microenvironment (TME) of carcinomas can play an important role in the initiation, progression, and metastasis of cancer. Here we test the hypothesis that specific benign fibrous soft tissue tumor gene expression profiles may represent distinct stromal fibroblastic reaction types that occur in different breast cancers. The discovered stromal profiles could classify breast cancer based on the type of stromal reaction patterns in the TME.Next generation sequencing-based gene expression profiling (3SEQ) was performed on formalin fixed, paraffin embedded (FFPE) samples of 10 types of fibrous soft tissue tumors. We determined the extent to which these signatures could identify distinct subsets of breast cancers in four publicly available breast cancer datasets.A total of 53 fibrous tumors were sequenced by 3SEQ with an average of 29 million reads per sample. Both the gene signatures derived from elastofibroma (EF) and fibroma of tendon sheath (FOTS) demonstrated robust outcome results for survival in the four breast cancer datasets. The breast cancers positive for the EF signature (20-33% of the cohort) demonstrated significantly better outcome for survival. In contrast, the FOTS signature-positive breast cancers (11-35% of the cohort) had a worse outcome.We defined and validated two new stromal signatures in breast cancer (EF and FOTS), which are significantly associated with prognosis. Our group has previously identified novel cancer stromal gene expression signatures associated with outcome differences in breast cancer by gene expression profiling of three soft tissue tumors, desmoid-type fibromatosis (DTF), solitary fibrous tumor (SFT), and tenosynovial giant cell tumor (TGCT/CSF1), as surrogates for stromal expression patterns. By combining the stromal signatures of EF and FOTS, with our previously identified DTF and TGCT/CSF1 signatures we can now characterize clinically relevant stromal expression profiles in the TME for between 74% to 90% of all breast cancers.

    View details for DOI 10.1186/bcr3586

    View details for Web of Science ID 000331544200013

    View details for PubMedCentralID PMC3978842

  • CDX2 is an amplified lineage-survival oncogene in colorectal cancer PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Salari, K., Spulak, M. E., Cuff, J., Forster, A. D., Giacomini, C. P., Huang, S., Ko, M. E., Lin, A. Y., van de Rijn, M., Pollack, J. R. 2012; 109 (46): E3196-E3205


    The mutational activation of oncogenes drives cancer development and progression. Classic oncogenes, such as MYC and RAS, are active across many different cancer types. In contrast, "lineage-survival" oncogenes represent a distinct and emerging class typically comprising transcriptional regulators of a specific cell lineage that, when deregulated, support the proliferation and survival of cancers derived from that lineage. Here, in a large collection of colorectal cancer cell lines and tumors, we identify recurrent amplification of chromosome 13, an alteration highly restricted to colorectal-derived cancers. A minimal region of amplification on 13q12.2 pinpoints caudal type homeobox transcription factor 2 (CDX2), a regulator of normal intestinal lineage development and differentiation, as a target of the amplification. In contrast to its described role as a colorectal tumor suppressor, CDX2 when amplified is required for the proliferation and survival of colorectal cancer cells. Further, transcriptional profiling, binding-site analysis, and functional studies link CDX2 to Wnt/β-catenin signaling, itself a key oncogenic pathway in colorectal cancer. These data characterize CDX2 as a lineage-survival oncogene deregulated in colorectal cancer. Our findings challenge a prevailing view that CDX2 is a tumor suppressor in colorectal cancer and uncover an additional piece in the multistep model of colorectal tumorigenesis.

    View details for DOI 10.1073/pnas.1206004109

    View details for Web of Science ID 000311576300010

    View details for PubMedID 23112155

    View details for PubMedCentralID PMC3503165

  • Flipping the script on macrophages in leiomyosarcoma ONCOIMMUNOLOGY Edris, B., Weiskopf, K., Weissman, I. L., van de Rijn, M. 2012; 1 (7): 1202-1204


    Macrophages promote the growth of leiomyosarcoma (LMS), a malignant soft-tissue tumor. CD47 on tumor cells binds to the macrophagic receptor signal regulatory protein α (SIRPα) and prevents phagocytosis. We showed that anti-CD47 monoclonal antibodies (mAbs) allow macrophages to engulf LMS cells and prevent tumor growth and metastases. Therefore, anti-CD47 mAbs represent a promising targeted immunotherapy for LMS.

    View details for DOI 10.4161/onci.20799

    View details for Web of Science ID 000316279900033

  • Cyclin D1 as a Diagnostic Immunomarker for Endometrial Stromal Sarcoma With YWHAE-FAM22 Rearrangement AMERICAN JOURNAL OF SURGICAL PATHOLOGY Lee, C., Ali, R. H., Rouzbahman, M., Marino-Enriquez, A., Zhu, M., Guo, X., Brunner, A. L., Chiang, S., Leung, S., Nelnyk, N., Huntsman, D. G., Gilks, C. B., Nielsen, T. O., Dal Cin, P., van de Rijn, M., Oliva, E., Fletcher, J. A., Nucci, M. R. 2012; 36 (10): 1562-1570


    Endometrial stromal sarcoma (ESS) characterized by YWHAE-FAM22 genetic fusion is histologically higher grade and clinically more aggressive than ESS with JAZF1-SUZ12 or equivalent genetic rearrangements, hence it is clinically important to recognize this subset of ESS. To identify diagnostic immunomarkers for this biologically defined ESS subset, we compared gene expression profiles between YWHAE-FAM22 ESS and JAZF1-rearranged ESS. These studies showed consistent upregulation of cyclin D1 in YWHAE-FAM22 ESS compared with JAZF1-SUZ12 ESS. Immunohistochemically, the high-grade round cell component of all 12 YWHAE-FAM22 ESS demonstrated diffuse (≥70%) moderate to strong nuclear cyclin D1 staining, and this diffuse positivity was not seen in 34 ESSs with JAZF1 and equivalent genetic rearrangements or in 21 low-grade ESS with no demonstrable genetic rearrangements. In a series of 243 non-ESS pure uterine mesenchymal and mixed epithelial-mesenchymal tumors, only 2 of 8 undifferentiated endometrial sarcomas with nuclear uniformity and 1 of 80 uterine leiomyosarcomas demonstrate diffuse cyclin D1 immunoreactivity. Both cyclin D1-positive undifferentiated endometrial sarcomas showed diffuse strong CD10 staining, which is consistently absent in the high-grade round cell component of YWHAE-FAM22 ESS. The low-grade spindle cell component of YWHAE-FAM22 ESS showed a spatially heterogenous cyclin D1 staining pattern that was weaker and less diffuse overall. Our findings indicate that cyclin D1 is a sensitive and specific diagnostic immunomarker for YWHAE-FAM22 ESS. When evaluating high-grade uterine sarcomas, cyclin D1 can be included in the immunohistochemical panel as an indicator of YWHAE-FAM22 ESS.

    View details for DOI 10.1097/PAS.0b013e31825fa931

    View details for Web of Science ID 000309115100018

    View details for PubMedID 22982899

    View details for PubMedCentralID PMC3444748

  • Sox10 and S100 in the Diagnosis of Soft-tissue Neoplasms APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY Karamchandani, J. R., Nielsen, T. O., van de Rijn, M., West, R. B. 2012; 20 (5): 445-450


    Despite a well-characterized lack of specificity, pathologists routinely employ S100 in the diagnosis of neural crest-derived tumors. Recent studies have shown that Sox10 is a reliable marker of neural crest differentiation that is consistently expressed in schwannian and melanocytic tumors. We sought to validate these results in a larger series of soft tissue neoplasms of both neural crest and non-neural crest origin, and to further characterize the sensitivity and specificity of Sox10 for use in clinical diagnosis. We evaluated Sox10 and S100 mRNA levels in 122 cases of peripheral nerve sheath tumors and synovial sarcoma and used immunohistochemistry for Sox10 and S100 protein expression in 1012 tissue specimens. This study includes 174 tissue microarray cases previously reported by Nonaka and colleagues, which include cases of melanoma, dermatofibrosarcoma protuberans, neurofibroma, synovial sarcoma, clear-cell sarcoma, malignant peripheral nerve sheath tumor (MPNST), perineurioma, and schwannoma. Synovial sarcomas expressed significantly higher levels of S100B than Sox10 (P=7.9×10), and no significant Sox10 mRNA expression was identified in synovial sarcoma (n=40), whereas 18/40 cases showed comparatively increased levels of S100 mRNA. The majority of schwannomas (n=26) and neurofibromas (n=28) showed relatively an increased expression of both Sox10 and S100 mRNA. MPNSTs (n=28) showed variable levels of Sox10 and S100 mRNA expression, and these expression levels were highly correlated (Pearson correlation coefficient r=0.79). In contrast, immunohistochemistry performed on a larger and more varied number of cases highlighted significant differences between the 2 proteins. We identified 5 non-neural, nonmelanocytic sarcoma types in which a subset of cases showed S100 protein expression: synovial sarcoma (12/79, 15%), Ewing sarcoma (3/14, 21%), rhabdomyosarcoma (4/17, 24%), chondrosarcoma (3/4, 75%), and extraskeletal myxoid chondrosarcoma (5/11, 45%). For each of these entities, we identified cases with strong and diffuse S100 staining. Of these cases, only 1 case of rhabdomyosarcoma showed focal Sox10 positivity. In 78 cases of MPNST, S100 increased the sensitivity (31/78, 40%) as compared with Sox10 (21/78, 27%), but the majority of these cases were negative for both Sox10 and S100 (44/78, 56%). Sox10 proved superior to S100 in the detection of desmoplastic melanoma (7/9, 78%) and clear-cell sarcoma (4/7, 57%). We also report for the first time Sox10 expression in 26 cases of granular cell tumor, further supporting the neural crest derivation of this tumor. Excluding MPNST, S100 and Sox10 showed similar sensitivity in tumors of neural crest origin (140/148, 95% and 137/148, 93%, respectively). In summary, Sox10 shows an increased specificity for tumors of neural crest origin compared with S100: Sox10 was positive in only 5 of 668 cases (99% specificity) in nonschwannian, nonmelanocytic tumors, whereas S100 was positive in 53 of 668 cases (91% specificity). Sox10 should be used in the place of or along with S100 in soft tissue tumor diagnosis.

    View details for DOI 10.1097/PAI.0b013e318244ff4b

    View details for Web of Science ID 000309551700002

    View details for PubMedID 22495377

  • ROR2 is a novel prognostic biomarker and a potential therapeutic target in leiomyosarcoma and gastrointestinal stromal tumour JOURNAL OF PATHOLOGY Edris, B., Espinosa, I., Muehlenberg, T., Mikels, A., Lee, C., Steigen, S. E., Zhu, S., Montgomery, K. D., Lazar, A. J., Lev, D., Fletcher, J. A., Beck, A. H., West, R. B., Nusse, R., van de Rijn, M. 2012; 227 (2): 223-233


    Soft-tissue sarcomas are a group of malignant tumours whose clinical management is complicated by morphological heterogeneity, inadequate molecular markers and limited therapeutic options. Receptor tyrosine kinases (RTKs) have been shown to play important roles in cancer, both as therapeutic targets and as prognostic biomarkers. An initial screen of gene expression data for 48 RTKs in 148 sarcomas showed that ROR2 was expressed in a subset of leiomyosarcoma (LMS), gastrointestinal stromal tumour (GIST) and desmoid-type fibromatosis (DTF). This was further confirmed by immunohistochemistry (IHC) on 573 tissue samples from 59 sarcoma tumour types. Here we provide evidence that ROR2 expression plays a role in the invasive abilities of LMS and GIST cells in vitro. We also show that knockdown of ROR2 significantly reduces tumour mass in vivo using a xenotransplantation model of LMS. Lastly, we show that ROR2 expression, as measured by IHC, predicts poor clinical outcome in patients with LMS and GIST, although it was not independent of other clinico-pathological features in a multivariate analysis, and that ROR2 expression is maintained between primary tumours and their metastases. Together, these results show that ROR2 is a useful prognostic indicator in the clinical management of these soft-tissue sarcomas and may represent a novel therapeutic target.

    View details for DOI 10.1002/path.3986

    View details for Web of Science ID 000303193100012

    View details for PubMedID 22294416

    View details for PubMedCentralID PMC3992120

  • The Clinicopathologic Features of YWHAE-FAM22 Endometrial Stromal Sarcomas: A Histologically High-grade and Clinically Aggressive Tumor USCAP Annual Meeting Lee, C., Marino-Enriquez, A., Ou, W., Zhu, M., Ali, R. H., Chiang, S., Amant, F., Gilks, C. B., van de Rijn, M., Oliva, E., Debiec-Rychter, M., Dal Cin, P., Fletcher, J. A., Nucci, M. R. LIPPINCOTT WILLIAMS & WILKINS. 2012: 641–53


    Endometrial stromal sarcoma (ESS) is a genetically heterogenous group of uterine sarcomas, of which almost half are associated with JAZF1 rearrangement. We recently identified a novel genetic fusion between YWHAE and FAM22A/B in ESS harboring t(10;17)(q22;p13) and herein describe the clinicopathologic features of 13 YWHAE-FAM22 ESS cases (11 primary and 3 metastatic) and compare them with 20 ESS cases with JAZF1 rearrangement. Ten of 11 primary uterine tumors contained morphologically high-grade areas composed of round cells arranged in nests with a delicate stromal capillary network. The tumor cells showed large nuclei with irregular nuclear contours and significant mitotic activity (>10 mitoses/10 HPF) in addition to focal tumor necrosis, in contrast to JAZF1 ESS, which lacked a nested growth pattern, were composed of cells with small round/oval nuclei, and typically had <5 MF/10 HPF. In 7 of the 11 uterine tumors, there was an additional cytologically bland and mitotically weakly active spindle cell component with a fibrous/fibromyxoid stroma (ESS, fibromyxoid variant). Two metastatic tumors (pulmonary) also contained round cell and spindle cell components, whereas 1 metastasis (vaginal) was composed solely of the spindle cell component. In both primary and metastatic tumors, the spindle cells were diffusely positive for estrogen and progesterone receptors and CD10, in contrast to the round cell areas, which were negative. Clinically, 10 of 12 patients with YWHAE-FAM22 ESS presented with FIGO stages II to III disease, in contrast to only 4 of 16 patients with JAZF1 ESS presenting with stages II to III disease (P<0.05). Tumors with YWHAE-FAM22 rearrangements constitute a distinct group of ESS, which is associated with high-grade morphology and aggressive clinical behavior compared to JAZF1 ESS. Thus, their distinction from typical JAZF1 ESS is important for prognostic and therapeutic purposes.

    View details for DOI 10.1097/PAS.0b013e31824a7b1a

    View details for Web of Science ID 000302814000001

    View details for PubMedID 22456610

  • Antibody therapy targeting the CD47 protein is effective in a model of aggressive metastatic leiomyosarcoma PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Edris, B., Weiskopf, K., Volkmer, A. K., Volkmer, J., Willingham, S. B., Contreras-Trujillo, H., Liu, J., Majeti, R., West, R. B., Fletcher, J. A., Beck, A. H., Weissman, I. L., van de Rijn, M. 2012; 109 (17): 6656-6661


    Antibodies against CD47, which block tumor cell CD47 interactions with macrophage signal regulatory protein-α, have been shown to decrease tumor size in hematological and epithelial tumor models by interfering with the protection from phagocytosis by macrophages that intact CD47 bestows upon tumor cells. Leiomyosarcoma (LMS) is a tumor of smooth muscle that can express varying levels of colony-stimulating factor-1 (CSF1), the expression of which correlates with the numbers of tumor-associated macrophages (TAMs) that are found in these tumors. We have previously shown that the presence of TAMs in LMS is associated with poor clinical outcome and the overall effect of TAMs in LMS therefore appears to be protumorigenic. However, the use of inhibitory antibodies against CD47 offers an opportunity to turn TAMs against LMS cells by allowing the phagocytic behavior of resident macrophages to predominate. Here we show that interference with CD47 increases phagocytosis of two human LMS cell lines, LMS04 and LMS05, in vitro. In addition, treatment of mice bearing subcutaneous LMS04 and LMS05 tumors with a novel, humanized anti-CD47 antibody resulted in significant reductions in tumor size. Mice bearing LMS04 tumors develop large numbers of lymph node and lung metastases. In a unique model for neoadjuvant treatment, mice were treated with anti-CD47 antibody starting 1 wk before resection of established primary tumors and subsequently showed a striking decrease in the size and number of metastases. These data suggest that treatment with anti-CD47 antibodies not only reduces primary tumor size but can also be used to inhibit the development of, or to eliminate, metastatic disease.

    View details for DOI 10.1073/pnas.1121629109

    View details for Web of Science ID 000303249100064

    View details for PubMedID 22451919

    View details for PubMedCentralID PMC3340056

  • The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Willingham, S. B., Volkmer, J., Gentles, A. J., Sahoo, D., Dalerba, P., Mitra, S. S., Wang, J., Contreras-Trujillo, H., Martin, R., Cohen, J. D., Lovelace, P., Scheeren, F. A., Chao, M. P., Weiskopf, K., Tang, C., Volkmer, A. K., Naik, T. J., Storm, T. A., Mosley, A. R., Edris, B., Schmid, S. M., Sun, C. K., Chua, M., Murillo, O., Rajendran, P., Cha, A. C., Chin, R. K., Kim, D., Adorno, M., Raveh, T., Tseng, D., Jaiswal, S., Enger, P. O., Steinberg, G. K., Li, G., So, S. K., Majeti, R., Harsh, G. R., van de Rijn, M., Teng, N. N., Sunwoo, J. B., Alizadeh, A. A., Clarke, M. F., Weissman, I. L. 2012; 109 (17): 6662-6667


    CD47, a "don't eat me" signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies.

    View details for DOI 10.1073/pnas.1121623109

    View details for Web of Science ID 000303249100065

    View details for PubMedID 22451913

    View details for PubMedCentralID PMC3340046

  • Three differentiation states risk-stratify bladder cancer into distinct subtypes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volkmer, J., Sahoo, D., Chin, R. K., Ho, P. L., Tang, C., Kurtova, A. V., Willingham, S. B., Pazhanisamy, S. K., Contreras-Trujillo, H., Storm, T. A., Lotan, Y., Beck, A. H., Chung, B. I., Alizadeh, A. A., Godoy, G., Lerner, S. P., van de Rijng, M., Shortliffe, L. D., Weissman, I. L., Chan, K. S. 2012; 109 (6): 2078-2083


    Current clinical judgment in bladder cancer (BC) relies primarily on pathological stage and grade. We investigated whether a molecular classification of tumor cell differentiation, based on a developmental biology approach, can provide additional prognostic information. Exploiting large preexisting gene-expression databases, we developed a biologically supervised computational model to predict markers that correspond with BC differentiation. To provide mechanistic insight, we assessed relative tumorigenicity and differentiation potential via xenotransplantation. We then correlated the prognostic utility of the identified markers to outcomes within gene expression and formalin-fixed paraffin-embedded (FFPE) tissue datasets. Our data indicate that BC can be subclassified into three subtypes, on the basis of their differentiation states: basal, intermediate, and differentiated, where only the most primitive tumor cell subpopulation within each subtype is capable of generating xenograft tumors and recapitulating downstream populations. We found that keratin 14 (KRT14) marks the most primitive differentiation state that precedes KRT5 and KRT20 expression. Furthermore, KRT14 expression is consistently associated with worse prognosis in both univariate and multivariate analyses. We identify here three distinct BC subtypes on the basis of their differentiation states, each harboring a unique tumor-initiating population.

    View details for DOI 10.1073/pnas.1120605109

    View details for Web of Science ID 000299925000058

    View details for PubMedID 22308455

  • CD47 Is a Therapeutic Antibody Target in Leiomyosarcoma 101st Annual Meeting of United-States-and-Canadian-Academy-of-Pathology (USCAP) Edris, B., Weiskopf, K., Volkmer, J., Willingham, S., Volkmer, A., Fletcher, J., Beck, A., Weissman, I., van de Rijn, M. NATURE PUBLISHING GROUP. 2012: 12A–12A
  • Cyclin 131 Is a Sensitive and Specific Diagnostic Immunomarker for YWHAE-FAM22A/B Endometrial Stromal Sarcoma 101st Annual Meeting of United-States-and-Canadian-Academy-of-Pathology (USCAP) Lee, C., Ali, R., Marino-Enriquez, A., Ou, W., Zhu, M., Guo, X., Brunner, A. L., Chiang, S., Oliva, E., Rouzbahman, M., Gilks, C. B., Dal Cin, P., West, P. B., van de Rijn, M., Fletcher, J. A., Nucci, M. R. NATURE PUBLISHING GROUP. 2012: 282A–282A
  • Cyclin D1 Is a Sensitive and Specific Diagnostic Immunomarker for YWHAE-FAM22A/B Endometrial Stromal Sarcoma 101st Annual Meeting of United-States-and-Canadian-Academy-of-Pathology (USCAP) Lee, C., Ali, R., Marino-Enriquez, A., Ou, W., Zhu, M., Guo, X., Brunner, A. L., Chiang, S., Oliva, E., Rouzbahman, M., Gilks, C. B., Dal Cin, P., West, P. B., van de Rijn, M., Fletcher, J. A., Nucci, M. R. NATURE PUBLISHING GROUP. 2012: 282A–282A
  • The Receptor Tyrosine Kinase ROR2 Is a Novel Marker for TSC-Associated Lesions and a Potential Therapeutic Target Independent of the TSC/mTOR Pathway 101st Annual Meeting of United-States-and-Canadian-Academy-of-Pathology (USCAP) SWEENEY, R. T., Badreddin, E., Montgomery, K. D., Nusse, R., van de Rijn, M. NATURE PUBLISHING GROUP. 2012: 491A–491A
  • 14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lee, C., Ou, W., Marino-Enriquez, A., Zhu, M., Mayeda, M., Wang, Y., Guo, X., Brunner, A. L., Amant, F., French, C. A., West, R. B., McAlpine, J. N., Gilks, C. B., Yaffe, M. B., Prentice, L. M., McPherson, A., Jones, S. J., Marra, M. A., Shah, S. P., van de Rijn, M., Huntsman, D. G., Dal Cin, P., Debiec-Rychter, M., Nucci, M. R., Fletcher, J. A. 2012; 109 (3): 929-934


    14-3-3 proteins are ubiquitously expressed regulators of various cellular functions, including proliferation, metabolism, and differentiation, and altered 14-3-3 expression is associated with development and progression of cancer. We report a transforming 14-3-3 oncoprotein, which we identified through conventional cytogenetics and whole-transcriptome sequencing analysis as a highly recurrent genetic mechanism in a clinically aggressive form of uterine sarcoma: high-grade endometrial stromal sarcoma (ESS). The 14-3-3 oncoprotein results from a t(10;17) genomic rearrangement, leading to fusion between 14-3-3ε (YWHAE) and either of two nearly identical FAM22 family members (FAM22A or FAM22B). Expression of YWHAE-FAM22 fusion oncoproteins was demonstrated by immunoblot in t(10;17)-bearing frozen tumor and cell line samples. YWHAE-FAM22 fusion gene knockdowns were performed with shRNAs and siRNAs targeting various FAM22A exons in an t(10;17)-bearing ESS cell line (ESS1): Fusion protein expression was inhibited, with corresponding reduction in cell growth and migration. YWHAE-FAM22 maintains a structurally and functionally intact 14-3-3ε (YWHAE) protein-binding domain, which is directed to the nucleus by a FAM22 nuclear localization sequence. In contrast to classic ESS, harboring JAZF1 genetic fusions, YWHAE-FAM22 ESS display high-grade histologic features, a distinct gene-expression profile, and a more aggressive clinical course. Fluorescence in situ hybridization analysis demonstrated absolute specificity of YWHAE-FAM22A/B genetic rearrangement for high-grade ESS, with no fusions detected in other uterine and nonuterine mesenchymal tumors (55 tumor types, n = 827). These discoveries reveal diagnostically and therapeutically relevant models for characterizing aberrant 14-3-3 oncogenic functions.

    View details for DOI 10.1073/pnas.1115528109

    View details for Web of Science ID 000299154000058

    View details for PubMedID 22223660

    View details for PubMedCentralID PMC3271913

  • Comparative gene expression profiling of benign and malignant lesions reveals candidate therapeutic compounds for leiomyosarcoma. Sarcoma Edris, B., Fletcher, J. A., West, R. B., van de Rijn, M., Beck, A. H. 2012; 2012: 805614-?


    Leiomyosarcoma (LMS) is a malignant, soft-tissue tumor for which few effective therapies exist. Previously, we showed that there are three molecular subtypes of LMS. Here, we analyzed genes differentially expressed in each of the three LMS subtypes as compared to benign leiomyomas and then used the Connectivity Map (cmap) to calculate enrichment scores for the 1309 cmap drugs in order to identify candidate molecules with the potential to induce a benign, leiomyoma-like phenotype in LMS cells. 11 drugs were selected and tested for their ability to inhibit the growth of three human LMS cell lines. We identified two drugs with in vitro efficacy against LMS, one of which had a strongly negative enrichment score (Cantharidin) and the other of which had a strongly positive enrichment score (MG-132). Given MG-132's strong inhibitory effect on LMS cell viability, we hypothesized that LMS cells may be sensitive to treatment with other proteasome inhibitors and demonstrated that bortezomib, a clinically-approved proteasome inhibitor not included in the original cmap screen, potently inhibited the viability of the LMS cell lines. These findings suggest that systematically linking LMS subtype-specific expression signatures with drug-associated expression profiles represents a promising approach for the identification of new drugs for LMS.

    View details for DOI 10.1155/2012/805614

    View details for PubMedID 22919280

    View details for PubMedCentralID PMC3420093

  • Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers GENOME BIOLOGY Brunner, A. L., Beck, A. H., Edris, B., Sweeney, R. T., Zhu, S. X., Li, R., Montgomery, K., Varma, S., Gilks, T., Guo, X., Foley, J. W., Witten, D. M., Giacomini, C. P., Flynn, R. A., Pollack, J. R., Tibshirani, R., Chang, H. Y., van de Rijn, M., West, R. B. 2012; 13 (8)


    BACKGROUND: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. RESULTS: We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We found that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors. It was shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. CONCLUSIONS: This study provides the first large survey of long non-coding RNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research.

    View details for Web of Science ID 000315867500009

  • Increased midkine expression correlates with desmoid tumour recurrence: a potential biomarker and therapeutic target JOURNAL OF PATHOLOGY Colombo, C., Creighton, C. J., Ghadimi, M. P., Bolshakov, S., Warneke, C. L., Zhang, Y., Lusby, K., Zhu, S., Lazar, A. J., West, R. B., van de Rijn, M., Lev, D. 2011; 225 (4): 574-582


    Desmoid tumours (DTs) are soft tissue monoclonal neoplasms exhibiting a unique phenotype, consisting of aggressive local invasiveness without metastatic capacity. While DTs can infrequently occur as part of familial adenomatosis polyposis, most cases arise sporadically. Sporadic DTs harbour a high prevalence of CTNNB1 mutations and hence increased β-catenin signalling. However, β-catenin downstream transcriptional targets and other molecular deregulations operative in DT inception and progression are currently not well defined, contributing to the lack of sensitive molecular prognosticators and efficacious targeted therapeutic strategies. We compared the gene expression profiles of 14 sporadic DTs to those of five corresponding normal tissues and six solitary fibrous tumour specimens. A DT expression signature consisting of 636 up- and 119 down-regulated genes highly enriched for extracellular matrix, cell adhesion and wound healing-related proteins was generated. Furthermore, 98 (15%) of the over-expressed genes were demonstrated to contain a TCF/LEF consensus binding site in their promoters, possibly heralding direct β-catenin downstream targets relevant to DT. The protein products of three of the up-regulated DT genes: ADAM12, MMP2 and midkine, were found to be commonly expressed in a large cohort of human DT samples assembled on a tissue microarray. Interestingly, enhanced midkine expression significantly correlated with a higher propensity and decreased time for primary DT recurrence (log-rank p = 0.0025). Finally, midkine was found to enhance the migration and invasion of primary DT cell cultures. Taken together, these studies provide insights into potential DT molecular aberrations and novel β-catenin transcriptional targets. Further studies to confirm the utility of midkine as a clinical DT molecular prognosticator and a potential therapeutic target are therefore warranted. Raw gene array data can be found at:

    View details for DOI 10.1002/path.2951

    View details for Web of Science ID 000297299500011

    View details for PubMedID 21826666

  • Immature T-Cell Populations in Lymph Nodes of Castleman Disease and Angioimmunoblastic T-Cell Lymphoma Suggest Alternate Sites of T-Cell Development 53rd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Ohgami, R. S., Chun, S., Ohgami, J., Zehnder, J. L., Van de Rijn, M., Arber, D. A., Natkunam, Y., Warnke, R. AMER SOC HEMATOLOGY. 2011: 1395–96
  • Systematic Analysis of Breast Cancer Morphology Uncovers Stromal Features Associated with Survival SCIENCE TRANSLATIONAL MEDICINE Beck, A. H., Sangoi, A. R., Leung, S., Marinelli, R. J., Nielsen, T. O., van de Vijver, M. J., West, R. B., van de Rijn, M., Koller, D. 2011; 3 (108)


    The morphological interpretation of histologic sections forms the basis of diagnosis and prognostication for cancer. In the diagnosis of carcinomas, pathologists perform a semiquantitative analysis of a small set of morphological features to determine the cancer's histologic grade. Physicians use histologic grade to inform their assessment of a carcinoma's aggressiveness and a patient's prognosis. Nevertheless, the determination of grade in breast cancer examines only a small set of morphological features of breast cancer epithelial cells, which has been largely unchanged since the 1920s. A comprehensive analysis of automatically quantitated morphological features could identify characteristics of prognostic relevance and provide an accurate and reproducible means for assessing prognosis from microscopic image data. We developed the C-Path (Computational Pathologist) system to measure a rich quantitative feature set from the breast cancer epithelium and stroma (6642 features), including both standard morphometric descriptors of image objects and higher-level contextual, relational, and global image features. These measurements were used to construct a prognostic model. We applied the C-Path system to microscopic images from two independent cohorts of breast cancer patients [from the Netherlands Cancer Institute (NKI) cohort, n = 248, and the Vancouver General Hospital (VGH) cohort, n = 328]. The prognostic model score generated by our system was strongly associated with overall survival in both the NKI and the VGH cohorts (both log-rank P ≤ 0.001). This association was independent of clinical, pathological, and molecular factors. Three stromal features were significantly associated with survival, and this association was stronger than the association of survival with epithelial characteristics in the model. These findings implicate stromal morphologic structure as a previously unrecognized prognostic determinant for breast cancer.

    View details for DOI 10.1126/scitranslmed.3002564

    View details for Web of Science ID 000296765800004

    View details for PubMedID 22072638

  • CSF1 Expression in Nongynecological Leiomyosarcoma Is Associated with Increased Tumor Angiogenesis AMERICAN JOURNAL OF PATHOLOGY Espinosa, I., Edris, B., Lee, C., Cheng, H. W., Gilks, C. B., Wang, Y., Montgomery, K. D., Varma, S., Li, R., Marinelli, R. J., West, R. B., Nielsen, T., Beck, A. H., van de Rijn, M. 2011; 179 (4): 2100-2107


    Leiomyosarcoma (LMS) is a malignant tumor of smooth muscle cells for which few effective therapies exist. A subset of LMS cases express macrophage colony-stimulating factor (CSF1) and the resultant tumor-associated macrophage (TAM) infiltration predicts poor clinical outcome. Further, TAMs have been shown to increase tumor angiogenesis. Here, we analyzed 149 LMS cases by immunohistochemistry for vascular marker CD34 and show that high microvessel density (MVD) in nongynecological LMS cases significantly predicts poor patient outcome. The majority of high MVD cases were also CSF1-positive, and when combining high MVD with CSF1 expression, an even stronger prognostic correlation with patient outcome was obtained. Gene expression profiling revealed that MVD has a stronger correlation with CSF1 expression than with expression of vascular endothelial growth factor isoforms, which have traditionally been used as markers of angiogenesis and as anti-angiogenic therapeutic targets. Finally, patterns of CSF1 expression and TAM recruitment remained consistent between primary tumors and their metastases, and between primary tumors and those grown as xenografts in mice, highlighting the stability of these features to the biology of LMS tumors. Together, these findings suggest an important role for CSF1 and the resulting TAM infiltration in the pathological neovascularization of LMS tumors and provide a rationale for CSF1-targeted therapies in LMS.

    View details for DOI 10.1016/j.ajpath.2011.06.021

    View details for Web of Science ID 000298307400049

    View details for PubMedID 21854753

    View details for PubMedCentralID PMC3181338

  • SMURF1 Amplification Promotes Invasiveness in Pancreatic Cancer PLOS ONE Kwei, K. A., Shain, A. H., Bair, R., Montgomery, K., Karikari, C. A., van de Rijn, M., Hidalgo, M., Maitra, A., Bashyam, M. D., Pollack, J. R. 2011; 6 (8)


    Pancreatic cancer is a deadly disease, and new therapeutic targets are urgently needed. We previously identified DNA amplification at 7q21-q22 in pancreatic cancer cell lines. Now, by high-resolution genomic profiling of human pancreatic cancer cell lines and human tumors (engrafted in immunodeficient mice to enrich the cancer epithelial fraction), we define a 325 Kb minimal amplicon spanning SMURF1, an E3 ubiquitin ligase and known negative regulator of transforming growth factor β (TGFβ) growth inhibitory signaling. SMURF1 amplification was confirmed in primary human pancreatic cancers by fluorescence in situ hybridization (FISH), where 4 of 95 cases (4.2%) exhibited amplification. By RNA interference (RNAi), knockdown of SMURF1 in a human pancreatic cancer line with focal amplification (AsPC-1) did not alter cell growth, but led to reduced cell invasion and anchorage-independent growth. Interestingly, this effect was not mediated through altered TGFβ signaling, assayed by transcriptional reporter. Finally, overexpression of SMURF1 (but not a catalytic mutant) led to loss of contact inhibition in NIH-3T3 mouse embryo fibroblast cells. Together, these findings identify SMURF1 as an amplified oncogene driving multiple tumorigenic phenotypes in pancreatic cancer, and provide a new druggable target for molecularly directed therapy.

    View details for DOI 10.1371/journal.pone.0023924

    View details for Web of Science ID 000294251800040

    View details for PubMedID 21887346

    View details for PubMedCentralID PMC3161761

  • A Tri-Marker Proliferation Index Predicts Biochemical Recurrence after Surgery for Prostate Cancer PLOS ONE Malhotra, S., Lapointe, J., Salari, K., Higgins, J. P., Ferrari, M., Montgomery, K., van de Rijn, M., Brooks, J. D., Pollack, J. R. 2011; 6 (5)


    Prostate cancer exhibits tremendous variability in clinical behavior, ranging from indolent to lethal disease. Better prognostic markers are needed to stratify patients for appropriately aggressive therapy. By expression profiling, we can identify a proliferation signature variably expressed in prostate cancers. Here, we asked whether one or more tissue biomarkers might capture that information, and provide prognostic utility. We assayed three proliferation signature genes: MKI67 (Ki-67; also a classic proliferation biomarker), TOP2A (DNA topoisomerase II, alpha), and E2F1 (E2F transcription factor 1). Immunohistochemical staining was evaluable on 139 radical prostatectomy cases (in tissue microarray format), with a median clinical follow-up of eight years. Each of the three proliferation markers was by itself prognostic. Notably, combining the three markers together as a "proliferation index" (0 or 1, vs. 2 or 3 positive markers) provided superior prognostic performance (hazard ratio = 2.6 (95% CI: 1.4-4.9); P = 0.001). In a multivariate analysis that included preoperative serum prostate specific antigen (PSA) levels, Gleason grade and pathologic tumor stage, the composite proliferation index remained a significant predictor (P = 0.005). Analysis of receiver-operating characteristic (ROC) curves confirmed the improved prognostication afforded by incorporating the proliferation index (compared to the clinicopathologic data alone). Our findings highlight the potential value of a multi-gene signature-based diagnostic, and define a tri-marker proliferation index with possible utility for improved prognostication and treatment stratification in prostate cancer.

    View details for DOI 10.1371/journal.pone.0020293

    View details for Web of Science ID 000291005200049

    View details for PubMedID 21629784

    View details for PubMedCentralID PMC3100337

  • Uterine leiomyosarcomas: Tumor size, mitotic index, and biomarkers Ki67, and Bcl-2 identify two groups with different prognosis GYNECOLOGIC ONCOLOGY D'angelo, E., Espinosa, I., Ali, R., Gilks, C. B., van de Rijn, M., Lee, C., Prat, J. 2011; 121 (2): 328-333


    Prognostic factors for uterine leiomyosarcomas are not well established. Although most tumors are associated with poor prognosis even when apparently confined to the uterus (stage I), some cases that exhibited morphologic features of malignancy had prolonged survival.Using tissue microarrays of 84 uterine leiomyosarcomas, we investigated conventional clinico-pathologic parameters, including International Federation of Gynecology and Obstetrics (FIGO) stage, together with expression of Ki67, p53, p16, and Bcl-2, attempting to distinguish leiomyosarcomas with different prognosis. The rate of CD163 immunoreactive tumor macrophages was also investigated.Tumor size and mitotic index were significant prognostic factors by univariate (p=0.018 and p=0.003, respectively) and multivariate (p=0.006 and p=0.001) analyses. Of the biomarkers investigated, only Ki67 immunoreaction was significant by univariate analysis and was associated with adverse prognosis (p=0.01). However, combination of tumor size, mitotic index, Ki67, and Bcl-2 worked even better. Using these 4 parameters, unsupervised hierarchical clustering identified 2 groups of tumors with different prognosis (p=0.001): group 1 consisted mostly of smaller leiomyosarcomas (<10cm) with mitotic index <20 MF/10 HPF, negative Ki67, and positive or negative Bcl-2 immunostaining. These tumors were associated with better prognosis. In contrast, group 2 leiomyosarcomas which were mostly≥10cm in diameter had higher mitotic index (≥ 20 MF/10 HPF), and were positive for Ki67 and negative for Bcl-2 had worse prognosis. Also, the number of CD163-macrophages was greater in group 2 than group 1 (p=0.007).Tumor size and mitotic index are morphologic predictors of malignancy in uterine leiomyosarcomas. Combination of tumor size, mitotic index, Ki67, and Bcl-2 protein expression allows distinguishing 2 groups of leiomyosarcomas with different survival. Leiomyosarcomas associated with poor outcome had a higher number of CD163 stromal macrophages.

    View details for DOI 10.1016/j.ygyno.2011.01.022

    View details for Web of Science ID 000290292100017

    View details for PubMedID 21316747

  • Expression of Subtype-Specific Group 1 Leiomyosarcoma Markers in a Wide Variety of Sarcomas by Gene Expression Analysis and Immunohistochemistry AMERICAN JOURNAL OF SURGICAL PATHOLOGY Mills, A. M., Beck, A. H., Montgomery, K. D., Zhu, S. X., Espinosa, I., Lee, C., Subramanian, S., Fletcher, C. D., van de Rijn, M., West, R. B. 2011; 35 (4): 583-589


    Leiomyosarcomas (LMSs) constitute approximately one quarter of all sarcomas and are usually defined by morphologic criteria and/or immunoreactivity for actin or desmin. Among high-grade lesions, the distinction from undifferentiated pleomorphic sarcoma (UPS) can be problematic, and previous studies have shown that a significant number of LMS cases may be hiding under the diagnosis of UPS. We recently described 3 novel molecular LMS subtypes that are distributed similarly over LMSs of gyneocologic and non-gyneocologic origins. The group 1 subtype shows an improved disease-specific survival compared with the other 2 groups that is independent of histologic grade. Group 1 comprises approximately 25% of all LMSs, and is defined by a shared pattern of gene expression, a distinct pattern of genomic changes, and reactivity for at least 3 of 5 immunohistochemistry (IHC) markers (smooth muscle gamma actin, calsequestrin 2, human muscle cofilin2, myosin light chain kinase, and sarcolemmal membrane associated protein), as tested on 271 cases of LMS in tissue microarrays. These IHC markers have not been well characterized in non-LMS sarcomas. Here we provide a characterization of these 5 markers across normal tissues, an additional 59 cases of LMS, and a wide range of 565 non-LMS soft tissue tumors from 44 diagnostic categories, with a focus on UPS. When analyzed individually, the 5 markers were found to be expressed in many sarcomas other than LMSs. However, when analyzed by the same criteria used for the recognition of group 1 LMSs, in which a case is scored positive when at least 3 of 5 markers reacted, coordinate expression was seen in significant numbers of cases from only 3 diagnostic groups that included 22% of leiomyomas (n=22), 16% of gastrointestinal stromal tumors (n=43), and 18% of endometrial stromal sarcomas (n=11). In addition, 5% (n=57) of UPSs showed a staining pattern similar to that seen in group 1 LMSs. To further examine the possibility that group 1 LMS constitutes a small part of cases diagnosed as UPS, we examined the expression of the top 500 genes from the group 1 LMS expression signature in 29 UPSs by complementary DNA microarray. Unsupervised hierarchical clustering of 29 UPS expression showed that 2 (7%) had coordinated high levels of expression of genes from the group 1 LMS signature, a rate similar to that seen by IHC analysis. These findings show that group 1 LMS IHC markers smooth muscle gamma actin, calsequestrin 2, human muscle cofilin2, myosin light chain kinase, and sarcolemmal membrane associated protein when coordinately expressed have specificity for a subset of LMS when compared with other sarcomas, and may be useful for the recognition of group 1 LMS cases within cases diagnosed as UPS.

    View details for DOI 10.1097/PAS.0b013e318211abd6

    View details for Web of Science ID 000288491600014

    View details for PubMedID 21412072

    View details for PubMedCentralID PMC3440303

  • Comparative Profiling of Primary Colorectal Carcinomas and Liver Metastases Identifies LEF1 as a Prognostic Biomarker PLOS ONE Lin, A. Y., Chua, M., Choi, Y., Yeh, W., Kim, Y. H., Azzi, R., Adams, G. A., Sainani, K., van de Rijn, M., So, S. K., Pollack, J. R. 2011; 6 (2)


    We sought to identify genes of clinical significance to predict survival and the risk for colorectal liver metastasis (CLM), the most common site of metastasis from colorectal cancer (CRC).We profiled gene expression in 31 specimens from primary CRC and 32 unmatched specimens of CLM, and performed Significance Analysis of Microarrays (SAM) to identify genes differentially expressed between these two groups. To characterize the clinical relevance of two highly-ranked differentially-expressed genes, we analyzed the expression of secreted phosphoprotein 1 (SPP1 or osteopontin) and lymphoid enhancer factor-1 (LEF1) by immunohistochemistry using a tissue microarray (TMA) representing an independent set of 154 patients with primary CRC.Supervised analysis using SAM identified 963 genes with significantly higher expression in CLM compared to primary CRC, with a false discovery rate of <0.5%. TMA analysis showed SPP1 and LEF1 protein overexpression in 60% and 44% of CRC cases, respectively. Subsequent occurrence of CLM was significantly correlated with the overexpression of LEF1 (chi-square p = 0.042), but not SPP1 (p = 0.14). Kaplan Meier analysis revealed significantly worse survival in patients with overexpression of LEF1 (p<0.01), but not SPP1 (p = 0.11). Both univariate and multivariate analyses identified stage (p<0.0001) and LEF1 overexpression (p<0.05) as important prognostic markers, but not tumor grade or SPP1.Among genes differentially expressed between CLM and primary CRC, we demonstrate overexpression of LEF1 in primary CRC to be a prognostic factor for poor survival and increased risk for liver metastasis.

    View details for DOI 10.1371/journal.pone.0016636

    View details for Web of Science ID 000287761700013

    View details for PubMedID 21383983

    View details for PubMedCentralID PMC3044708

  • The Prognostic Value of Tumor-Associated Macrophages in Leiomyosarcoma A Single Institution Study AMERICAN JOURNAL OF CLINICAL ONCOLOGY-CANCER CLINICAL TRIALS Ganjoo, K. N., Witten, D., Patel, M., Espinosa, I., La, T., Tibshirani, R., van de Rijn, M., Jacobs, C., West, R. B. 2011; 34 (1): 82-86


    High numbers of tumor-associated macrophages (TAMs) have been associated with poor outcome in several solid tumors. In 2 previous studies, we showed that colony stimulating factor-1 (CSF1) is secreted by leiomyosarcoma (LMS) and that the increase in macrophages and CSF1 associated proteins are markers for poor prognosis in both gynecologic and nongynecologic LMS in a multicentered study. The purpose of this study is to evaluate the outcome of patients with LMS from a single institution according to the number of TAMs evaluated through 3 CSF1 associated proteins.Patients with LMS treated at Stanford University with adequate archived tissue and clinical data were eligible for this retrospective study. Data from chart reviews included tumor site, size, grade, stage, treatment, and disease status at the time of last follow-up. The 3 CSF1 associated proteins (CD163, CD16, and cathepsin L) were evaluated by immunohistochemistry on tissue microarrays. Kaplan-Meier survival curves and univariate Cox proportional hazards models were fit to assess the association of clinical predictors as well as CSF1 associated proteins with overall survival.A total of 52 patients diagnosed from 1983 to 2007 were evaluated. Univariate Cox proportional hazards models were fit to assess the significance of grade, size, stage, and the 3 CSF1 associated proteins in predicting OS. Grade, size, and stage were not significantly associated with survival in the full patient cohort, but grade and stage were significant predictors of survival in the gynecologic (GYN) LMS samples (P = 0.038 and P = 0.0164, respectively). Increased cathepsin L was associated with a worse outcome in GYN LMS (P = 0.049). Similar findings were seen with CD16 (P < 0.0001). In addition, CSF1 response enriched (all 3 stains positive) GYN LMS had a poor overall survival when compared with CSF1 response poor tumors (P = 0.001). These results were not seen in non-GYN LMS.Our data form an independent confirmation of the prognostic significance of TAMs and the CSF1 associated proteins in LMS. More aggressive or targeted therapies could be considered in the subset of LMS patients that highly express these markers.

    View details for DOI 10.1097/COC.0b013e3181d26d5e

    View details for Web of Science ID 000286624100017

    View details for PubMedID 23781555

  • CSF1-Response Signature Is Associated with Tumor Angiogenesis in Non-Gynecological Leiomyosarcoma 100th Annual Meeting United States-and-Canadian-Academy-of-Pathology Espinosa, I., Beck, A., Edris, B., Lee, C., West, R., van de Rijn, M. NATURE PUBLISHING GROUP. 2011: 13A–13A
  • CSF1-Response Signature Is Associated with Tumor Angiogenesis in Non-Gynecological Leiomyosarcoma 100th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Espinosa, I., Beck, A., Edris, B., Lee, C., West, R., van de Rijn, M. NATURE PUBLISHING GROUP. 2011: 13A–13A
  • The Histologic Features of Endometrial Stromal Sarcomas Characterized by YWHAE Rearrangement - Distinction from Usual Low-Grade Endometrial Stromal Sarcoma with JAZF1 Rearrangement 100th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Lee, C., Marino-Enriquez, A., van de Rijn, M., Gilks, C. B., Debiec-Rychter, M., Dal Cin, P., Fletcher, J. A., Nucci, M. R. NATURE PUBLISHING GROUP. 2011: 255A–255A
  • Endogenous Versus Tumor-Specific Host Response to Breast Carcinoma: A Study of Stromal Response in Synchronous Breast Primaries and Biopsy Site Changes CLINICAL CANCER RESEARCH Wu, J. M., Beck, A. H., Pate, L. L., Witten, D., Zhu, S. X., Montgomery, K. D., Allison, K. H., van de Rijn, M., West, R. B. 2011; 17 (3): 437-446


    We recently described two types of stromal response in breast cancer derived from gene expression studies of tenosynovial giant cell tumors and fibromatosis. The purpose of this study is to elucidate the basis of this stromal response--whether they are elicited by individual tumors or whether they represent an endogenous host reaction produced by the patient.Stromal signatures from patients with synchronous dual primaries were analyzed by immunohistochemistry on a tissue microarray (n = 26 pairs) to evaluate the similarity of stromal responses in different tumors within the same patient. We also characterized the extent to which the stromal signatures were conserved between stromal response to injury compared to the stromal response to carcinoma using gene expression profiling and tissue microarray immunohistochemistry.The two stromal response signatures showed divergent associations in synchronous primaries: the DTF fibroblast response is more likely to be similar in a patient with multiple breast primaries (permutation analysis P = 0.0027), whereas CSF1 macrophage response shows no significant concordance in separate tumors within a given patient. The DTF fibroblast signature showed more concordance across normal, cancer, and biopsy site samples from within a patient, than across normal, cancer, and biopsy site samples from a random group of patients, whereas the CSF1 macrophage response did not.The results suggest that the DTF fibroblast response is host-specific, whereas the CSF1 response may be tumor-elicited. Our findings provide further insight into stromal response and may facilitate the development of therapeutic strategies to target particular stromal subtypes.

    View details for DOI 10.1158/1078-0432.CCR-10-1709

    View details for Web of Science ID 000286873400007

    View details for PubMedID 21098336

    View details for PubMedCentralID PMC3033467

  • Variations in stromal signatures in breast and colorectal cancer metastases JOURNAL OF PATHOLOGY Webster, J. A., Beck, A. H., Sharma, M., Espinosa, I., Weigelt, B., Schreuder, M., Montgomery, K. D., Jensen, K. C., van de Rijn, M., West, R. 2010; 222 (2): 158-165


    The tumour microenvironment (TME) plays an important role in tumour survival and growth, but little is known about the degree of preservation between different stromal response patterns found in primary tumours and their metastases. We have previously identified gene expression profiles for two distinct stromal signatures in breast carcinoma of fibroblast (aka DTF) and macrophage (aka CSF1) response and found them to be correlated with clinicopathological features, including outcome. In this study, we compare the DTF fibroblast and CSF1 macrophage stromal response patterns in primary breast and colorectal cancers to their matched lymph node metastases. In both breast and colorectal cancer, there was a significant positive correlation between the CSF1 macrophage signature in the primary tumours and the matched lymph node metastases, as assessed by immunohistochemical markers. No such correlation was observed for the DTF fibroblast signature. A similar result was seen in independent analysis of two published gene expression microarray datasets. The variations of these stromal reaction patterns from the primary to the metastasis shed light on the relationship between the neoplastic cells and the non-neoplastic cells in the TME. The preservation of the CSF1 macrophage response pattern in metastases lends support to targeting the CSF1 pathway in cancer.

    View details for DOI 10.1002/path.2738

    View details for Web of Science ID 000282725700006

    View details for PubMedID 20593409

    View details for PubMedCentralID PMC2935495

  • Gross genomic alterations and gene expression profiles of high- grade serous carcinoma of the ovary with and without BRCA1 inactivation BMC CANCER Pradhan, M., Risberg, B. A., Trope, C. G., van de Rijn, M., Gilks, C. B., Lee, C. 2010; 10


    BRCA1 gene inactivation causes chromosomal instability, leading to rapid accumulation of chromosomal rearrangements and mutations. The loss of BRCA1 function due to either germline/somatic mutation or epigenetic silencing is observed in most high-grade serous carcinomas of the ovary.DNA ploidy and gene expression profile were used in order to compare gross genomic alteration and gene expression pattern between cases with BRCA1 loss through mutation, BRCA1 epigenetic loss, and no BRCA1 loss in cases of high-grade serous carcinoma with known BRCA1 and BRCA 2 status.Using image cytometry and oligonucleotide microarrays, we analyzed DNA ploidy, S-phase fraction and gene expression profile of 28 consecutive cases of ovarian high-grade serous adenocarcinomas, which included 8 tumor samples with BRCA1 somatic or germline mutation, 9 samples with promoter hypermethylation of BRCA1, and 11 samples with no BRCA1 loss. None had BRCA2 mutations. The prevalence of aneuploidy and tetraploidy was not statistically different in the three groups with different BRCA1 status. The gene expression profiles were also very similar between the groups, with only two genes showing significant differential expression when comparison was made between the group with BRCA1 mutation and the group with no demonstrable BRCA1 loss. There were no genes showing significant differences in expression when the group with BRCA1 loss through epigenetic silencing was compared to either of the other two groups.In this series of 28 high-grade serous carcinomas, gross genomic alteration characterized by aneuploidy did not correlate with BRCA1 status. In addition, the gene expression profiles of the tumors showed negligible differences between the three defined groups based on BRCA1 status. This suggests that all ovarian high-grade serous carcinomas arise through oncogenic mechanisms that result in chromosomal instability, irrespective of BRCA status; the molecular abnormalities underlying this in the BRCA intact tumors remains unknown.

    View details for DOI 10.1186/1471-2407-10-493

    View details for Web of Science ID 000282723000001

    View details for PubMedID 20843305

    View details for PubMedCentralID PMC2946313

  • Analysis of stromal signatures in the tumor microenvironment of ductal carcinoma in situ BREAST CANCER RESEARCH AND TREATMENT Sharma, M., Beck, A. H., Webster, J. A., Espinosa, I., Montgomery, K., Varma, S., van de Rijn, M., Jensen, K. C., West, R. B. 2010; 123 (2): 397-404


    Recent advances in the study of the tumor microenvironment have revealed significant interaction between tumor cells and their surrounding stroma in model systems. We have previously shown that two distinct stromal signatures derived from a macrophage (CSF1) response and a fibroblastic (DTF-like) response are present in subsets of invasive breast cancers and show a correlation with clinical outcome. In the present study we explore whether these signatures also exist in the stroma of ductal carcinoma in situ (DCIS). We studied the signatures by both gene expression profile analysis of a publically available data set of DCIS and by immunohistochemistry (IHC) on a tissue microarray of DCIS and invasive breast cancer cases. Both the gene expression and immunohistochemical data show that the macrophage response and fibroblast expression signatures are present in the stroma of subsets of DCIS cases. The incidence of the stromal signatures in DCIS is similar to the incidence in invasive breast cancer that we have previously reported. We also find that the macrophage response signature is associated with higher grade DCIS and cases which are ER and PR negative, whereas the fibroblast signature was not associated with any clinicopathologic features in DCIS. A comparison of 115 matched cases of DCIS and invasive breast cancer found a correlation between the type of stromal response in DCIS and invasive ductal carcinoma (IDC) within the same patient for both the macrophage response and the fibroblast stromal signatures (P = 0.03 and 0.08, respectively). This study is a first characterization of these signatures in DCIS. These signatures have significant clinicopathologic associations and tend to be conserved as the tumor progresses from DCIS to invasive breast cancer.

    View details for DOI 10.1007/s10549-009-0654-0

    View details for Web of Science ID 000280807900008

    View details for PubMedID 19949854

    View details for PubMedCentralID PMC2976659

  • Human melanoma-initiating cells express neural crest nerve growth factor receptor CD271 NATURE Boiko, A. D., Razorenova, O. V., van de Rijn, M., Swetter, S. M., Johnson, D. L., Ly, D. P., Butler, P. D., Yang, G. P., Joshua, B., Kaplan, M. J., Longaker, M. T., Weissman, I. L. 2010; 466 (7302): 133-U155


    The question of whether tumorigenic cancer stem cells exist in human melanomas has arisen in the last few years. Here we show that in melanomas, tumour stem cells (MTSCs, for melanoma tumour stem cells) can be isolated prospectively as a highly enriched CD271(+) MTSC population using a process that maximizes viable cell transplantation. The tumours sampled in this study were taken from a broad spectrum of sites and stages. High-viability cells isolated by fluorescence-activated cell sorting and re-suspended in a matrigel vehicle were implanted into T-, B- and natural-killer-deficient Rag2(-/-)gammac(-/-) mice. The CD271(+) subset of cells was the tumour-initiating population in 90% (nine out of ten) of melanomas tested. Transplantation of isolated CD271(+) melanoma cells into engrafted human skin or bone in Rag2(-/-)gammac(-/-) mice resulted in melanoma; however, melanoma did not develop after transplantation of isolated CD271(-) cells. We also show that in mice, tumours derived from transplanted human CD271(+) melanoma cells were capable of metastatsis in vivo. CD271(+) melanoma cells lacked expression of TYR, MART1 and MAGE in 86%, 69% and 68% of melanoma patients, respectively, which helps to explain why T-cell therapies directed at these antigens usually result in only temporary tumour shrinkage.

    View details for DOI 10.1038/nature09161

    View details for Web of Science ID 000279343800049

    View details for PubMedID 20596026

    View details for PubMedCentralID PMC2898751

  • DOG1 for the Diagnosis of Gastrointestinal Stromal Tumor (GIST): Comparison Between 2 Different Antibodies APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY Lopes, L. F., West, R. B., Bacchi, L. M., van de Rijn, M., Bacchi, C. E. 2010; 18 (4): 333-337


    Gastrointestinal stromal tumor (GIST) is the most common mesenchymal neoplasm of the gastrointestinal tract. Discovered on GIST-1 (DOG1) is a recently described protein expressed in GISTs irrespective of mutation status. The aim of this study was to investigate the immunohistochemical expression of DOG1 using 2 different monoclonal antibodies (DOG1.1 and the commercially available K9 antibody) in 668 GIST cases and to compare the results with the expression of KIT. DOG1 and KIT expression also were studied in most human normal tissues and several nonmesenchymal and mesenchymal tumors other than GIST. KIT was expressed in 643 (96.3%) GISTs. DOG1.1 and K9 were positive in 538 (80.5%) and 642 (96.1%) GIST cases, respectively. In 25 (3.7%) KIT-negative GIST cases, DOG1 was expressed in 5 (20.0%) and 19 (76.0%) using DOG1.1 and K9 antibodies, respectively. Only 0.9% of GISTs were negative for KIT, DOG1.1, and K9. Most normal human tissues did not reveal KIT and DOG1 expression. DOG1.1 was positive in only 2 of 57 synovial sarcomas and 1 of 61 soft tissue leiomyosarcomas. K9 was positive in 5 of 57 synovial sarcomas, 1 of 14 angiosarcomas, 1 of 61 soft tissue leiomyosarcomas, 3 of 4 adenoid cystic carcinomas of the head and neck, and in myoepithelial cells of 9 of 11 fibroadenomas of the breast. In conclusion, the commercially available K9 is of great utility for the diagnosis of most KIT-negative GISTs, and the combination of both KIT and K9 antibody in a panel of immunohistochemistry can define the diagnosis of GIST in more than 99% of cases.

    View details for DOI 10.1097/PAI.0b013e3181d27ec8

    View details for Web of Science ID 000279059900004

    View details for PubMedID 20571340

  • Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling ONCOGENE Beck, A. H., Lee, C., WITTEN, D. M., Gleason, B. C., Edris, B., Espinosa, I., Zhu, S., Li, R., Montgomery, K. D., Marinelli, R. J., Tibshirani, R., Hastie, T., Jablons, D. M., Rubin, B. P., Fletcher, C. D., West, R. B., van de Rijn, M. 2010; 29 (6): 845-854


    Leiomyosarcoma (LMS) is a soft tissue tumor with a significant degree of morphologic and molecular heterogeneity. We used integrative molecular profiling to discover and characterize molecular subtypes of LMS. Gene expression profiling was performed on 51 LMS samples. Unsupervised clustering showed three reproducible LMS clusters. Array comparative genomic hybridization (aCGH) was performed on 20 LMS samples and showed that the molecular subtypes defined by gene expression showed distinct genomic changes. Tumors from the 'muscle-enriched' cluster showed significantly increased copy number changes (P=0.04). A majority of the muscle-enriched cases showed loss at 16q24, which contains Fanconi anemia, complementation group A, known to have an important role in DNA repair, and loss at 1p36, which contains PRDM16, of which loss promotes muscle differentiation. Immunohistochemistry (IHC) was performed on LMS tissue microarrays (n=377) for five markers with high levels of messenger RNA in the muscle-enriched cluster (ACTG2, CASQ2, SLMAP, CFL2 and MYLK) and showed significantly correlated expression of the five proteins (all pairwise P<0.005). Expression of the five markers was associated with improved disease-specific survival in a multivariate Cox regression analysis (P<0.04). In this analysis that combined gene expression profiling, aCGH and IHC, we characterized distinct molecular LMS subtypes, provided insight into their pathogenesis, and identified prognostic biomarkers.

    View details for DOI 10.1038/onc.2009.381

    View details for Web of Science ID 000274397800007

    View details for PubMedID 19901961

    View details for PubMedCentralID PMC2820592

  • Gene expression profiling for the investigation of soft tissue sarcoma pathogenesis and the identification of diagnostic, prognostic, and predictive biomarkers VIRCHOWS ARCHIV Beck, A. H., West, R. B., van de Rijn, M. 2010; 456 (2): 141-151


    Soft tissue sarcomas are malignant neoplasms derived from mesenchymal tissues. Their pathogenesis is poorly understood and there are few effective treatment options for advanced disease. In the past decade, gene expression profiling has been applied to sarcomas to facilitate understanding of sarcoma pathogenesis and to identify diagnostic, prognostic, and predictive markers. In this paper, we review this body of work and discuss how gene expression profiling has led to advancements in the understanding of sarcoma pathobiology, the identification of clinically useful biomarkers, and the refinement of sarcoma classification schemes. Lastly, we conclude with a discussion of strategies to further optimize the translation of gene expression data into a greater understanding of sarcoma pathogenesis and improved clinical outcomes for sarcoma patients.

    View details for DOI 10.1007/s00428-009-0774-2

    View details for Web of Science ID 000274951700004

    View details for PubMedID 19412622

  • Fibroblast-Like Stromal Response Is Host-Dependent While Macrophage-Associated Stromal Response Is Tumor-Dependent: A Study of Stromal Response in Paired Breast Carcinomas from Patients with Dual Primaries 99th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Wu, J. M., Beck, A. H., WITTEN, D., Allison, K., van de Rijn, M., West, R. B. NATURE PUBLISHING GROUP. 2010: 79A–79A
  • Variations in Stromal Signatures in Breast Cancer Metastases 99th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Webster, J. A., Beck, A. H., Sharma, M., Espinosa, I., Schreuder, M., Montgomery, K. D., Jensen, K. C., van de Rijn, M., West, R. B. NATURE PUBLISHING GROUP. 2010: 77A–77A
  • Meta-Mining of Gene Expression Profiles Identifies MG132 and Cantharidin as Therapeutic Agents with In Vitro Activity Against Leiomyosarcoma 99th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Edris, B., West, R. B., Lee, C. H., Zhu, M., Fletcher, J., van de Rijn, M., Beck, A. H. NATURE PUBLISHING GROUP. 2010: 19A–19A
  • Clinicopathological and Immunohistochemical Study in 148 Uterine Sarcomas: Bcl-2 and Proliferative Markers Identify Different Prognostic Groups of Uterine Leiomyosarcomas 99th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology D'Angelo, E., Ali, R., Espinosa, I., Gilks, C. B., van de Rijn, M., Lee, C., Prat, J. NATURE PUBLISHING GROUP. 2010: 239A–239A
  • Differing Prognostic Significance of Tumor Associated Macrophages in Gastrointestinal Leiomyosarcomas and Gastrointestinal Stromal Tumors 99th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Lee, C. H., Steigen, S. E., Espinosa, I., Lopes, L. F., Bacchi, C. E., Gilks, C. B., Nielsen, T. O., van de Rijn, M. NATURE PUBLISHING GROUP. 2010: 23A–23A
  • 3 '-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples PLOS ONE Beck, A. H., Weng, Z., Witten, D. M., Zhu, S., Foley, J. W., Lacroute, P., Smith, C. L., Tibshirani, R., van de Rijn, M., Sidow, A., West, R. B. 2010; 5 (1)


    Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3'-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF) and solitary fibrous tumor (SFT)) (total n = 23 samples, which were each profiled by at least one of the four platform-tissue preparation combinations). Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR<0.01) on both the frozen tissue (approximately 9.6K genes) and FFPET (approximately 8.1K genes). Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (approximately 4.64K), and analysis of microarray data on FFPET revealed very few (69) differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research.

    View details for DOI 10.1371/journal.pone.0008768

    View details for Web of Science ID 000273778900012

    View details for PubMedID 20098735

    View details for PubMedCentralID PMC2808244

  • Genome-wide transcriptome analyses reveal p53 inactivation mediated loss of miR-34a expression in malignant peripheral nerve sheath tumours JOURNAL OF PATHOLOGY Subramanian, S., Thayanithy, V., West, R. B., Lee, C., Beck, A. H., Zhu, S., Downs-Kelly, E., Montgomery, K., Goldblum, J. R., Hogendoom, P. C., Corless, C. L., Oliveira, A. M., Dry, S. M., Nielsen, T. O., Rubin, B. P., Fletcher, J. A., Fletcher, C. D., van de Rijn, M. 2010; 220 (1): 58-70


    Malignant peripheral nerve sheath tumours (MPNSTs) are aggressive soft tissue tumours that occur either sporadically or in patients with neurofibromatosis type 1. The malignant transformation of the benign neurofibroma to MPNST is incompletely understood at the molecular level. We have determined the gene expression signature for benign and malignant PNSTs and found that the major trend in malignant transformation from neurofibroma to MPNST consists of the loss of expression of a large number of genes, rather than widespread increase in gene expression. Relatively few genes are expressed at higher levels in MPNSTs and these include genes involved in cell proliferation and genes implicated in tumour metastasis. In addition, a gene expression signature indicating p53 inactivation is seen in the majority of MPNSTs. Subsequent microRNA profiling of benign and malignant PNSTs indicated a relative down-regulation of miR-34a in most MPNSTs compared to neurofibromas. In vitro studies using the cell lines MPNST-14 (NF1 mutant) and MPNST-724 (from a non-NF1 individual) show that exogenous expression of p53 or miR-34a promotes apoptotic cell death. In addition, exogenous expression of p53 in MPNST cells induces miR-34a and other miRNAs. Our data show that p53 inactivation and subsequent loss of expression of miR-34a may significantly contribute to the MPNST development. Collectively, our findings suggest that deregulation of miRNAs has a potential role in the malignant transformation process in peripheral nerve sheath tumours.

    View details for DOI 10.1002/path.2633

    View details for Web of Science ID 000273186100008

    View details for PubMedID 19890883

  • A panel of antibodies to determine site of origin and malignancy in smooth muscle tumors MODERN PATHOLOGY Lee, C., Turbin, D. A., Sung, Y. V., Espinosa, I., Montgomery, K., van de Rijn, M., Gilks, C. B. 2009; 22 (12): 1519-1531


    Leiomyosarcomas are malignant smooth muscle tumors that occur most commonly in the gynecologic tract and soft tissue. There are different diagnostic criteria of malignancy for smooth muscle tumors arising at gynecologic and soft tissue sites and they may be managed differently but determining the primary site of a smooth muscle tumor can be difficult in some cases. In addition, the distinction between malignant and benign gynecologic tract smooth muscle tumors on morphologic grounds can be challenging. Using a series of tissue microarrays that contain 245 cases of leiomyosarcomas (102 gynecologic) with survival data, and 49 cases of uterine leiomyoma, we examined the ability of selected immune-markers (estrogen receptor (ER) and WT1) to distinguish between leiomyosarcomas of gynecologic and nongynecologic origin. In addition, we examined whether immunostains for p16, p53 and Ki-67 could distinguish between malignant and benign gynecologic smooth muscle tumors. ER nuclear positivity was observed in 3 and 50% of the nongynecologic and gynecologic leiomyosarcomas, respectively (P<0.001). Nuclear WT1 positivity was seen in 0 and 8% of the nongynecologic and gynecologic leiomyosarcomas, respectively (P<0.001). 87% of primary gynecologic leiomyosarcomas and 2% of uterine leiomyomas showed diffuse (>or=50% of cells) p16 staining (P<0.001). 23% of gynecologic leiomyosarcomas showed p53 immunopositivity (>or=50% of cells) whereas none of the leiomyomas were positive for p53 (P<0.001). 65% of the gynecologic leiomyosarcomas and 0% of the leiomyomas exhibited >10% Ki-67 proliferation index (P<0.001). Diffuse p16 and p53 immunopositivity and high Ki-67 proliferation index, singly or in combination, yielded an overall sensitivity of 92% and specificity of 98% for distinguishing between gynecologic leiomyosarcomas and leiomyomas and can be used as indicators of malignancy for gynecologic smooth muscle tumors. Although ER positivity can be used to support the gynecologic origin of a leiomyosarcomas, nuclear WT1 immunostaining is of little use.

    View details for DOI 10.1038/modpathol.2009.122

    View details for Web of Science ID 000272207200001

    View details for PubMedID 19734847

  • MicroRNA Profiling of BRCA1/2 Mutation-Carrying and Non-Mutation-Carrying High-Grade Serous Carcinomas of Ovary PLOS ONE Lee, C., Subramanian, S., Beck, A. H., Espinosa, I., Senz, J., Zhu, S. X., Huntsman, D., van de Rijn, M., Gilks, C. B. 2009; 4 (10)


    MicroRNAs (miRNA) are 20 approximately 25 nucleotide non-coding RNAs that inhibit the translation of targeted mRNA, and they have been implicated in the development of human malignancies. High grade serous ovarian carcinomas, the most common and lethal subtype of ovarian cancer, can occur sporadically or in the setting of BRCA1/2 syndromes. Little is known regarding the miRNA expression profiles of high grade serous carcinoma in relation to BRCA1/2 status, and compared to normal tubal epithelium, the putative tissue of origin for high grade serous carcinomas.Global miRNA expression profiling was performed on a series of 33 high grade serous carcinomas, characterized with respect to BRCA1/2 status (mutation, epigenetic silencing with loss of expression or normal), and with clinical follow-up, together with 2 low grade serous carcinomas, 2 serous borderline tumors, and 3 normal fallopian tube samples, using miRNA microarrays (328 human miRNA). Unsupervised hierarchical clustering based on miRNA expression profiles showed no clear separation between the groups of carcinomas with different BRCA1/2 status. There were relatively few miRNAs that were differentially expressed between the genotypic subgroups. Comparison of 33 high grade serous carcinomas to 3 normal fallopian tube samples identified several dysregulated miRNAs (false discovery rate <5%), including miR-422b and miR-34c. Quantitative RT-PCR analysis performed on selected miRNAs confirmed the pattern of differential expression shown by microarray analysis. Prognostically, lower level miR-422b and miR-34c in high grade serous carcinomas were both associated with decreased disease-specific survival by Kaplan-Meier analysis (p<0.05).High grade serous ovarian carcinomas with and without BRCA1/2 abnormalities demonstrate very similar miRNA expression profiles. High grade serous carcinomas as a group exhibit significant miRNA dysregulation in comparison to tubal epithelium and the levels of miR-34c and miR-422b appear to be prognostically important.

    View details for DOI 10.1371/journal.pone.0007314

    View details for Web of Science ID 000270593300013

    View details for PubMedID 19798417

  • Validation of immature adipogenic status and identification of prognostic biomarkers in myxoid liposarcoma using tissue microarrays HUMAN PATHOLOGY Cheng, H., Dodge, J., Mehl, E., Liu, S., Poulin, N., van de Rijn, M., Nielsen, T. O. 2009; 40 (9): 1244-1251


    Myxoid liposarcoma displays variably aggressive behavior and responds poorly to available systemic therapies. Expression profiling followed by tissue microarray validation linked to patient outcome is a powerful approach for validating biological mechanisms and identifying prognostic biomarkers. We applied these techniques to independent series of primary myxoid liposarcomas in an effort to assess markers of adipose differentiation in myxoid liposarcoma and to identify prognostic markers that can be efficiently assessed by immunohistochemistry. Candidate genes were selected based on analysis of expression profiles from 9 primary myxoid/round liposarcomas and 45 other soft tissue tumors, and by reference to publicly available data sets. Protein products were validated on an adipose neoplasm tissue microarray, including 32 myxoid liposarcomas linked to patient outcome. Results were scored visually and correlated with clinical outcome by Kaplan-Meier and Cox regression analyses. In the study, by examining expression patterns of several lipogenic regulatory gene products, an immature adipogenic status was verified in myxoid liposarcomas. We also found that expression levels of the ret proto-oncogene, insulin-like growth factor 1 receptor, and insulin-like growth factor 2 correlate with poor metastasis-free survival, supporting a role for ERK/MAPK and PI3K/AKT pathways in clinically aggressive myxoid liposarcomas.

    View details for DOI 10.1016/j.humpath.2009.01.011

    View details for Web of Science ID 000269368800004

    View details for PubMedID 19368956

  • Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Chan, K. S., Espinosa, I., Chao, M., Wong, D., Ailles, L., Diehn, M., Gill, H., Presti, J., Chang, H. Y., van de Rijn, M., Shortliffe, L., Weissman, I. L. 2009; 106 (33): 14016-14021


    Major clinical issues in bladder cancer include the identification of prediction markers and novel therapeutic targets for invasive bladder cancer. In the current study, we describe the isolation and characterization of a tumor-initiating cell (T-IC) subpopulation in primary human bladder cancer, based on the expression of markers similar to that of normal bladder basal cells (Lineage-CD44(+)CK5(+)CK20(-)). The bladder T-IC subpopulation was defined functionally by its enriched ability to induce xenograft tumors in vivo that recapitulated the heterogeneity of the original tumor. Further, molecular analysis of more than 300 bladder cancer specimens revealed heterogeneity among activated oncogenic pathways in T-IC (e.g., 80% Gli1, 45% Stat3, 10% Bmi-1, and 5% beta-catenin). Despite this molecular heterogeneity, we identified a unique bladder T-IC gene signature by gene chip analysis. This T-IC gene signature, which effectively distinguishes muscle-invasive bladder cancer with worse clinical prognosis from non-muscle-invasive (superficial) cancer, has significant clinical value. It also can predict the progression of a subset of recurring non-muscle-invasive cancers. Finally, we found that CD47, a protein that provides an inhibitory signal for macrophage phagocytosis, is highly expressed in bladder T-ICs compared with the rest of the tumor. Blockade of CD47 by a mAb resulted in macrophage engulfment of bladder cancer cells in vitro. In summary, we have identified a T-IC subpopulation with potential prognostic and therapeutic value for invasive bladder cancer.

    View details for DOI 10.1073/pnas.0906549106

    View details for Web of Science ID 000269078700071

    View details for PubMedID 19666525

    View details for PubMedCentralID PMC2720852

  • Other Targetable Sarcomas SEMINARS IN ONCOLOGY de Camargo, V. P., van de Rijn, M., de Alava, E., Madoz-Gurpide, J., Pilotti, S., von Mehren, M., Pedeutour, F., Maki, R. G., Rutkowski, P., Thomas, D. M. 2009; 36 (4): 358-371


    Despite complex genetics, aneuploid tumors like dedifferentiated liposarcoma have specific and reproducible chromosomal changes such as amplification of HDM2 and CDK4 that represent potential targets for systemic therapy. In addition, there are cancer cell survival pathways that may not be the target of chromosomal translocations or mutations that are still estimable targets for new systemic therapeutics, be it pathways involved in angiogenesis or apoptosis. In this review, we examine target selection for specific sarcoma subtypes, and demonstrate with a few examples new techniques being used to delineate novel therapeutic inroads for patients with sarcoma.

    View details for DOI 10.1053/j.seminoncol.2009.06.008

    View details for Web of Science ID 000268899600008

    View details for PubMedID 19664496

  • Ror2, a developmentally regulated kinase, promotes tumor growth potential in renal cell carcinoma ONCOGENE Wright, T. M., Brannon, A. R., Gordan, J. D., Mikels, A. J., Mitchell, C., Chen, S., Espinosa, I., van de Rijn, M., Pruthi, R., Wallen, E., Edwards, L., Nusse, R., Rathmell, W. K. 2009; 28 (27): 2513-2523


    Inappropriate kinase expression and subsequent promiscuous activity defines the transformation of many solid tumors including renal cell carcinoma (RCC). Thus, the expression of novel tumor-associated kinases has the potential to dramatically shape tumor cell behavior. Further, identifying tumor-associated kinases can lend insight into patterns of tumor growth and characteristics. Here, we report the identification of the RTK-like orphan receptor 2 (Ror2), a new tumor-associated kinase in RCC cell lines and primary tumors. Ror2 is an orphan receptor tyrosine kinase with physiological expression normally seen in the embryonic kidney. However, in RCC, Ror2 expression correlated with expression of genes involved at the extracellular matrix, including Twist and matrix metalloprotease-2 (MMP2). Expression of MMP2 in RCC cells was suppressed by Ror2 knockdown, placing Ror2 as a mediator of MMP2 regulation in RCC and a potential regulator of extracellular matrix remodeling. The suppression of Ror2 not only inhibited cell migration, but also inhibited anchorage-independent growth in soft agar and growth in an orthotopic xenograft model. These findings suggest a novel pathway of tumor-promoting activity by Ror2 within a subset of renal carcinomas, with significant implications for unraveling the tumorigenesis of RCC.

    View details for DOI 10.1038/onc.2009.116

    View details for Web of Science ID 000267806800004

    View details for PubMedID 19448672

    View details for PubMedCentralID PMC2771692

  • Coordinate Expression of Colony-Stimulating Factor-1 and Colony-Stimulating Factor-1-Related Proteins Is Associated with Poor Prognosis in Gynecological and Nongynecological Leiomyosarcoma AMERICAN JOURNAL OF PATHOLOGY Espinosa, I., Beck, A. H., Lee, C., Zhu, S., Montgomery, K. D., Marinelli, R. J., Ganjoo, K. N., Nielsen, T. O., Gilks, C. B., West, R. B., van de Rijn, M. 2009; 174 (6): 2347-2356


    Previously, we showed that the presence of high numbers of macrophages correlates with poor prognosis in nongynecological leiomyosarcoma (LMS). In gynecological LMS, a similar trend was noted but did not reach statistical significance. Colony-stimulating factor-1 (CSF1) is a major chemoattractant for macrophages. Here we show that in a subset of LMS cases, CSF1 is expressed by the malignant cells. Previously, we found that CSF1 is translocated and highly expressed in tenosynovial giant cell tumors (TGCTs), and this observation allowed us to identify genes that showed a coordinate expression with CSF1. Here, we evaluated the expression of CSF1 and TGCT-associated proteins in 149 cases of LMS. The coordinate expression of CSF1 and three TGCT-associated proteins (CD163, FCGR3a, and CTSL1) identified cases with poor prognosis in both gynecological LMS (P = 0.00006) and nongynecological LMS (P = 0.03). In gynecological LMS, the coordinate expression of these four markers was the only independent prognosticator in multivariate analysis (hazard ratio, 4.2; 95% CI, 1.12 to 16; P = 0.03). Our findings indicate that CSF1 may play an important role in the clinical behavior of LMS that may open a window for new therapeutic reagents.

    View details for DOI 10.2353/ajpath.2009.081037

    View details for Web of Science ID 000266370600037

    View details for PubMedID 19443701

    View details for PubMedCentralID PMC2684198

  • Ano1 is a selective marker of interstitial cells of Cajal in the human and mouse gastrointestinal tract AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY Gomez-Pinilla, P. J., Gibbons, S. J., Bardsley, M. R., Lorincz, A., Pozo, M. J., Pasricha, P. J., van de Rijn, M., West, R. B., Sarr, M. G., Kendrick, M. L., Cima, R. R., Dozois, E. J., Larson, D. W., Ordog, T., Farrugia, G. 2009; 296 (6): G1370-G1381


    Populations of interstitial cells of Cajal (ICC) are altered in several gastrointestinal neuromuscular disorders. ICC are identified typically by ultrastructure and expression of Kit (CD117), a protein that is also expressed on mast cells. No other molecular marker currently exists to independently identify ICC. The expression of ANO1 (DOG1, TMEM16A), a Ca(2+)-activated Cl(-) channel, in gastrointestinal stromal tumors suggests it may be useful as an ICC marker. The aims of this study were therefore to determine the distribution of Ano1 immunoreactivity compared with Kit and to establish whether Ano1 is a reliable marker for human and mouse ICC. Expression of Ano1 in human and mouse stomach, small intestine, and colon was investigated by immunofluorescence labeling using antibodies to Ano1 alone and in combination with antibodies to Kit. Colocalization of immunoreactivity was demonstrated by epifluorescence and confocal microscopy. In the muscularis propria, Ano1 immunoreactivity was restricted to cells with the morphology and distribution of ICC. All Ano1-positive cells in the muscularis propria were also Kit positive. Kit-expressing mast cells were not Ano1 positive. Some non-ICC in the mucosa and submucosa of human tissues were Ano1 positive but Kit negative. A few (3.2%) Ano1-positive cells in the human gastric muscularis propria were labeled weakly for Kit. Ano1 labels all classes of ICC and represents a highly specific marker for studying the distribution of ICC in mouse and human tissues with an advantage over Kit since it does not label mast cells.

    View details for DOI 10.1152/ajpgi.00074.2009

    View details for Web of Science ID 000266453300023

    View details for PubMedID 19372102

    View details for PubMedCentralID PMC2697941

  • LC3-mediated fibronectin mRNA translation induces fibrosarcoma growth by increasing connective tissue growth factor JOURNAL OF CELL SCIENCE Ying, L., Lau, A., Alvira, C. M., West, R., Cann, G. M., Zhou, B., Kinnear, C., Jan, E., Sarnow, P., van de Rijn, M., Rabinovitch, M. 2009; 122 (9): 1441-1451


    Previously, we related fibronectin (Fn1) mRNA translation to an interaction between an AU-rich element in the Fn1 3' UTR and light chain 3 (LC3) of microtubule-associated proteins 1A and 1B. Since human fibrosarcoma (HT1080) cells produce little fibronectin and LC3, we used these cells to investigate how LC3-mediated Fn1 mRNA translation might alter tumor growth. Transfection of HT1080 cells with LC3 enhanced fibronectin mRNA translation. Using polysome analysis and RNA-binding assays, we show that elevated levels of translation depend on an interaction between a triple arginine motif in LC3 and the AU-rich element in Fn1 mRNA. Wild-type but not mutant LC3 accelerated HT1080 cell growth in culture and when implanted in SCID mice. Comparison of WT LC3 with vector-transfected HT1080 cells revealed increased fibronectin-dependent proliferation, adhesion and invasion. Microarray analysis of genes differentially expressed in WT and vector-transfected control cells indicated enhanced expression of connective tissue growth factor (CTGF). Using siRNA, we show that enhanced expression of CTGF is fibronectin dependent and that LC3-mediated adhesion, invasion and proliferation are CTGF dependent. Expression profiling of soft tissue tumors revealed increased expression of both LC3 and CTGF in some locally invasive tumor types.

    View details for DOI 10.1242/jcs.025957

    View details for Web of Science ID 000265443300020

    View details for PubMedID 19366727

    View details for PubMedCentralID PMC2672968

  • A compact VEGF signature associated with distant metastases and poor outcomes BMC MEDICINE Hu, Z., Fan, C., Livasy, C., He, X., Oh, D. S., Ewend, M. G., Carey, L. A., Subramanian, S., West, R., Ikpatt, F., Olopade, O. I., van de Rijn, M., Perou, C. M. 2009; 7


    Tumor metastases pose the greatest threat to a patient's survival, and thus, understanding the biology of disseminated cancer cells is critical for developing effective therapies.Microarrays and immunohistochemistry were used to analyze primary breast tumors, regional (lymph node) metastases, and distant metastases in order to identify biological features associated with distant metastases.When compared with each other, primary tumors and regional metastases showed statistically indistinguishable gene expression patterns. Supervised analyses comparing patients with distant metastases versus primary tumors or regional metastases showed that the distant metastases were distinct and distinguished by the lack of expression of fibroblast/mesenchymal genes, and by the high expression of a 13-gene profile (that is, the 'vascular endothelial growth factor (VEGF) profile') that included VEGF, ANGPTL4, ADM and the monocarboxylic acid transporter SLC16A3. At least 8 out of 13 of these genes contained HIF1alpha binding sites, many are known to be HIF1alpha-regulated, and expression of the VEGF profile correlated with HIF1alpha IHC positivity. The VEGF profile also showed prognostic significance on tests of sets of patients with breast and lung cancer and glioblastomas, and was an independent predictor of outcomes in primary breast cancers when tested in models that contained other prognostic gene expression profiles and clinical variables.These data identify a compact in vivo hypoxia signature that tends to be present in distant metastasis samples, and which portends a poor outcome in multiple tumor types.This signature suggests that the response to hypoxia includes the ability to promote new blood and lymphatic vessel formation, and that the dual targeting of multiple cell types and pathways will be needed to prevent metastatic spread.

    View details for DOI 10.1186/1741-7015-7-9

    View details for Web of Science ID 000265841300001

    View details for PubMedID 19291283

    View details for PubMedCentralID PMC2671523

  • Intraepithelial T cells and prognosis in ovarian carcinoma: novel associations with stage, tumor type, and BRCA1 loss MODERN PATHOLOGY Clarke, B., Tinker, A. V., Lee, C., Subramanian, S., van de Rijn, M., Turbin, D., Kalloger, S., Han, G., Ceballos, K., Cadungog, M. G., Huntsman, D. G., Coukos, G., Gilks, C. B. 2009; 22 (3): 393-402


    Intraepithelial tumor-infiltrating T cells have been correlated with improved outcomes in ovarian carcinoma, however, it is not known whether there is an association with disease stage, histological subtype, or BRCA mutation/expression. Two case series of ovarian carcinomas were included in the study; a retrospective series of 500 patients, and 40 prospectively collected cases fully characterized for BRCA1 mutation status and expression. Intraepithelial immune cells were assessed as present or absent by immunohistochemical staining of tissue microarrays. In the retrospective case series, the presence of intraepithelial CD8(+) T-cells correlated with improved disease-specific survival (P=0.027), whereas intraepithelial CD3(+) T cells did not (P=0.49). For serous ovarian carcinomas, the presence of intraepithelial CD3(+) and CD8(+) T-cells correlated with improved disease-specific survival (P=0.0016 and P

    View details for DOI 10.1038/modpathol.2008.191

    View details for Web of Science ID 000263722600007

    View details for PubMedID 19060844

  • The Macrophage Colony-Stimulating Factor 1 Response Signature in Breast Carcinoma CLINICAL CANCER RESEARCH Beck, A. H., Espinosa, I., Edris, B., Li, R., Montgomery, K., Zhu, S., Varma, S., Marinelli, R. J., van de Rijn, M., West, R. B. 2009; 15 (3): 778-787


    Macrophages play an important role in breast carcinogenesis. The pathways that mediate the macrophage contribution to breast cancer and the heterogeneity that exists within macrophages are incompletely understood. Macrophage colony-stimulating factor 1 (CSF1) is the primary regulator of tissue macrophages. The purpose of this study was to define a novel CSF1 response signature and to evaluate its clinical and biological significance in breast cancer.We defined the CSF1 response signature by identifying genes overexpressed in tenosynovial giant cell tumor and pigmented villonodular synovitis (tumors composed predominantly of macrophages recruited in response to the overexpression of CSF1) compared with desmoid-type fibromatosis and solitary fibrous tumor. To characterize the CSF1 response signature in breast cancer, we analyzed the expression of CSF1 response signature genes in eight published breast cancer gene expression data sets (n = 982) and did immunohistochemistry and in situ hybridization for CSF1 response genes on a breast cancer tissue microarray (n = 283).In both the gene microarray and tissue microarray analyses, a consistent subset (17-25%) of breast cancers shows the CSF1 response signature. The signature is associated with higher tumor grade, decreased expression of estrogen receptor, decreased expression of progesterone receptor, and increased TP53 mutations (P < 0.001).Our data show that the CSF1 response signature is consistently seen in a subset of breast carcinomas and correlates with biological features of the tumor. Our findings provide insight into macrophage biology and may facilitate the development of personalized therapy for patients most likely to benefit from CSF1-targeted treatments.

    View details for DOI 10.1158/1078-0432.CCR-08-1283

    View details for Web of Science ID 000263213600006

    View details for PubMedID 19188147

    View details for PubMedCentralID PMC2987696

  • Discovery of Molecular Subtypes in Leiomyosarcoma through Integrative Molecular Profiling 98th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Beck, A. H., Lee, C. H., WITTEN, D. M., Zhou, S., Montgomery, K., Tibshirani, R., Hastie, T., West, R. B., van de Rijn, M. NATURE PUBLISHING GROUP. 2009: 368A–368A
  • CSF-1 and Fibromatosis Expression in Stroma of Ductal Carcinoma In Situ 98th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Sharma, M., Espinosa, I., Beck, A. H., Webster, J. A., Montgomery, K. D., van de Rijn, M., Jensen, K. C., West, R. B. NATURE PUBLISHING GROUP. 2009: 67A–67A
  • Discovery of Molecular Subtypes in Leiomyosarcoma through Integrative Molecular Profiling 98th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Beck, A. H., Lee, C. H., WITTEN, D. M., Zhou, S., Montgomery, K., Tibshirani, R., Hastie, T., West, R. B., van de Rijn, M. NATURE PUBLISHING GROUP. 2009: 368A–368A
  • Immunohistochemical Profiling of 312 Gynecologic and Soft Tissue Smooth Muscle Tumors 98th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Lee, C. H., Sung, V., Montgomery, K., van de Rijn, M., Gilks, C. B. NATURE PUBLISHING GROUP. 2009: 223A–224A
  • Characterization of a novel anti-fatty acid synthase (FASN) antiserum in breast tissue 97th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Jensen, K. C., Schaeffer, D. F., Cheang, M., Montgomery, K., West, R. B., Gilks, C. B., Ross, D., Turashvili, G., Schnitt, S., van de Rijn, M. NATURE PUBLISHING GROUP. 2008: 1413–20


    Fatty acid synthase (FASN) expression has been reported in many different tumors, including breast cancer. In gene microarray studies, the fatty acid synthase gene co-clustered with cytokeratins 5 and 17 and other genes that defined the basal-like subset of breast cancers. To define the use of this marker in breast pathology, a rabbit polyclonal antiserum (S143) to a peptide fragment of this gene was produced and compared with a commercially available monoclonal antibody by immunohistochemistry on various tissue microarrays and whole tissue sections. The tissue microarrays included 1090 breast cancers and 244 normal breast tissues. Whole tissue sections consisted of benign and malignant tissues from breast resection specimens. In contrast to other 'basal' markers identified by gene expression profiling data, the fatty acid synthase (FASN) expression pattern in normal breast was notable for its expression in only a small subset of basal and suprabasal cells. Dual staining experiments revealed that the subpopulation of cells labeling with FASN did not coexpress myoepithelial markers CK5/6 or p63, but did coexpress e-cadherin. In addition to staining a subset of basal and suprabasal cells, the antiserum highlighted apocrine differentiation, and stained 106/144 (74%) cases of columnar cell lesions and five of five cases of flat epithelial atypia. Despite its association with basal keratins in gene array studies, FASN expression did not correlate significantly with the outcome in breast cancer. We describe an expression pattern that highlights only a subset of basal and suprabasal cells in normal breast ducts and we show by dual expression studies that this subset of cells is different from myoepithelial and basal cytokeratin-positive cells. In addition, FASN expression is described in apocrine metaplasia, columnar cell lesions, and flat epithelial atypia.

    View details for DOI 10.1038/modpathol.2008.163

    View details for Web of Science ID 000261109000001

    View details for PubMedID 18820672

  • Immunohistochemical and Biogenetic Features of Diffuse-Type Tenosynovial Giant Cell Tumors: The Potential Roles of Cyclin A, P53, and Deletion of 15q in Sarcomatous Transformation CLINICAL CANCER RESEARCH Huang, H., West, R. B., Tzeng, C., van de Rijn, M., Wang, J., Chou, S., Huang, W., Eng, H., Lin, C., Yu, S., Wu, J., Lu, C., Li, C. 2008; 14 (19): 6023-6032


    Diffuse-type tenosynovial giant cell tumor (D-TSGCT) is an aggressive proliferation of synovial-like mononuclear cells with inflammatory infiltrates. Despite the COL6A3-CSF1 gene fusion discovered in benign lesions, molecular aberrations of malignant D-TSGCTs remain unidentified.We used fluorescent in situ hybridization and in situ hybridization to evaluate CSF1 translocation and mRNA expression in six malignant D-TSGCTs, which were further immunohistochemically compared with 24 benign cases for cell cycle regulators involving G(1) phase and G(1)-S transition. Comparative genomic hybridization, real-time reverse transcription-PCR, and a combination of laser microdissection and sequencing were adopted to assess chromosomal imbalances, cyclin A expression, and TP53 gene, respectively.Five of six malignant D-TSGCTs displayed CSF1 mRNA expression by in situ hybridization, despite only one having CSF1 translocation. Cyclin A (P = 0.008) and P53 (P < 0.001) could distinguish malignant from benign lesions without overlaps in labeling indices. Cyclin A transcripts were more abundant in malignant D-TSGCTs (P < 0.001). All malignant cases revealed a wild-type TP53 gene, which was validated by an antibody specifically against wild-type P53 protein. Chromosomal imbalances were only detected in malignant D-TSGCTs, with DNA losses predominating over gains. Notably, -15q was recurrently identified in five malignant D-TSGCTs, four of which showed a minimal overlapping deletion at 15q22-24.Deregulated CFS1 overexpression is frequent in malignant D-TSGCTs. The sarcomatous transformation involves aberrations of cyclin A, P53, and chromosome arm 15q. Cyclin A mRNA is up-regulated in malignant D-TSGCTs. Non-random losses at 15q22-24 suggest candidate tumor suppressor gene(s) in this region. However, P53 overexpression is likely caused by alternative mechanisms rather than mutations in hotspot exons.

    View details for DOI 10.1158/1078-0432.CCR-08-0252

    View details for Web of Science ID 000260142500013

    View details for PubMedID 18829481

  • Diffuse myogenin expression by immunohistochemistry is an independent marker of poor survival in pediatric rhabdomyosarcoma - A tissue microarray study of 71 primary tumors including correlation with molecular phenotype AMERICAN JOURNAL OF SURGICAL PATHOLOGY Heerema-McKenney, A., Wijnaendts, L. C., Pulliam, J. F., Lopez-Terrada, D., McKenney, J. K., Zhu, S., Montgomery, K., Mitchell, J., Marinelli, R. J., Hart, A. A., van de Rijn, M., Linn, S. C. 2008; 32 (10): 1513-1522


    The pathologic classification of rhabdomyosarcoma (RMS) into embryonal or alveolar subtype is an important prognostic factor guiding the therapeutic protocol chosen for an individual patient. Unfortunately, this classification is not always straightforward, and the diagnostic criteria are controversial in a subset of cases. Ancillary studies are used to aid in the classification, but their potential use as independent prognostic factors is rarely studied. The aim of this study is to identify immunohistochemical markers of potential prognostic significance in pediatric RMS and to correlate their expression with PAX-3/FKHR and PAX-7/FKHR fusion status. A single tissue microarray containing 71 paraffin-embedded pediatric RMSs was immunostained with antibodies against p53, bcl-2, Ki-67, CD44, myogenin, and MyoD1. The tissue microarray and whole paraffin blocks were studied for PAX-3/FKHR and PAX-7/FKHR gene fusions by fluorescence in situ hybridization and reverse transcription-polymerase chain reaction. Clinical follow-up data were available for each patient. Immunohistochemical staining results and translocation status were correlated with recurrence-free interval (RFI) and overall survival (OS) using the Kaplan-Meier method, the log-rank test, and Cox proportional hazard regression. The minimum clinical follow-up interval was 24 months (median follow-up=57 mo). On univariable analysis, immunohistochemical expression of myogenin, bcl-2, and identification of a gene fusion were associated with decreased 5-year RFI and 10-year OS (myogenin RFI P=0.0028, OS P=0.0021; bcl-2 RFI P=0.037, OS P=0.032; gene fusion RFI P=0.0001, OS P=0.0058). After adjustment for Intergroup Rhabdomyosarcoma Study-TNM stage, tumor site, age, tumor histology, and translocation status by multivariable analysis, only myogenin retained an independent association with RFI (P=0.034) and OS (P=0.0069). In this retrospective analysis, diffuse immunohistochemical reactivity for myogenin in RMS correlates with decreased RFI and OS, independent of histologic subtype, translocation status, tumor site, or stage.

    View details for Web of Science ID 000259684300010

    View details for PubMedID 18708938

  • Automated quantitative analysis of estrogen receptor expression in breast carcinoma does not differ from expert pathologist scoring: a tissue microarray study of 3,484 cases BREAST CANCER RESEARCH AND TREATMENT Turbin, D. A., Leung, S., Cheang, M. C., Kennecke, H. A., Montgomery, K. D., McKinney, S., Treaba, D. O., Boyd, N., Goldstein, L. C., Badve, S., Gown, A. M., van de Rijn, M., Nielsen, T. O., Gilks, C. B., Huntsman, D. G. 2008; 110 (3): 417-426


    Estrogen receptor (ER) expression is routinely assessed by immunohistochemistry (IHC) in breast carcinoma. Our study compares visual scoring of ER in invasive breast cancer by histopathologists to quantitation of staining using a fully automated system.A tissue microarray was constructed from 4,049 cases (3,484 included in analysis) of invasive breast carcinoma linked to treatment and outcome information. Slides were scored independently by two pathologists and scores were dichotomised, with ER positivity recognized at a cut-off of >1% positive nuclei. The slides were scanned and analyzed with an Ariol automated system.Using data dichotomised as ER positive or negative, both visual and automated scores were highly consistent: there was excellent concordance between two pathologists (kappa = 0.918 (95%CI: 0.903-0.932)) and between two Ariol machines (kappa = 0.913 (95%CI: 0.897-0.928)). The prognostic significance of ER positivity was similar whether determined by pathologist or automated scoring for both the entire patient cohort and subsets of patients treated with tamoxifen alone or receiving no systemic adjuvant therapy. The optimal cut point for the automated scores using breast cancer disease-specific survival as an endpoint was >0.4% positive nuclei. The concordance between dextran-coated charcoal ER biochemical assay data and automated scores (kappa = 0.728 (95%CI: 0.69-0.75); 0.74 (95%CI: 0.71-0.77)) was similar to the concordance between biochemical assay and pathologist scores (kappa = 0.72 (95%CI: 0.70-0.75; 0.70 (95%CI: 0.67-0.72)).Fully automated quantitation of ER immunostaining yields results that do not differ from human scoring against both biochemical assay and patient outcome gold standards.

    View details for DOI 10.1007/s10549-007-9736-z

    View details for Web of Science ID 000257486600003

    View details for PubMedID 17912629

  • The fibromatosis signature defines a robust stromal response in breast carcinoma LABORATORY INVESTIGATION Beck, A. H., Espinosa, I., Gilks, C. B., van de Rijn, M., West, R. B. 2008; 88 (6): 591-601


    Breast cancer is a heterogeneous disease, and the influence of stromal gene and protein expression patterns on the biological and clinical heterogeneity of the disease is poorly understood. We previously demonstrated that evaluation of the gene expression patterns of two soft-tissue tumors (desmoid-type fibromatosis (DTF) and solitary fibrous tumor) could be used to identify distinct stromal reaction patterns in breast carcinoma. In the current study, we examined four additional data sets obtained from four different institutions and containing gene expression data from a total of 561 breast cancer patients. We identified a core set of 66 DTF-associated genes that were consistently coordinately expressed in a subset of 25-35% of breast cancers. Breast carcinomas defined by high levels of coordinated expression of DTF core genes tend to be lower grade, express estrogen receptor, and show significantly longer survival across the four data sets. Using multiple tissue microarrays of archival breast cancer specimens obtained from a total of 745 patients, we demonstrated that a subset of breast cancers show coordinate expression of DTF core proteins by stromal cells in the tumor microenvironment. We evaluated the protein expression of a single DTF core protein (SPARC) on a tissue microarray with clinical outcome data and demonstrated that breast cancers with strong stromal protein expression of SPARC show a trend for increased survival. Our data demonstrate that the DTF core gene set is a robust descriptor of a distinct stromal response that is associated with improved clinical outcome in breast cancer patients.

    View details for DOI 10.1038/labinvest.2008.31

    View details for Web of Science ID 000256114600003

    View details for PubMedID 18414401

  • Histone deacetylase inhibitors reverse SS18-SSX-mediated polycomb silencing of the tumor suppressor early growth response 1 in synovial sarcoma CANCER RESEARCH Lubieniecka, J. M., de Bruijn, D. R., Su, L., van Dijk, A. H., Subramanian, S., van de Rijn, M., Poulin, N., van Kessel, A. G., Nielsen, T. O. 2008; 68 (11): 4303-4310


    Synovial sarcoma is a soft tissue malignancy characterized by the fusion of SS18 to either SSX1, SSX2, or SSX4 genes. SS18 and SSX are transcriptional cofactors involved in activation and repression of gene transcription, respectively. SS18 interacts with SWI/SNF, whereas SSX associates with the polycomb chromatin remodeling complex. Thus, fusion of these two proteins brings together two opposing effects on gene expression and chromatin structure. Recent studies have shown that a significant number of genes are down-regulated by the SS18-SSX fusion protein and that the clinically applicable histone deacetylase (HDAC) inhibitor romidepsin inhibits synovial sarcoma growth. Therefore, we set out to identify direct targets of SS18-SSX among genes down-regulated in synovial sarcoma and investigated if romidepsin can specifically counteract SS18-SSX-mediated transcriptional dysregulation. Here, we report that the tumor suppressor early growth response 1 (EGR1) is repressed by the SS18-SSX protein through a direct association with the EGR1 promoter. This SS18-SSX binding correlates with trimethylation of Lys(27) of histone H3 (H3K27-M3) and recruitment of polycomb group proteins to this promoter. In addition, we found that romidepsin treatment reverts these modifications and reactivates EGR1 expression in synovial sarcoma cell models. Our data implicate polycomb-mediated epigenetic gene repression as a mechanism of oncogenesis in synovial sarcoma. Furthermore, our work highlights a possible mechanism behind the efficacy of a clinically applicable HDAC inhibitor in synovial sarcoma treatment.

    View details for DOI 10.1158/0008-5472.CAN-08-0092

    View details for Web of Science ID 000256484000035

    View details for PubMedID 18519690

  • Diagnostic implications of podoplanin expression in peripheral nerve sheath neoplasms AMERICAN JOURNAL OF CLINICAL PATHOLOGY Jokinen, C. H., Dadras, S. S., Goldblum, J. R., van de Rijn, M., West, R. B., Rubin, B. P. 2008; 129 (6): 886-893


    By using the D2-40 antibody, we have observed podoplanin expression in Schwann cells and perineurial cells. Podoplanin expression has not been well characterized in peripheral nerve sheath tumors. Because neoplasms of neural crest lineage, including peripheral nerve sheath and melanocytic neoplasms, may share histologic and immunohistochemical characteristics, we evaluated podoplanin and S-100 expression in these lesions to determine the usefulness of podoplanin as a diagnostic marker. Diffuse podoplanin and S-100 expression was observed in 16 (76%) of 21 classical schwannomas, 6 (100%) of 6 cellular schwannomas, and 3 (75%) of 4 epithelioid malignant peripheral nerve sheath tumors (EMPNSTs). Podoplanin was expressed in 3 (7%) of 43 neurofibromas, 16 (21%) of 75 spindle cell MPNSTs (SMPNSTs), and 1 (10%) of 10 spindle cell melanomas but was absent in conventional melanoma. Only rare neurofibromas and SMPNSTs showed strong coexpression of podoplanin and S-100. These results suggest diffuse podoplanin expression or coexpression of podoplanin and S-100 is limited to schwannoma and EMPNST and may be useful in the evaluation of these neoplasms.

    View details for DOI 10.1309/M7D5KTVYYE51XYQA

    View details for Web of Science ID 000255959700006

    View details for PubMedID 18480004

  • Predictive value of tumor associated histiocytes in patients with leiomyosarcoma Ganjoo, K. N., WITTEN, D., Patel, M., Espinosa, I., La, T., West, R., Jacobs, C., van de Rijn, M. AMER SOC CLINICAL ONCOLOGY. 2008
  • Gene expression profiling identifies p63 as a diagnostic marker for giant cell tumor of the bone MODERN PATHOLOGY Lee, C., Espinosa, I., Jensen, K. C., Subramanian, S., Zhu, S. X., Varma, S., Montgomery, K. D., Nielsen, T. O., van de Rijn, M., West, R. B. 2008; 21 (5): 531-539


    Giant cell tumor of the bone (GCTOB) is a primary bone tumor that occurs mainly in young adults and is capable of locally aggressive growth. Its histologic appearance can resemble a number of benign and malignant tumors but no useful diagnostic marker is known currently. To identify diagnostic markers for this tumor, global gene expression profiling using cDNA microarray was performed on 6 fresh-frozen GCTOB, 3 aneurysmal bone cysts, 4 fibrous dysplasias and 12 giant cell tumors of tendon sheath/diffuse-type giant cell tumors. Unsupervised hierarchical clustering separated the tumors based on their histopathologic types, and significance analysis of microarray identified several genes including TP73L (encoding the p63 protein) that are significantly highly expressed in GCTOB relative to these other tumors. The diagnostic utility of p63 was subsequently confirmed using anti-p63 antibody on a series of 26 GCTOB, 25 aneurysmal bone cysts, 15 chondroblastomas, 13 giant cell reparative granulomas, 13 chondromyxoid fibromas, 4 brown tumors, 4 fibrous dysplasias, 53 giant cell tumors of tendon sheath/diffuse-type giant cell tumors and 385 additional mesenchymal tumors in tissue microarrays. Strong p63 nuclear staining was present in 18 of 26 (69%) GCTOB, 3 of 15 (20%) chondroblastomas and in 1 of 25 (4%) aneurysmal bone cysts while none of the other tumors commonly considered in the differential diagnosis of GCTOB showed any detectable p63 staining. Strong p63 staining is rare in bone and soft-tissue tumors in general. In contrast to the pattern of p63 staining, the majority of the chondroblastomas (70%) demonstrated S-100 immunoreactivity while only a minority of the GCTOB (8%) was immunoreactive for S-100. These findings altogether show that p63 can be used as a diagnostic marker to aid the clinical diagnosis of GCTOB.

    View details for DOI 10.1038/modpathol.3801023

    View details for Web of Science ID 000255256600004

    View details for PubMedID 18192965

  • Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer PLOS GENETICS Kwei, K. A., Bashyam, M. D., Kao, J., Ratheesh, R., Reddy, E. C., Kim, Y. H., Montgomery, K., Giacomini, C. P., Choi, Y., Chatterjee, S., Karikari, C. A., Salari, K., Wang, P., Hernandez-Boussard, T., Swarnalata, G., van de Rijn, M., Maitra, A., Pollack, J. R. 2008; 4 (5)


    Pancreatobiliary cancers have among the highest mortality rates of any cancer type. Discovering the full spectrum of molecular genetic alterations may suggest new avenues for therapy. To catalogue genomic alterations, we carried out array-based genomic profiling of 31 exocrine pancreatic cancers and 6 distal bile duct cancers, expanded as xenografts to enrich the tumor cell fraction. We identified numerous focal DNA amplifications and deletions, including in 19% of pancreatobiliary cases gain at cytoband 18q11.2, a locus uncommonly amplified in other tumor types. The smallest shared amplification at 18q11.2 included GATA6, a transcriptional regulator previously linked to normal pancreas development. When amplified, GATA6 was overexpressed at both the mRNA and protein levels, and strong immunostaining was observed in 25 of 54 (46%) primary pancreatic cancers compared to 0 of 33 normal pancreas specimens surveyed. GATA6 expression in xenografts was associated with specific microarray gene-expression patterns, enriched for GATA binding sites and mitochondrial oxidative phosphorylation activity. siRNA mediated knockdown of GATA6 in pancreatic cancer cell lines with amplification led to reduced cell proliferation, cell cycle progression, and colony formation. Our findings indicate that GATA6 amplification and overexpression contribute to the oncogenic phenotypes of pancreatic cancer cells, and identify GATA6 as a candidate lineage-specific oncogene in pancreatobiliary cancer, with implications for novel treatment strategies.

    View details for DOI 10.1371/journal.pgen.1000081

    View details for Web of Science ID 000256869100012

    View details for PubMedID 18535672

    View details for PubMedCentralID PMC2413204

  • A systems biology approach to anatomic diversity of skin JOURNAL OF INVESTIGATIVE DERMATOLOGY Rinn, J. L., Wang, J. K., Liu, H., Montgomery, K., van de Rijn, M., Chang, H. Y. 2008; 128 (4): 776-782


    Human skin exhibits exquisite site-specific morphologies and functions. How are these site-specific differences specified during development, maintained in adult homeostasis, and potentially perturbed by disease processes? Here, we review progress in understanding the anatomic patterning of fibroblasts, a major constituent cell type of the dermis and key participant in epithelial-mesenchymal interactions. The gene expression programs of human fibroblasts largely reflect the superimposition of three gene expression profiles that demarcate the fibroblast's position relative to three developmental axes. The HOX family of homeodomain transcription factors is implicated in specifying site-specific transcriptional programs. The use of gene, tiling, and tissue microarrays together gives a comprehensive view of the gene regulation involved in patterning the skin.

    View details for DOI 10.1038/sj.jid.5700986

    View details for Web of Science ID 000254330300005

    View details for PubMedID 18337710

  • MicroRNA expression signature of human sarcomas ONCOGENE Subramanian, S., Lui, W. O., Lee, C. H., Espinosa, I., Nielsen, T. O., Heinrich, M. C., Corless, C. L., Fire, A. Z., van de Rijn, M. 2008; 27 (14): 2015-2026


    MicroRNAs (miRNAs) are approximately 22 nucleotide-long noncoding RNAs involved in several biological processes including development, differentiation and proliferation. Recent studies suggest that knowledge of miRNA expression patterns in cancer may have substantial value for diagnostic and prognostic determinations as well as for eventual therapeutic intervention. We performed comprehensive analysis of miRNA expression profiles of 27 sarcomas, 5 normal smooth muscle and 2 normal skeletal muscle tissues using microarray technology and/or small RNA cloning approaches. The miRNA expression profiles are distinct among the tumor types as demonstrated by an unsupervised hierarchical clustering, and unique miRNA expression signatures were identified in each tumor class. Remarkably, the miRNA expression patterns suggested that two of the sarcomas had been misdiagnosed and this was confirmed by reevaluation of the tumors using histopathologic and molecular analyses. Using the cloning approach, we also identified 31 novel miRNAs or other small RNA effectors in the sarcomas and normal skeletal muscle tissues examined. Our data show that different histological types of sarcoma have distinct miRNA expression patterns, reflecting the apparent lineage and differentiation status of the tumors. The identification of unique miRNA signatures in each tumor type may indicate their role in tumorigenesis and may aid in diagnosis of soft tissue sarcomas.

    View details for DOI 10.1038/sj.onc.1210836

    View details for Web of Science ID 000254359100006

    View details for PubMedID 17922033

  • Prognostic significance of macrophage infiltration in leiomyosarcomas CLINICAL CANCER RESEARCH Lee, C., Espinosa, I., Vrijaldenhoven, S., Subramanian, S., Montgomery, K. D., Zhu, S., Marinelli, R. J., Peterse, J. L., Poulin, N., Nielsen, T. O., West, R. B., Gilks, C. B., van de Rijn, M. 2008; 14 (5): 1423-1430


    Macrophages are migratory cells that are frequently recruited to the site of tumors. Their presence is associated with poor clinical outcome in a variety of epithelial malignancies. The aim of this study is to examine the prognostic significance of tumor-associated macrophages in sarcomas.Global gene expression profiling data of a series of soft tissue tumors were analyzed for macrophage-associated gene expression. Immunohistochemistry on tissue microarrays containing leiomyosarcoma cases with known clinical outcome was used to verify the presence of macrophages and to examine the relationship between tumor-associated macrophages and clinical outcome.Gene expression profiling revealed high-level expression of several macrophage-associated genes such as CD163 and CD68 in a subset of leiomyosarcomas, indicating the presence of variable numbers of tumor-infiltrating macrophages. This was confirmed by CD68 and CD163 immunostaining of a tissue microarray containing 149 primary leiomyosarcomas. Kaplan-Meier survival analysis showed that high density of tumor-infiltrating macrophages as identified by CD163 or CD68 staining is associated with a significantly worse disease-specific survival in nongynecologic leiomyosarcomas, whereas leiomyosarcomas arising from the gynecologic tract showed no significant association between macrophage infiltration and survival. The presence of tumor necrosis did not correlate significantly with outcome.An increased density of CD163- or CD68-positive tumor-infiltrating macrophages is associated with poor outcome in nongynecologic leiomyosarcomas. This may help the clinical management of patients with leiomyosarcomas.

    View details for DOI 10.1158/1078-0432.CCR-07-1712

    View details for Web of Science ID 000253565000023

    View details for PubMedID 18316565

  • A novel monoclonal antibody against DOG1 is a sensitive and specific marker for gastrointestinal stromal tumors AMERICAN JOURNAL OF SURGICAL PATHOLOGY Espinosa, I., Lee, C., Kim, M. K., Rouse, B., Subramanian, S., Montgomery, K., Varma, S., Corless, C. L., Heinrich, M. C., Smith, K. S., Wang, Z., Rubin, B., Nielsen, T. O., Seitz, R. S., Ross, D. T., West, R. B., Cleary, M. L., van de Rijn, M. 2008; 32 (2): 210-218


    Gastrointestinal stromal tumors (GIST) occur primarily in the wall of the intestine and are characterized by activating mutations in the receptor tyrosine kinases genes KIT or PDGFRA. The diagnosis of GIST relies heavily on the demonstration of KIT/CD117 protein expression by immunohistochemistry. However, KIT expression is absent in approximately 4% to 15% of GIST and this can complicate the diagnosis of GIST in patients who may benefit from treatment with receptor tyrosine kinase inhibitors. We previously identified DOG1/TMEM16A as a novel marker for GIST using a conventional rabbit antipeptide antiserum and an in situ hybridization probe. Here, we describe 2 new monoclonal antibodies against DOG1 (DOG1.1 and DOG1.3) and compare their staining profiles with KIT and CD34 antibodies on 447 cases of GIST. These included 306 cases with known mutational status for KIT and PDGFRA from a molecular consultation service. In addition, 935 other mesenchymal tumors and 432 nonsarcomatous tumors were studied. Both DOG1 antibodies showed high sensitivity and specificity for GIST, with DOG1.1 showing some advantages. This antibody yielded positive staining in 370 of 425 (87%) scorable GIST, whereas CD117 was positive in 317 of 428 (74%) GIST and CD34 in 254 of 430 (59%) GIST. In GIST with mutations in PDGFRA, 79% (23/29) showed DOG1.1 immunoreactivity while only 9% (3/32) and 27% (9/33) stained for CD117 and CD34, respectively. Only 1 of 326 (0.3%) leiomyosarcomas and 1 of 39 (2.5%) synovial sarcomas among the 935 soft tissue tumors examined showed positive immunostaining for DOG1.1. In addition, DOG1.1 immunoreactivity was seen in fewer cases of carcinoma, melanoma, and seminoma as compared with KIT.

    View details for Web of Science ID 000252759900005

    View details for PubMedID 18223323

  • hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature AMERICAN JOURNAL OF SURGICAL PATHOLOGY Lapointe, J., Malhotra, S., Higgins, J. P., Bair, E., Thompson, M., Salari, K., Giacomini, C. P., Ferrari, M., Montgomery, K., Tibshirani, R., van de Rijn, M., Brooks, J. D., Pollack, J. R. 2008; 32 (2): 205-209


    Growing evidence suggests that only a fraction of prostate cancers detected clinically are potentially lethal. An important clinical issue is identifying men with indolent cancer who might be spared aggressive therapies with associated morbidities. Previously, using microarray analysis we defined 3 molecular subtypes of prostate cancer with different gene-expression patterns. One, subtype-1, displayed features consistent with more indolent behavior, where an immunohistochemical marker (AZGP1) for subtype-1 predicted favorable outcome after radical prostatectomy. Here we characterize a second candidate tissue biomarker, hCAP-D3, expressed in subtype-1 prostate tumors. hCAP-D3 expression, assayed by RNA in situ hybridization on a tissue microarray comprising 225 cases, was associated with decreased tumor recurrence after radical prostatectomy (P=0.004), independent of pathologic tumor stage, Gleason grade, and preoperative prostate-specific antigen levels. Simultaneous assessment of hCAP-D3 and AZGP1 expression in this tumor set improved outcome prediction. We have previously demonstrated that hCAP-D3 is induced by androgen in prostate cells. Extending this finding, Gene Set Enrichment Analysis revealed enrichment of androgen-responsive genes in subtype-1 tumors (P=0.019). Our findings identify hCAP-D3 as a new biomarker for subtype-1 tumors that improves prognostication, and reveal androgen signaling as an important biologic feature of this potentially clinically favorable molecular subtype.

    View details for Web of Science ID 000252759900004

    View details for PubMedID 18223322

  • The Stanford Tissue Microarray Database NUCLEIC ACIDS RESEARCH Marinelli, R. J., Montgomery, K., Liu, C. L., Shah, N. H., Prapong, W., Nitzberg, M., Zachariah, Z. K., Sherlock, G. J., Natkunam, Y., West, R. B., van de Rijn, M., Brown, P. O., Ball, C. A. 2008; 36: D871-D877


    The Stanford Tissue Microarray Database (TMAD; is a public resource for disseminating annotated tissue images and associated expression data. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance (Immunohistochemistry; IHC), or by labeled nucleic acids (in situ hybridization; ISH) to detect transcript abundance. TMAD archives multi-wavelength fluorescence and bright-field images of tissue microarrays for scoring and analysis. As of July 2007, TMAD contained 205 161 images archiving 349 distinct probes on 1488 tissue microarray slides. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. To date, 12 publications have been based on these raw public data. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. Image processing researchers can extract images and scores for training and testing classification algorithms. The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license.

    View details for DOI 10.1093/nar/gkm861

    View details for Web of Science ID 000252545400154

    View details for PubMedID 17989087

    View details for PubMedCentralID PMC2238948

  • Gene expression profiling of breast cancer ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE Cheang, M. C., van de Rijn, M., Nielsen, T. O. 2008; 3: 67-97


    DNA microarray platforms for gene expression profiling were invented relatively recently, and breast cancer has been among the earliest and most intensely studied diseases using this technology. The molecular signatures so identified help reveal the biologic spectrum of breast cancers, provide diagnostic tools as well as prognostic and predictive gene signatures, and may identify new therapeutic targets. Data are best presented in an open access format to facilitate external validation, the most crucial step in identifying robust, reproducible gene signatures suitable for clinical translation. Clinically practical applications derived from full expression profile studies already in use include reduced versions of microarrays representing key discriminatory genes and therapeutic targets, quantitative polymerase chain reaction assays, or immunohistochemical surrogate panels (suitable for application to standard pathology blocks). Prospective trials are now underway to determine the value of such tools for clinical decision making in breast cancer; these efforts may serve as a model for using such approaches in other tumor types.

    View details for DOI 10.1146/annurev.pathol.3.121806.151505

    View details for Web of Science ID 000254085800004

    View details for PubMedID 18039137

  • A novel breast carcinoma stromal response defined by the Nodular Fasciitis gene signature 50th Annual Meeting of the American-Society-for-Therapeutic-Radiology-and-Oncology (ASTRO) Cho, N. K., Beck, A. H., Espinosa, I., Montgomery, K., Zhu, S., van de Rijn, M., West, R. B. ELSEVIER SCIENCE INC. 2008: S686–S686
  • The CSF-1 response signature in breast carcinoma 97th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Beck, A. B., Espinosa, I., van de Rijn, M., West, R. B. NATURE PUBLISHING GROUP. 2008: 22A–22A
  • Identification of prognostically relevant and reproducible subsets of endometrial adenocarcinoma based on clustering analysis of immunostaining data MODERN PATHOLOGY Alkushi, A., Clarke, B. A., Akbari, M., Makretsov, N., Lim, P., Miller, D., Magliocco, A., Coldman, A., van de Rijn, M., Huntsman, D., Parker, R., Gilks, C. B. 2007; 20 (11): 1156-1165


    Panels of immunomarkers can provide greater information than single markers, but the problem of how to optimally interpret data from multiple immunomarkers is unresolved. We examined the expression profile of 12 immunomarkers in 200 endometrial carcinomas using a tissue microarray. The outcomes of groups of patients were analyzed by using the Kaplan-Meier method, using the log-rank statistic for comparison of survival curves. Correlation between clustering results and traditional prognosticators of endometrial carcinoma was examined by either Fisher's exact test or chi2-test. Multivariate analysis was performed using a proportional hazards method (Cox regression modeling). Seven of the 12 immunomarkers studied showed prognostic significance in univariate analysis (P<0.05) and 1 marker showed a trend toward significance (P=0.06). These eight markers were used in unsupervised hierarchical clustering of the cases, and resulted in identification of three cluster groups. There was a statistically significant difference in patient survival between these cluster groups (P=0.0001). The prognostic significance of the cluster groups was independent of tumor stage and patient age on multivariate analysis (P=0.014), but was not of independent significance when either tumor grade or cell type was added to the model. The cluster group designation was strongly correlated with tumor grade, stage, and cell type (P<0.0001 for each). Interlaboratory reproducibility of subclassification of endometrial adenocarcinoma by hierarchical clustering analysis was verified by showing highly reproducible assignment of individual cases to specific cluster groups when the immunostaining was performed, interpreted, and clustered in a second laboratory (kappa=0.79, concordance rate=89.6%). Unsupervised hierarchical clustering of immunostaining data identifies prognostically relevant subsets of endometrial adenocarcinoma. Such analysis is reproducible, showing less interobserver variability than histopathological assessment of tumor cell type or grade.

    View details for DOI 10.1038/modpathol.3800950

    View details for Web of Science ID 000250226200006

    View details for PubMedID 17717550

  • Experimental approaches to the study of cancer-stroma interactions: recent findings suggest a pivotal role for stroma in carcinogenesis LABORATORY INVESTIGATION West, R. B., De Rijn, M. V. 2007; 87 (10): 967-970


    An increasing body of research indicates that stroma surrounding cancer cells plays an important role in the development and subsequent behavior of the tumor. Studies using a wide range of techniques, including stromal cell isolation, modification of stromal-specific gene expression, and recreation of specific microenvironment conditions in culture, have demonstrated that stroma can promote cancer and that the expression patterns within the stroma can influence clinical outcome. Major hurdles in the study of the cancer stroma revolve around the cellular complexity of the tumor microenvironment, both in modeling the microenvironment and discovering/isolating pure populations of stromal cell types.

    View details for DOI 10.1038/labinvest.3700666

    View details for Web of Science ID 000249557400001

    View details for PubMedID 17700561

  • Gene expression programs of human smooth muscle cells: Tissue-specific differentiation and prognostic significance in breast cancers PLOS GENETICS Chi, J., Rodriguez, E. H., Wang, Z., Nuyten, D. S., Mukherjee, S., van de Rijn, M., van de Vijver, M. J., Hastie, T., Brown, P. O. 2007; 3 (9): 1770-1784


    Smooth muscle is present in a wide variety of anatomical locations, such as blood vessels, various visceral organs, and hair follicles. Contraction of smooth muscle is central to functions as diverse as peristalsis, urination, respiration, and the maintenance of vascular tone. Despite the varied physiological roles of smooth muscle cells (SMCs), we possess only a limited knowledge of the heterogeneity underlying their functional and anatomic specializations. As a step toward understanding the intrinsic differences between SMCs from different anatomical locations, we used DNA microarrays to profile global gene expression patterns in 36 SMC samples from various tissues after propagation under defined conditions in cell culture. Significant variations were found between the cells isolated from blood vessels, bronchi, and visceral organs. Furthermore, pervasive differences were noted within the visceral organ subgroups that appear to reflect the distinct molecular pathways essential for organogenesis as well as those involved in organ-specific contractile and physiological properties. Finally, we sought to understand how this diversity may contribute to SMC-involving pathology. We found that a gene expression signature of the responses of vascular SMCs to serum exposure is associated with a significantly poorer prognosis in human cancers, potentially linking vascular injury response to tumor progression.

    View details for DOI 10.1371/journal.pgen.0030164

    View details for Web of Science ID 000249767800019

    View details for PubMedID 17907811

  • The utility of PAX5 immunohistochemistry in the diagnosis of undifferentiated malignant neoplasms MODERN PATHOLOGY Jensen, K. C., Higgins, J. P., Montgomery, K., Kaygusuz, G., van de Rijn, M., Natkunam, Y. 2007; 20 (8): 871-877


    PAX5 is a B-cell transcription factor whose expression at the protein level is reliably detected by immunohistochemistry in routine biopsies. The purpose of this study was to investigate whether PAX5 immunohistochemistry has diagnostic benefit as a B-cell marker in the work-up of undifferentiated malignant neoplasms. Twenty-five cases previously diagnosed as undifferentiated malignant neoplasms were selected. In addition, 59 hematolymphoid and 884 non-hematolymphoid malignancies were studied such that the specificity of PAX5 immunohistochemistry could be addressed. Two of the 25 (8%) undifferentiated neoplasms showed diffuse staining for PAX5, which indicated a B-cell derivation for these neoplasms that was not appreciated at the time of initial diagnosis. PAX5 staining was detected in the vast majority of hematolymphoid tumors of B-cell derivation but only in 5 of 884 (less than 1%) non-hematolymphoid tumors. Our results further show that PAX5 may be the only detectable marker of B lineage in lymphomas that lack or show equivocal CD45RB and CD20 expression. We conclude that the addition of PAX5 to a panel of immunohistologic markers used in the interrogation of undifferentiated neoplasms is of diagnostic benefit. Its expression can also facilitate the diagnosis of classical and nodular lymphocyte-predominant Hodgkin lymphoma with atypical morphologic and immunohistologic features. Lastly, we have shown that the lack of its expression at the protein level in many epithelial and mesenchymal neoplasms renders PAX5 expression an extremely specific marker of the B lineage.

    View details for Web of Science ID 000248219700008

    View details for PubMedID 17529924

  • Translocation and expression of CSF1 in pigmented villonodular synovitis, tenosynovial giant cell tumor, rheumatoid arthritis and other reactive synovitides AMERICAN JOURNAL OF SURGICAL PATHOLOGY Cupp, J. S., Miller, M. A., Montgomery, K. D., Nielsen, T. O., O'Connell, J. X., Huntsman, D., van de Rijn, M., Gilks, C. B., West, R. B. 2007; 31 (6): 970-976


    We recently demonstrated that CSF1, the ligand of the tyrosine kinase receptor, CSF1R, can be translocated in pigmented villonodular synovitis (PVNS) and tenosynovial giant cell tumor (TGCT). In this study, we evaluated the staining characteristics of PVNS/TGCT and reactive synovitides for CSF1 and CSF1R by in situ hybridization and immunohistochemistry on tissue microarrays and correlated these findings with the recently described translocation. We collected specimens of TGCT/PVNS from 60 patients and of rheumatoid arthritis and other reactive synovitides from 74 patients. We identify 2 groups of PVNS and TGCT cases by the presence of CSF1 translocation and CSF1 expression. The first group (35 of 57 cases; 61%) had both the CSF1 translocation and high expression of CSF1 RNA, confirming our previous findings. Interestingly, a second group (22 of 57 cases; 39%) was identified that showed high expression of CSF1 RNA or CSF1 protein but did not have the translocation. The rheumatoid arthritis and reactive synovitis specimens showed localization of CSF1 RNA and protein to the synovial lining cells, implying a possible role for CSF1 in the pathogenesis of these lesions. As the CSF1 translocation is postulated to play an important role in the biology of PVNS/TGCT, the consistent presence of CSF1 expression in translocation-negative cases implies that other mechanisms can lead to CSF1 up-regulation. The consistent presence of CSF1 overexpression in all cases of PVNS/TGCT and reactive synovitides suggests both an important role for CSF1 in the spectrum of synovial pathologies and the possibility of targeting the CSF1/CSF1R interaction therapeutically.

    View details for Web of Science ID 000246872500022

    View details for PubMedID 17527089

  • Oncogenic regulators and substrates of the anaphase promoting complex/cyclosome are frequently overexpressed in malignant tumors AMERICAN JOURNAL OF PATHOLOGY Lehman, N. L., Tibshirani, R., Hsu, J. Y., Natkunam, Y., Harris, B. T., West, R. B., Masek, M. A., Montgomery, K., van de Rijn, M., Jackson, P. K. 2007; 170 (5): 1793-1805


    The fidelity of cell division is dependent on the accumulation and ordered destruction of critical protein regulators. By triggering the appropriately timed, ubiquitin-dependent proteolysis of the mitotic regulatory proteins securin, cyclin B, aurora A kinase, and polo-like kinase 1, the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase plays an essential role in maintaining genomic stability. Misexpression of these APC/C substrates, individually, has been implicated in genomic instability and cancer. However, no comprehensive survey of the extent of their misregulation in tumors has been performed. Here, we analyzed more than 1600 benign and malignant tumors by immunohistochemical staining of tissue microarrays and found frequent overexpression of securin, polo-like kinase 1, aurora A, and Skp2 in malignant tumors. Positive and negative APC/C regulators, Cdh1 and Emi1, respectively, were also more strongly expressed in malignant versus benign tumors. Clustering and statistical analysis supports the finding that malignant tumors generally show broad misregulation of mitotic APC/C substrates not seen in benign tumors, suggesting that a "mitotic profile" in tumors may result from misregulation of the APC/C destruction pathway. This profile of misregulated mitotic APC/C substrates and regulators in malignant tumors suggests that analysis of this pathway may be diagnostically useful and represent a potentially important therapeutic target.

    View details for DOI 10.2353/ajpath.2007.060767

    View details for Web of Science ID 000246050400033

    View details for PubMedID 17456782

    View details for PubMedCentralID PMC1854971

  • Placental S100 (S100P) and GATA3: Markers for transitional epithelium and urothelial carcinoma discovered by complementary DNA microarray AMERICAN JOURNAL OF SURGICAL PATHOLOGY Higgins, J. P., Kaygusuz, G., Wang, L., Montgomery, K., Mason, V., Zhu, S. X., Marinelli, R. J., Presti, J. C., van de Rijn, M., Brooks, J. D. 2007; 31 (5): 673-680


    The morphologic distinction between prostate and urothelial carcinoma can be difficult. To identify novel diagnostic markers that may aid in the differential diagnosis of prostate versus urothelial carcinoma, we analyzed expression patterns in prostate and bladder cancer tissues using complementary DNA microarrays. Together with our prior studies on renal neoplasms and normal kidney, these studies suggested that the gene for placental S100 (S100P) is specifically expressed in benign and malignant urothelial cells. Using tissue microarrays, a polyclonal antiserum against S100P protein stained 86% of 295 urothelial carcinomas while only 3% of 260 prostatic adenocarcinomas and 1% of 133 renal cell carcinomas stained. A commercially available monoclonal antibody against S100P stained 78% of 300 urothelial carcinomas while only 2% of 256 prostatic adenocarcinomas and none of 137 renal cell carcinomas stained. A second gene, GATA3, also showed high level expression in urothelial tumors by cDNA array. A commercially available monoclonal antibody against GATA3 stained 67% of 308 urothelial carcinomas, but none of the prostate or renal carcinomas. For comparison, staining was also performed for p63 and cytokeratin 5/6. p63 stained 87% of urothelial carcinomas whereas CK5/6 stained 54%. Importantly, when S100P and p63 were combined 95% of urothelial carcinomas were labeled by one or both markers. We conclude that the detection of S100P and GATA3 protein expression may help distinguish urothelial carcinomas from other genitourinary neoplasms that enter into the differential diagnosis.

    View details for Web of Science ID 000246135600003

    View details for PubMedID 17460449

  • A variant TMPRSS2 isoform and ERG fusion product in prostate cancer with implications for molecular diagnosis MODERN PATHOLOGY Lapointe, J., Kim, Y. H., Miller, M. A., Li, C., Kaygusuz, G., van de Rijn, M., Huntsman, D. G., Brooks, J. D., Pollack, J. R. 2007; 20 (4): 467-473


    Prostate cancer is the most commonly diagnosed cancer among men in the United States. Recently, fusion of TMPRSS2 with ETS family oncogenic transcription factors has been identified as a common molecular alteration in prostate cancer, where most often the rearrangement places ERG under the androgen-regulated transcriptional control of TMPRSS2. Here, we carried out rapid amplification of cDNA ends (RACE) on a prostate cancer specimen carrying an atypical aberration discovered by array-based comparative genomic hybridization (array CGH), suggesting an alternative fusion partner of ERG. We identified novel transcribed sequences fused to ERG, mapping 4 kb upstream of the TMPRSS2 start site. The sequences derive from an apparent second TMPRSS2 isoform, which we found also expressed in some prostate tumors, suggesting similar androgen-regulated control. In a reverse transcription-polymerase chain reaction (RT-PCR)-based survey of 63 prostate tumor specimens (54 primary and nine lymph node metastases), 44 (70%) cases expressed either the known or novel variant TMPRSS2-ERG fusion, 28 (44%) expressed both, 10 (16%) expressed only the known, and notably six (10%) expressed only the variant isoform fusion. In this specimen set, the presence of a TMPRSS2-ERG fusion showed no statistical association with tumor stage, Gleason grade or recurrence-free survival. Nonetheless, the discovery of a novel variant TMPRSS2 isoform-ERG fusion adds to the characterization of ETS-family rearrangements in prostate cancer, and has important implications for the accurate molecular diagnosis of TMPRSS2-ETS fusions.

    View details for DOI 10.1038/modpathol.3800759

    View details for Web of Science ID 000245271000007

    View details for PubMedID 17334351

  • Gene Expression Patterns in Pancreatic Tumors, Cells and Tissues PLOS ONE Lowe, A. W., Olsen, M., Hao, Y., Lee, S. P., Lee, K. T., Chen, X., van de Rijn, M., Brown, P. O. 2007; 2 (3)


    Cancers of the pancreas originate from both the endocrine and exocrine elements of the organ, and represent a major cause of cancer-related death. This study provides a comprehensive assessment of gene expression for pancreatic tumors, the normal pancreas, and nonneoplastic pancreatic disease.DNA microarrays were used to assess the gene expression for surgically derived pancreatic adenocarcinomas, islet cell tumors, and mesenchymal tumors. The addition of normal pancreata, isolated islets, isolated pancreatic ducts, and pancreatic adenocarcinoma cell lines enhanced subsequent analysis by increasing the diversity in gene expression profiles obtained. Exocrine, endocrine, and mesenchymal tumors displayed unique gene expression profiles. Similarities in gene expression support the pancreatic duct as the origin of adenocarcinomas. In addition, genes highly expressed in other cancers and associated with specific signal transduction pathways were also found in pancreatic tumors.The scope of the present work was enhanced by the inclusion of publicly available datasets that encompass a wide spectrum of human tissues and enabled the identification of candidate genes that may serve diagnostic and therapeutic goals.

    View details for DOI 10.1371/journal.pone.0000323

    View details for Web of Science ID 000207445200006

    View details for PubMedID 17389914

    View details for PubMedCentralID PMC1824711

  • TLE1 as a diagnostic immunohistochemical marker for synovial sarcoma emerging from gene expression profiling studies AMERICAN JOURNAL OF SURGICAL PATHOLOGY Terry, J., Saito, T., Subramanian, S., Ruttan, C., Antonescu, C. R., Goldblum, J. R., Downs-Kelly, E., Corless, C. L., Rubin, B. P., van de Rijn, M., Ladanyi, M., Nielsen, T. O. 2007; 31 (2): 240-246


    Synovial sarcoma is a soft tissue malignancy defined by the SYT-SSX fusion oncogene. Demonstration of the t(X;18) by cytogenetics, fluorescence in situ hybridization or reverse-transcriptase polymerase chain reaction has become the gold standard for diagnosis, but practical considerations limit the availability of these methods. Gene expression profiling studies performed by several independent groups have consistently identified TLE1 as an excellent discriminator of synovial sarcoma from other sarcomas, including histologically similar tumors such as malignant peripheral nerve sheath tumor. TLE proteins (human homologues of Groucho) are transcriptional corepressors that inhibit Wnt signaling and other cell fate determination signals, and so have an established role in repressing differentiation. We examined the expression of TLE proteins in synovial sarcoma and in a broad range of mesenchymal tumors using tissue microarrays to assess the value of anti-TLE antibodies in the immunohistochemical confirmation of synovial sarcoma. We demonstrate that TLE expression is a consistent feature of synovial sarcoma using both a well-characterized monoclonal antibody recognizing the TLE family of proteins and a commercially available polyclonal antibody raised against TLE1. Both antibodies gave intense and/or diffuse nuclear staining in 91/94 molecularly confirmed synovial sarcomas. Moderate staining is occasionally seen in schwannoma and solitary fibrous tumor/hemangiopericytoma. In contrast, TLE staining is detected much less frequently and at lower levels, if at all, in 40 other mesenchymal tumors. Our findings establish TLE as a robust immunohistochemical marker for synovial sarcoma, and may have implications for understanding the biology of synovial sarcoma and for developing experimental therapies for this cancer.

    View details for Web of Science ID 000243831400010

    View details for PubMedID 17255769

  • Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Sneddon, J. B., Zhen, H. H., Montgomery, K., van de Rijn, M., Tward, A. D., West, R., Gladstone, H., Chang, H. Y., Morganroth, G. S., Oro, A. E., Brown, P. O. 2006; 103 (40): 14842-14847


    Although tissue microenvironments play critical roles in epithelial development and tumorigenesis, the factors mediating these effects are poorly understood. In this work, we used a genomic approach to identify factors produced by cells in the microenvironment of basal cell carcinoma (BCC) of the skin, one of the most common human cancers. The global gene expression programs of stromal cell cultures derived from human BCCs showed consistent, systematic differences from those derived from nontumor skin. The gene most consistently expressed at a higher level in BCC tumor stromal cells compared with those from nontumor skin was GREMLIN 1, which encodes a secreted antagonist of the bone morphogenetic protein (BMP) pathway. BMPs and their antagonists are known to play a crucial role in stem and progenitor cell biology as regulators of the balance between expansion and differentiation. Consistent with the hypothesis that BMP antagonists might have a similar role in cancer, we found GREMLIN 1 expression in the stroma of human BCC tumors but not in normal skin in vivo. Furthermore, BMP 2 and 4 are expressed by BCC cells. Ex vivo, BMP inhibits, and Gremlin 1 promotes, proliferation of cultured BCC cells. We further found that GREMLIN 1 is expressed by stromal cells in many carcinomas but not in the corresponding normal tissue counterparts that we examined. Our data suggest that BMP antagonists may be important constituents of tumor stroma, providing a favorable microenvironment for cancer cell survival and expansion in many cancers.

    View details for DOI 10.1073/pnas.0606857103

    View details for Web of Science ID 000241069300037

    View details for PubMedID 17003113

    View details for PubMedCentralID PMC1578503

  • Ossifying fibromyxoid tumor of soft parts presenting as a scalp cyst JOURNAL OF CUTANEOUS PATHOLOGY Seykora, J. T., Kutcher, C., van de Rijn, M., Dzubow, L., Junkins-Hopkins, J., Ioffreda, M. 2006; 33 (8): 569-572


    Ossifying fibromyxoid tumor of soft parts (OFMT) is a rare mesenchymal neoplasm of intermediate malignant potential. The tumor most commonly occurs on the extremities with a male predominance. We present an unusual case of OFMT occurring as a cystic lesion on the scalp of a female.A 67-year-old woman presented with a 6-year history of a well demarcated cystic scalp mass. Physical examination revealed a slightly movable, multilobular mass of the left parietal scalp which was subsequently excised. Histological evaluation revealed an OFMT comprised of bland, small cells and a thick collagenous capsule containing an incomplete rim of lamellar bone.OFMT is an unusual tumor which can usually be considered as having an intermediate risk of malignancy. It generally occurs in the extremities with a male predominance. The clinical differential for a cystic mass on the scalp is broadened by this unusual case of an OFMT.

    View details for DOI 10.1111/j.1600-0560.2006.00444.x

    View details for Web of Science ID 000239635900006

    View details for PubMedID 16919031

  • Upregulation of histidine decarboxylase expression in superficial cortical nephrons during pregnancy in mice and women KIDNEY INTERNATIONAL Morgan, T. K., Montgomery, K., Mason, V., West, R. B., Wang, L., van de Rijn, M., Higgins, J. P. 2006; 70 (2): 306-314


    Mechanisms regulating pregnancy-induced changes in renal function are incompletely understood. Few candidate genes have been identified and data suggest that alternate mechanisms remain to be elucidated. Our objective was to screen thousands of genes expressed in kidneys from mice throughout gestation to identify possible key regulators of renal function during pregnancy. Mouse complementary DNA microarrays were used to screen for differences in expression during pregnancy in C57BL/6 mice. Interesting candidate genes whose expression varied with pregnancy were further analyzed by reverse transcription-PCR and Northern blot. Expression was localized by in situ hybridization and immunohistochemistry. Follow-up immunohistochemical analyses in archival human kidney sections from the fetus, non-pregnant, and pregnant women were also performed. Histidine decarboxylase (HDC), the enzyme that synthesizes histamine, was markedly upregulated in the mouse kidney during pregnancy. HDC expression localized to proximal tubule cells of fetal and adult mice. Females showed strong expression in the juxtamedullary zone before pregnancy and upregulation in the superficial cortical zone (SCZ) by mid-gestation. Histamine colocalized with HDC. Male mice showed only low HDC expression. Similar expression patterns were observed in human kidneys. Our results show that HDC expression and histamine production are increased in the SCZ during pregnancy. If histamine acts as a vasodilator, we speculate that increasing production in the SCZ may increase renal blood flow to this zone and recruit superficial cortical nephrons during pregnancy.

    View details for DOI 10.1038/

    View details for Web of Science ID 000239118900011

    View details for PubMedID 16760908

  • A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA West, R. B., Rubin, B. P., Miller, M. A., Subramanian, S., Kaygusuz, G., Montgomery, K., Zhu, S., Marinelli, R. J., De Luca, A., Downs-Kelly, E., Goldblum, J. R., Corless, C. L., Brown, P. O., Gilks, C. B., Nielsen, T. O., Huntsman, D., van de Rijn, M. 2006; 103 (3): 690-695


    Tenosynovial giant-cell tumor (TGCT) and pigmented villonodular synovitis (PVNS) are related conditions with features of both reactive inflammatory disorders and clonal neoplastic proliferations. Chromosomal translocations involving chromosome 1p13 have been reported in both TGCT and PVNS. We confirm that translocations involving 1p13 are present in a majority of cases of TGCT and PVNS and show that CSF1 is the gene at the chromosome 1p13 breakpoint. In some cases of both TGCT and PVNS, CSF1 is fused to COL6A3 (2q35). The CSF1 translocations result in overexpression of CSF1. In cases of TGCT and PVNS carrying this translocation, it is present in a minority of the intratumoral cells, leading to CSF1 expression only in these cells, whereas the majority of cells express CSF1R but not CSF1, suggesting a tumor-landscaping effect with aberrant CSF1 expression in the neoplastic cells, leading to the abnormal accumulation of nonneoplastic cells that form a tumorous mass.

    View details for DOI 10.1073/pnas.0507321103

    View details for Web of Science ID 000234727800035

    View details for PubMedID 16407111

    View details for PubMedCentralID PMC1325107

  • Genetics of soft tissue tumors ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE van de Rijn, M., Fletcher, J. A. 2006; 1 (1): 435-466


    Sarcomas form a highly diverse group of rare tumors that are derived from connective tissue. More than 100 different malignant and benign soft tissue neoplasms can be recognized by histologic examination. Few diagnostic markers exist, and the cell of origin for many soft tissue tumors is unknown. The accurate diagnosis of many of these tumors therefore remains a challenge. The study of sarcomas has yielded many insights that can be applied to other neoplasms such as carcinoma. For example, the success of the treatment of gastrointestinal stromal tumor with Imatinib has led to an increased effort to find targeted therapies for other malignancies. Here we describe the known molecular changes in a number of sarcomas and focus on novel scientific approaches that can be expected to lead to improved diagnosis, prognostication, and therapy of sarcoma.

    View details for DOI 10.1146/annurev.pathol.1.110304.100052

    View details for Web of Science ID 000245565500017

    View details for PubMedID 18039122

  • Heat-shock protein-90 (HSP-90) expression in a spectrum of benign and malignant spindle cell neoplasms: An immunohistochemical study 95th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Larson, A. J., Downs-Kelley, E., Skacel, M., Nielsen, T. O., Ruttan, C., van de Rijn, M., West, R. B., Rubin, B. P., Corless, C., Goldblum, J. R. NATURE PUBLISHING GROUP. 2006: 13A–14A
  • Epidermal growth factor receptor (EGFR) expression and gene amplification in a spectrum of spindle cell soft tissue neoplasms: A fluorescence in situ hybridization (FISH) and immunohistochemical (IHC) study 95th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Larson, A. J., Downs-Kelley, E., Skacel, M., Tubbs, R. R., Rubin, B. P., van de Rijn, M., West, R. B., Corless, C., Chiesa, A., Goldblum, J. R. NATURE PUBLISHING GROUP. 2006: 14A–14A
  • S100p: A marker for transitional epithelium and urothelial carcinoma 95th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Higgins, J. P., Kaygusuz, G., Wang, L., Montgomery, K., Mason, V., Brooks, J. D., van de Rijn, M. NATURE PUBLISHING GROUP. 2006: 142A–142A
  • Lack of expression of platelet-derived growth factor receptor beta (PDGFR beta) in langerhans cell tumors: An in situ hybridization study 95th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology George, T. I., Mest, R. B., Blais, S., Montgomery, K., Gotlib, J., van de Rijn, M., Arber, D. A. NATURE PUBLISHING GROUP. 2006: 227A–227A
  • Translocation and expression of CSF1 in pigmented villonodular synovitis, tenosynovial giant cell tumors, and reactive synovial lesions 95th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Cupp, J. S., Rubin, B. P., Miller, M. A., Subramanian, S., Montgomery, K., Marinelli, R. J., De Luca, A., Nielsen, T. O., O'Connell, J. X., Huntsman, D., van de Rijn, M., Gilks, C. B., West, R. B. NATURE PUBLISHING GROUP. 2006: 10A–10A
  • The role of microarray technologies in the study of soft tissue tumours HISTOPATHOLOGY West, R. B., van de Rijn, M. 2006; 48 (1): 22-31


    Array technologies (gene array, tissue microarray and others) are being used in a growing number of research projects involving soft tissue tumours. Gene array techniques allow for measurements of RNA expression levels or gene copy number changes for a large number of genes in a single specimen. A complementary technique, tissue microarrays, allows for the measurement of expression of a single gene in a large number of specimens. These techniques and similar ones have created a fundamentally new approach to the investigation of soft tissue tumours. This review addresses some of the advantages, problems, and solutions to those problems that come with these technologies.

    View details for DOI 10.1111/j.1365-2559.2005.02286.x

    View details for Web of Science ID 000234030700004

    View details for PubMedID 16359534

  • TMA-combiner, a simple software tool to permit analysis of replicate cores on tissue microarrays MODERN PATHOLOGY Liu, C. L., Montgomery, K. D., Natkunam, Y., West, R. B., Nielsen, T. O., Cheang, M. C., Turbin, D. A., Marinelli, R. J., van de Rijn, M., Higgins, J. P. 2005; 18 (12): 1641-1648


    We have previously published a suite of software tools that facilitates the reformulation of tissue microarray (TMA) data so that it may be analyzed using techniques originally devised for analysis of cDNA microarray data. However, current microarray data often feature multiple scores for a given tissue sample and antibody combination. Furthermore, an efficient and systematic method for combining scores that takes into account the differing staining properties of tissue epitopes has not been described. We thus present the TMA-Combiner, a new Microsoft Excel-based macro that permits analysis of data for which tissues may have two or more scores per antibody, and permits combination of data from multiple different tissue microarrays. It accomplishes this by rendering one score per tissue per antibody from two or more scores, using one of multiple user-selectable combination rules developed to account for the differing staining properties of tissue epitopes. This greatly facilitates analysis of tissue microarrays, particularly for users with large repositories of data, and may facilitate discovery of biological trends and help refine diagnostic accuracy of tissue markers in clinical samples.

    View details for DOI 10.1038/modpathol.3800491

    View details for Web of Science ID 000233372100016

    View details for PubMedID 16258508

  • The retinoic acid synthesis gene ALDH1a2 is a candidate tumor suppressor in prostate cancer CANCER RESEARCH Kim, H., Lapointe, J., Kaygusuz, G., Ong, D. E., Li, C. D., van de Rijn, M., Brooks, J. D., Pollack, J. R. 2005; 65 (18): 8118-8124


    Prostate cancer is the most common cancer among men in the United States, and aberrant DNA methylation is known to be an early molecular event in its development. Here, we have used expression profiling to identify novel hypermethylated genes whose expression is induced by treatment of prostate cancer cell lines with the DNA methyltransferase inhibitor 5-Aza-2'-deoxycytidine (5-aza-dC). Of the 271 genes that were induced by 5-aza-dC treatment, 25 also displayed reduced expression in primary prostate tumors compared with normal prostate tissue, and the decreased expression of only one gene, aldehyde dehydrogenase 1 family, member A2 (ALDH1a2), was also associated with shorter recurrence-free survival. ALDH1a2 encodes an enzyme responsible for synthesis of retinoic acid (RA), a compound with prodifferentiation properties. By immunohistochemistry, we observed that ALDH1a2 was expressed in epithelia from normal prostate but not prostate cancer. Using bisulfite sequencing, we determined that the ALDH1a2 promoter region was significantly hypermethylated in primary prostate tumors compared with normal prostate specimens (P = 0.01). Finally, transfection-mediated reexpression of wild-type ALDH1a2 (but not a presumptive catalytically dead mutant) in the prostate cancer cell line DU145 resulted in decreased colony growth (P < 0.0001), comparable with treatment with either 5-aza-dC or RA. Taken together, our findings implicate ALDH1a2 as a candidate tumor suppressor gene in prostate cancer and further support a role of retinoids in the prevention or treatment of prostate cancer.

    View details for DOI 10.1158/0008-5472.CAN-04-4562

    View details for Web of Science ID 000231848800010

    View details for PubMedID 16166285

  • The gene expression profile of extraskeletal myxoid chondrosarcoma JOURNAL OF PATHOLOGY Subramanian, S., West, R. B., Marinelli, R. J., Nielsen, T. O., Rubin, B. P., Goldblum, J. R., Patel, R. M., Zhu, S., Montgomery, K., Ng, T. L., Corless, C. L., Heinrich, M. C., van de Rijn, M. 2005; 206 (4): 433-444


    Extraskeletal myxoid chondrosarcoma (EMC) is a soft tissue tumour that occurs primarily in the extremities and is characterized by a balanced translocation most commonly involving t(9;22) (q22;q12). The morphological spectrum of EMC is broad and thus a diagnosis based on histology alone can be difficult. Currently, no systemic therapy exists that improves survival in patients with EMC. In the present study, gene expression profiling has been performed to discover new diagnostic markers and potential therapeutic targets for this tumour type. Global gene expression profiling of ten EMCs and 26 other sarcomas using 42,000 spot cDNA microarrays revealed that the cases of EMC were closely related to each other and distinct from the other tumours profiled. Significance analysis of microarrays (SAM) identified 86 genes that distinguished EMC from the other sarcomas with 0.25% likelihood of false significance. NMB, DKK1, DNER, CLCN3, and DEF6 were the top five genes in this analysis. In situ hybridization for NMB gene expression on tissue microarrays (TMAs) containing a total of 1164 specimens representing 62 different sarcoma types and 15 different carcinoma types showed that NMB was highly expressed in 17 of 22 EMC cases and very rarely expressed in other tumours and thus could function as a novel diagnostic marker. High levels of expression of PPARG and the gene encoding its interacting protein, PPARGC1A, in most EMCs suggest activation of lipid metabolism pathways in this tumour. Small molecule inhibitors for PPARG exist and PPARG could be a potential therapeutic target for EMC.

    View details for DOI 10.1002/path.1792

    View details for Web of Science ID 000230662100009

    View details for PubMedID 15920699

  • Determination of stromal signatures in breast carcinoma PLOS BIOLOGY West, R. B., Nuyten, D. S., Subramanian, S., Nielsen, T. O., Corless, C. L., Rubin, B. P., Montgomery, K., Zhu, S., Patel, R., Hernandez-Boussard, T., Goldblum, J. R., Brown, P. O., van De Vijver, M., van de Rijn, M. 2005; 3 (6): 1101-1110


    Many soft tissue tumors recapitulate features of normal connective tissue. We hypothesize that different types of fibroblastic tumors are representative of different populations of fibroblastic cells or different activation states of these cells. We examined two tumors with fibroblastic features, solitary fibrous tumor (SFT) and desmoid-type fibromatosis (DTF), by DNA microarray analysis and found that they have very different expression profiles, including significant differences in their patterns of expression of extracellular matrix genes and growth factors. Using immunohistochemistry and in situ hybridization on a tissue microarray, we found that genes specific for these two tumors have mutually specific expression in the stroma of nonneoplastic tissues. We defined a set of 786 gene spots whose pattern of expression distinguishes SFT from DTF. In an analysis of DNA microarray gene expression data from 295 previously published breast carcinomas, we found that expression of this gene set defined two groups of breast carcinomas with significant differences in overall survival. One of the groups had a favorable outcome and was defined by the expression of DTF genes. The other group of tumors had a poor prognosis and showed variable expression of genes enriched for SFT type. Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells.

    View details for DOI 10.1371/journal.pbio.0030187

    View details for Web of Science ID 000229992900019

    View details for PubMedID 15869330

    View details for PubMedCentralID PMC1088973

  • Familial gastrointestinal stromal tumor syndrome: Phenotypic and molecular features in a kindred JOURNAL OF CLINICAL ONCOLOGY Li, F. P., Fletcher, J. A., Heinrich, M. C., Garber, J. E., Sallan, S. E., Curiel-Lewandrowski, C., Duensing, A., van de Rijn, M. V., Schnipper, L. E., Demetri, G. D. 2005; 23 (12): 2735-2743


    Members of a family with hereditary gastrointestinal stromal tumors (GISTs) and a germline KIT oncogene mutation were evaluated for other potential syndrome manifestations. A tumor from the proband was analyzed to compare features with sporadic GISTs.Members of a kindred in which six relatives in four consecutive generations comprised an autosomal dominant pattern of documented GISTs and cutaneous lesions underwent physical examination, imaging studies, and germline KIT analysis. A recurrent GIST from the proband was studied using microarray, karyotypic, immunohistochemical, and immunoblotting techniques.In addition to evidence of multiple GISTs, lentigines, malignant melanoma, and an angioleiomyoma were identified in relatives. A previously reported gain-of-function missense mutation in KIT exon 11 (T --> C) that results in a V559A substitution within the juxtamembrane domain was identified in three family members. The proband's recurrent gastric GIST had a 44,XY-14,-22 karyotype and immunohistochemical evidence of strong diffuse cytoplasmic KIT expression without expression of actin, desmin, or S-100. Immunoblotting showed strong expression of phosphorylated KIT and downstream signaling intermediates (AKT and MAPK) at levels comparable with those reported in sporadic GISTs. cDNA array profiling demonstrated clustering with sporadic GISTs, and expression of GIST markers comparable to sporadic GISTs.These studies provide the first evidence that gene expression and mechanisms of cytogenetic progression and cell signaling are indistinguishable in familial and sporadic GISTs. Current investigations of molecularly targeted therapies in GIST patients provide opportunities to increase the understanding of features of the hereditary syndrome, and risk factors and molecular pathways of the neoplastic phenotypes.

    View details for DOI 10.1200/JCO.2005.06.009

    View details for Web of Science ID 000228563600021

    View details for PubMedID 15837988

  • Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Chang, H. Y., Nuyten, D. S., Sneddon, J. B., Hastie, T., Tibshirani, R., Sorlie, T., Dai, H. Y., He, Y. D., Van't Veer, L. J., Bartelink, H., van de Rijn, M., Brown, P. O., van de Vijver, M. J. 2005; 102 (10): 3738-3743


    Based on the hypothesis that features of the molecular program of normal wound healing might play an important role in cancer metastasis, we previously identified consistent features in the transcriptional response of normal fibroblasts to serum, and used this "wound-response signature" to reveal links between wound healing and cancer progression in a variety of common epithelial tumors. Here, in a consecutive series of 295 early breast cancer patients, we show that both overall survival and distant metastasis-free survival are markedly diminished in patients whose tumors expressed this wound-response signature compared to tumors that did not express this signature. A gene expression centroid of the wound-response signature provides a basis for prospectively assigning a prognostic score that can be scaled to suit different clinical purposes. The wound-response signature improves risk stratification independently of known clinico-pathologic risk factors and previously established prognostic signatures based on unsupervised hierarchical clustering ("molecular subtypes") or supervised predictors of metastasis ("70-gene prognosis signature").

    View details for DOI 10.1073/pnas.0409462102

    View details for Web of Science ID 000227533100040

    View details for PubMedID 15701700

  • Distinction between serous tumors of low malignant potential and serous carcinomas based on global mRNA expression profiling GYNECOLOGIC ONCOLOGY Gilks, C. B., Vanderhyden, B. C., Zhu, S., van de Rijn, M., Longacre, T. A. 2005; 96 (3): 684-694


    The molecular pathogenesis of ovarian serous tumors of low malignant potential (S-LMP) is not well understood, although the collective data suggest that they arise through molecular mechanisms distinct from those leading to conventional serous carcinomas (S-Ca). To further examine the molecular differences between these two diseases, we studied the gene expression pattern of ovarian S-LMP and S-Ca using high-density spotted cDNA and tissue microarrays.Total RNA from 23 ovarian S-LMP and S-Ca was analyzed on 43,200 spot cDNA microarrays and the differential expression of proteins encoded by differentially expressed genes was validated using tissue microarrays.Unsupervised hierarchical clustering analysis of filtered data showed a complete separation between S-LMP and S-Ca, based predominantly on a small set of genes expressed at higher levels in S-LMP than in S-Ca. Many genes previously identified as up-regulated in ovarian carcinoma relative to normal ovarian tissue were expressed at even higher levels in S-LMP. These genes included mucin-1, mesothelin, HE4, PAX 8, and apolipoprotein J/clusterin. Immunohistochemical staining of tissue microarrays confirmed higher expression of selected proteins encoded by these genes in the S-LMP. Few genes were expressed at a higher level in S-Ca; these included E2F1, topoisomerase IIalpha, and cyclin E, with higher levels of cyclin E protein confirmed by immunohistochemistry.S-LMP and S-Ca are distinguished at the molecular level by a relatively small gene set, suggesting the pathogenesis of S-LMP as well as S-Ca may involve molecular pathways that escape detection by global gene expression profiling. In order to obtain biologically and clinically relevant information about the mechanisms involved in ovarian carcinogenesis, future studies based on molecular profiles of ovarian cancer should include analyses of low malignant potential tumors. Inclusion of such tumors is also critical to the evaluation of the efficacy of potential new diagnostic and/or therapeutic biomarkers.

    View details for DOI 10.1016/j.ygyno.2004.11.039

    View details for Web of Science ID 000227615600017

    View details for PubMedID 15721412

  • A novel method for making "tissue" microarrays from small numbers of suspension cells APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY Montgomery, K., Zhao, S. C., van de Rijn, M., Natkunam, Y. 2005; 13 (1): 80-84


    Tissue microarrays (TMAs) are a highly efficient method for large-scale protein expression studies. To date most TMAs have been constructed using paraffin-embedded specimens. The authors developed a method that allows construction of TMAs from small numbers of cells in suspension. Spun pellets of 1x10 to 1x10 cells are directly processed and embedded in paraffin in an Eppendorf tube. Cylindrical cores of 0.6 mm are taken from these tubes and embedded in a recipient paraffin block to create a TMA. This relatively simple but versatile method enables very small numbers of cells in suspension to be analyzed using the TMA technology and allows for the study of hematolymphoid and related disorders of the blood and bone marrow for which solid tissue samples cannot be readily obtained. With the increasing trend toward obtaining small samples for screening and diagnostic purposes, this method provides a means to manipulate small volume samples for high-throughput immunohistochemical analysis. This method is also amenable for use for cultured cells.

    View details for Web of Science ID 000227276000013

    View details for PubMedID 15722798

  • Screening of tissue microarrays for ubiquitin proteasome system components in tumors UBIQUITIN AND PROTEIN DEGRADATION, PT B Lehman, N. L., van de Rijn, M., Jackson, P. K. 2005; 399: 334-?


    The turnover of key proteins that mediate development, cellular proliferation, and a host of essential biological processes is controlled by the ubiquitin proteasome system (UPS). In several well-studied examples, notably in the cell cycle, regulatory proteins that control ubiquitin-dependent destruction are themselves substrates of the UPS, creating a multilayered system to ensure precise and dynamic control of protein stability. UPS regulators controlled at the level of protein stability--including the F-box protein Skp2 and the VHL protein (substrate adapter proteins for multicomponent E3 ubiquitin ligases)-- seem to be misregulated in tumors. In these cases, especially, measuring levels of critical regulatory and target proteins will often present a more biologically meaningful picture than examining relative mRNA levels, which do not always reflect corresponding protein levels. Tissue microarrays (TMAs) allow simultaneous screening of large numbers of tumors for expression of specific proteins by immunohistochemical staining of a single microscope slide prepared from a TMA paraffin block. Replicate slides prepared from the same block can be immunostained for multiple proteins functioning in a related pathway, and a semiquantitative protein expression profile for a given subset of UPS pathway components, or other subsets of proteins of interest, can be assembled. Protein expression profiles of individual tumors or tissue types can be compared and visualized by hierarchical clustering methods. These expression profiles may be used as screening tools to investigate the relative abundance of components of a biochemical pathway in tumors or other tissues. TMAs have an exciting future as tools for basic research, diagnostic pathology, and drug targeting. In this article, we provide an introduction to the use of TMAs to study the expression of UPS component proteins and substrates in tumors by immunohistochemistry.

    View details for DOI 10.1016/S0076-6879(05)99023-X

    View details for Web of Science ID 000233597300023

    View details for PubMedID 16338367

  • CSF1 expression signature identifies a subset of breast carcinomas and influences outcome. 28th Annual San Antonio Breast Cancer Symposium West, R. B., Horlings, H., Nuyten, D. S., Subramanian, S., Zhu, S. X., Miller, M., Rubin, B. P., Nielsen, T. O., Gilks, C. B., Huntsman, D. G., Tibshirani, R., van De Vijver, M., van de Rijn, M. SPRINGER. 2005: S135–S135
  • Stromal expression signatures predict outcome in breast carcinoma 94th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology West, R. B., Nuyten, D. S., Subramanian, S., Corless, C., Rubin, B. P., Montgomergy, K., Zhu, S. X., Nielsen, T. O., Patel, R., Goldblum, J. R., Brown, P. O., van De Vijver, M., van de Rijn, M. NATURE PUBLISHING GROUP. 2005: 55A–55A
  • PAX5 protein expression in bladder tumors by tissue microarray immunohistochemistry 94th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Jensen, K. C., Kaygusuz, G., Montgomery, K., van de Rijn, M., Higgins, J. NATURE PUBLISHING GROUP. 2005: 148A–148A
  • A DNA microarray survey of gene expression in normal human tissues GENOME BIOLOGY Shyamsundar, R., Kim, Y. H., Higgins, J. P., Montgomery, K., Jorden, M., Sethuraman, A., van de Rijn, M., Botstein, D., Brown, P. O., Pollack, J. R. 2005; 6 (3)


    Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states. Comparatively little is known about the genes expressed across the gamut of normal human tissues. Systematic studies of global gene-expression patterns, by linking variation in the expression of specific genes to phenotypic variation in the cells or tissues in which they are expressed, provide clues to the molecular organization of diverse cells and to the potential roles of the genes.Here we describe a systematic survey of gene expression in 115 human tissue samples representing 35 different tissue types, using cDNA microarrays representing approximately 26,000 different human genes. Unsupervised hierarchical cluster analysis of the gene-expression patterns in these tissues identified clusters of genes with related biological functions and grouped the tissue specimens in a pattern that reflected their anatomic locations, cellular compositions or physiologic functions. In unsupervised and supervised analyses, tissue-specific patterns of gene expression were readily discernable. By comparative hybridization to normal genomic DNA, we were also able to estimate transcript abundances for expressed genes.Our dataset provides a baseline for comparison to diseased tissues, and will aid in the identification of tissue-specific functions. In addition, our analysis identifies potential molecular markers for detection of injury to specific organs and tissues, and provides a foundation for selection of potential targets for selective anticancer therapy.

    View details for Web of Science ID 000228246400007

    View details for PubMedID 15774023

    View details for PubMedCentralID PMC1088941

  • Gastrointestinal stromal tumors (GISTs) with KIT and PDGFRA mutations have distinct gene expression profiles ONCOGENE Subramanian, S., West, R. B., Corless, C. L., Ou, W. B., Rubin, B. P., Chu, K. M., Leung, S. Y., Yuen, S. T., Zhu, S., Hernandez-Boussard, T., Montgomery, K., Nielsen, T. O., Patel, R. M., Goldblum, J. R., Heinrich, M. C., Fletcher, J. A., van de Rijn, M. 2004; 23 (47): 7780-7790


    Most GISTs require oncogenic activation of the KIT or PDGFRA receptor tyrosine kinase proteins, and the genomic mechanisms of oncogene activation are heterogeneous. Notably, the kinase mutation type correlates with both tumor biology and imatinib response. For example, GISTs with KIT exon 11 mutations are typically gastric and have excellent imatinib response, whereas those with KIT exon 9 mutations generally arise in the small bowel and are less responsive to imatinib. To identify genes that might contribute to these biological differences, we carried out gene expression profiling of 26 GISTs with known KIT and PDGFRA mutational status. Expression differences were then evaluated further by RNA in situ hybridization, immunohistochemistry, and immunoblotting. Unsupervised hierarchical clustering grouped tumors with similar mutations together, but the distinction between the different groups was not absolute. Differentially expressed genes included ezrin, p70S6K, and PKCs, which are known to have key roles in KIT or PDGFRA signaling, and which might therefore contribute to the distinctive clinicopathological features in GISTs with different mutation types. These gene products could serve as highly selective therapeutic targets in GISTs containing the KIT or PDGFRA mutational types with which they are associated.

    View details for DOI 10.1038/sj.onc.1208056

    View details for Web of Science ID 000224331600004

    View details for PubMedID 15326474

  • Novel endothelial cell markers in hepatocellular carcinoma MODERN PATHOLOGY Chen, X., Higgins, J., Cheung, S. T., Li, R., Mason, V., Montgomery, K., Fan, S. T., van de Rijn, M., So, S. 2004; 17 (10): 1198-1210


    Hepatocellular carcinoma is characterized by hypervascularity and a propensity for vascular invasion. Detailed analysis of complementary DNA (cDNA) microarray global gene expression data and further validation on a smaller independent sample set by reverse transcription-polymerase chain reaction established the presence of two endothelial gene clusters in hepatocellular carcinoma. Cluster I, consists of 20 cDNA clones, representing 15 unique genes. Cluster II consists of nine unique genes. The expression of the cluster I genes appeared to be significantly upregulated in hepatocellular carcinoma compared with normal liver, cirrhotic liver, or nontumor liver tissues adjacent to the hepatocellular carcinoma. The pattern of gene expression of cluster I genes correlated positively with the 'proliferation gene cluster' and 'stromal cells cluster 2'. Expression of cluster II genes, in contrast, was not significantly different between hepatocellular carcinoma and non-neoplastic liver tissues. Studies conducted to localize the protein products of these genes by immunohistochemical staining of tissue arrays with up to 350 cores of tissues, and by in situ hybridization led to the discovery of novel sinusoidal endothelial cell markers in hepatocellular carcinoma: podocalyxin-like and regulator of G protein signaling-5. Our results underscore fundamental differences not only between neoplastic vs non-neoplastic liver cells but also between the hepatic sinusoidal endothelium of hepatocellular carcinoma and normal liver.

    View details for DOI 10.1038/modpathol.3800167

    View details for Web of Science ID 000224094600004

    View details for PubMedID 15154008

  • Hierarchical clustering analysis of tissue microarray immunostaining data identifies prognostically significant groups of breast carcinoma CLINICAL CANCER RESEARCH Makretsov, N. A., Huntsman, D. G., Nielsen, T. O., Yorida, E., Peacock, M., Cheang, M. C., Dunn, S. E., Hayes, M., van de Rijn, M., Bajdik, C., Gilks, C. B. 2004; 10 (18): 6143-6151


    Prognostically relevant cluster groups, based on gene expression profiles, have been recently identified for breast cancers, lung cancers, and lymphoma. Our aim was to determine whether hierarchical clustering analysis of multiple immunomarkers (protein expression profiles) improves prognostication in patients with invasive breast cancer. A cohort of 438 sequential cases of invasive breast cancer with median follow-up of 15.4 years was selected for tissue microarray construction. A total of 31 biomarkers were tested by immunohistochemistry on these tissue arrays. The prognostic significance of individual markers was assessed by using Kaplan-Meier survival estimates and log-rank tests. Seventeen of 31 markers showed prognostic significance in univariate analysis (P < or = 0.05) and 4 markers showed a trend toward significance (P < or = 0.2). Unsupervised hierarchical clustering analysis was done by using these 21 immunomarkers, and this resulted in identification of three cluster groups with significant differences in clinical outcome. chi2 analysis showed that expression of 11 markers significantly correlated with membership in one of the three cluster groups. Unsupervised hierarchical clustering analysis with this set of 11 markers reproduced the same three prognostically significant cluster groups identified by using the larger set of markers. These cluster groups were of prognostic significance independent of lymph node metastasis, tumor size, and tumor grade in multivariate analysis (P=0.0001). The cluster groups were as powerful a prognostic indicator as lymph node status. This work demonstrates that hierarchical clustering of immunostaining data by using multiple markers can group breast cancers into classes with clinical relevance and is superior to the use of individual prognostic markers.

    View details for Web of Science ID 000224080200023

    View details for PubMedID 15448001

  • Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma CLINICAL CANCER RESEARCH Nielsen, T. O., Hsu, F. D., Jensen, K., Cheang, M., Karaca, G., Hu, Z. Y., Hernandez-Boussard, T., Livasy, C., Cowan, D., Dressler, L., Akslen, L. A., Ragaz, J., GOWN, A. M., Gilks, C. B., van de Rijn, M. V., Perou, C. M. 2004; 10 (16): 5367-5374


    Expression profiling studies classified breast carcinomas into estrogen receptor (ER)+/luminal, normal breast-like, HER2 overexpressing, and basal-like groups, with the latter two associated with poor outcomes. Currently, there exist clinical assays that identify ER+/luminal and HER2-overexpressing tumors, and we sought to develop a clinical assay for breast basal-like tumors.To identify an immunohistochemical profile for breast basal-like tumors, we collected a series of known basal-like tumors and tested them for protein patterns that are characteristic of this subtype. Next, we examined the significance of these protein patterns using tissue microarrays and evaluated the prognostic significance of these findings.Using a panel of 21 basal-like tumors, which was determined using gene expression profiles, we saw that this subtype was typically immunohistochemically negative for estrogen receptor and HER2 but positive for basal cytokeratins, HER1, and/or c-KIT. Using breast carcinoma tissue microarrays representing 930 patients with 17.4-year mean follow-up, basal cytokeratin expression was associated with low disease-specific survival. HER1 expression was observed in 54% of cases positive for basal cytokeratins (versus 11% of negative cases) and was associated with poor survival independent of nodal status and size. c-KIT expression was more common in basal-like tumors than in other breast cancers but did not influence prognosis.A panel of four antibodies (ER, HER1, HER2, and cytokeratin 5/6) can accurately identify basal-like tumors using standard available clinical tools and shows high specificity. These studies show that many basal-like tumors express HER1, which suggests candidate drugs for evaluation in these patients.

    View details for Web of Science ID 000223454600011

    View details for PubMedID 15328174

  • Apo D in soft tissue tumors - A novel marker for dermatofibrosarcoma protuberans AMERICAN JOURNAL OF SURGICAL PATHOLOGY West, R. B., Harvell, J., Linn, S. C., Lui, C. L., Prapong, W., Hernandez-Boussard, T., Montgomery, K., Nielsen, T. O., Rubin, B. P., Patel, R., Goldblum, J. R., Brown, P. O., van de Rijn, M. 2004; 28 (8): 1063-1069


    Using gene microarray expression profiling, we previously found that apolipoprotein D (Apo D) was highly expressed in dermatofibrosarcoma protuberans (DFSP). In this study, we confirm that Apo D is highly and relatively specifically expressed in DFSP using immunohistochemistry. A tissue microarray containing 421 soft tissue tumors was constructed and stained with antibodies against Apo D and CD34. Cytoplasmic immunostaining for Apo D was found in 9 of 10 typical DFSPs. In addition, 3 of 3 Bednar tumors and 2 of 3 giant cell fibroblastomas stained in conventional sections. In contrast, Apo D was immunoreactive in only a very small subset of a diverse collection of other soft tissue tumors, including Malignant Fibrous Histiocytoma (MFH), glomus tumor, neurofibroma, and malignant peripheral nerve sheath tumors. Immunostains for Apo D were negative in conventional sections of 16 fibrous histiocytomas, and an additional 12 variants of fibrous histiocytoma. Digital images of all immunohistochemical and hematoxylin and eosin tissue microarray stains are available at the accompanying website ( We conclude that Apo D is strongly expressed in DFSPs and neural lesions and may be useful in differentiating DFSP from fibrous histiocytoma.

    View details for Web of Science ID 000222891400012

    View details for PubMedID 15252314

  • The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status AMERICAN JOURNAL OF PATHOLOGY West, R. B., Corless, C. L., Chen, X., Rubin, B. P., Subramanian, S., Montgomery, K., Zhu, S., Ball, C. A., Nielsen, T. O., Patel, R., Goldblum, J. R., Brown, P. O., Heinrich, M. C., van de Rijn, M. 2004; 165 (1): 107-113


    We recently characterized gene expression patterns in gastrointestinal stromal tumors (GISTs) using cDNA microarrays, and found that the gene FLJ10261 (DOG1, discovered on GIST-1), encoding a hypothetical protein, was specifically expressed in GISTs. The immunoreactivity of a rabbit antiserum to synthetic DOG1 peptides was assessed on two soft tissue tumor microarrays. The tissue microarrays included 587 soft tissue tumors, with 149 GISTs, including 127 GIST cases for which the KIT and PDGFRA mutation status was known. Immunoreactivity for DOG1 was found in 136 of 139 (97.8%) of scorable GISTs. All seven GIST cases with a PDGFRA mutation were DOG1-positive, while most of these failed to react for KIT. The immunohistochemical findings were confirmed with in situ hybridization probes for DOG1, KIT, and PDGFRA. Other neoplasms in the differential diagnosis of GIST, including desmoid fibromatosis (0 of 17) and Schwannoma (0 of 3), were immunonegative for DOG1. Only 4 of 438 non-GIST cases were immunoreactive for DOG1. DOG1, a protein of unknown function, is expressed strongly on the cell surface of GISTs and is rarely expressed in other soft tissue tumors. Reactivity for DOG1 may aid in the diagnosis of GISTs, including PDGFRA mutants that fail to express KIT antigen, and lead to appropriate treatment with imatinib mesylate, an inhibitor of the KIT tyrosine kinase.

    View details for Web of Science ID 000222216000010

    View details for PubMedID 15215166

  • High-resolution array-based comparative genomic hybridization for distinguishing paraffin-embedded Spitz nevi and melanomas DIAGNOSTIC MOLECULAR PATHOLOGY Harvell, J. D., Kohler, S., Zhu, S., Hernandez-Boussard, T., Pollack, J. R., van de Rijn, M. 2004; 13 (1): 22-25


    Distinguishing between Spitz nevus and melanoma presents a challenging task for clinicians and pathologists. Most of these lesions are submitted entirely in formalin for histologic analysis by conventional hematoxylin and eosin-stained sections, and fresh-frozen material for ancillary studies is rarely collected. Molecular techniques, such as comparative genomic hybridization (CGH), can detect chromosomal alterations in tumor DNA that differ between these 2 lesions. This study investigated the ability of high-resolution array-based CGH to serve as a diagnostic test in distinguishing Spitz nevus and melanoma using DNA isolated from formalin-fixed and paraffin-embedded samples. Two of 3 Spitz nevi exhibited no significant chromosomal alterations, while the third showed gain of the short arm of chromosome 11p. The latter finding has previously been described as characteristic of a subset of Spitz nevi. The 2 melanomas showed multiple copy number alterations characteristic of melanoma such as 1q amplification and chromosome 9 deletion. This study has shown the utility of array-based CGH as a potential molecular test in distinguishing Spitz nevus from melanoma. The assay is capable of using archival paraffin-embedded, formalin-fixed material; is technically easier to perform as compared with conventional CGH; is more sensitive than conventional CGH in being able to detect focal alterations; and can detect copy number alterations even with relatively small amounts of lesional tissue as is typical of many skin tumors.

    View details for Web of Science ID 000189276600004

    View details for PubMedID 15163005

  • Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS biology Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J., van de Rijn, M., Botstein, D., Brown, P. O. 2004; 2 (2): E7-?


    Cancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between these two processes and their prognostic implications are unclear. In this study, based on gene expression profiles of fibroblasts from ten anatomic sites, we identify a stereotyped gene expression program in response to serum exposure that appears to reflect the multifaceted role of fibroblasts in wound healing. The genes comprising this fibroblast common serum response are coordinately regulated in many human tumors, allowing us to identify tumors with gene expression signatures suggestive of active wounds. Genes induced in the fibroblast serum-response program are expressed in tumors by the tumor cells themselves, by tumor-associated fibroblasts, or both. The molecular features that define this wound-like phenotype are evident at an early clinical stage, persist during treatment, and predict increased risk of metastasis and death in breast, lung, and gastric carcinomas. Thus, the transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a powerful predictor of the clinical course in several common carcinomas.

    View details for PubMedID 14737219

    View details for PubMedCentralID PMC314300

  • Gene expression signature of fibroblast serum response predicts human cancer progression: Similarities between tumors and wounds PLOS BIOLOGY Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. T., van de Rijn, M., Botstein, D., Brown, P. O. 2004; 2 (2): 206-214
  • Gene expression in the normal adult human kidney assessed by complementary DNA microarray MOLECULAR BIOLOGY OF THE CELL Higgins, J. P., Wang, L. L., Kambham, N., Montgomery, K., Mason, V., Vogelmann, S. U., Lemley, K. V., Brown, P. O., Brooks, J. D., van de Rijn, M. 2004; 15 (2): 649-656


    The kidney is a highly specialized organ with a complex, stereotyped architecture and a great diversity of functions and cell types. Because the microscopic organization of the nephron, the functional unit of the kidney, has a consistent relationship to the macroscopic anatomy of the kidney, knowledge of the characteristic patterns of gene expression in different compartments of the kidney could provide insight into the functions and functional organization of the normal nephron. We studied gene expression in dissected renal lobes of five adult human kidneys using cDNA microarrays representing approximately 30,000 different human genes. Total RNA was isolated from sections of the inner and outer cortex, inner and outer medulla, papillary tips, and renal pelvis and from glomeruli isolated by sieving. The results revealed unique and highly distinctive patterns of gene expression for glomeruli, cortex, medulla, papillary tips, and pelvic samples. Immunohistochemical staining using selected antisera confirmed differential expression of several cognate proteins and provided histological localization of expression within the nephron. The distinctive patterns of gene expression in discrete portions of the kidney may serve as a resource for further understanding of renal physiology and the molecular and cellular organization of the nephron.

    View details for DOI 10.1091/mbc.E03-06-0432

    View details for Web of Science ID 000188718900024

    View details for PubMedID 14657249

    View details for PubMedCentralID PMC329285

  • Applications of microarrays to histopathology HISTOPATHOLOGY van de Rijn, M., Gilks, C. B. 2004; 44 (2): 97-108


    High-throughput microarray technologies have the potential to impact significantly on the practice of histopathology over the coming years. Global gene expression profiling allows for a systematic search of all human genes for novel diagnostic and prognostic markers and for potential therapeutic targets. Likewise, gene copy number changes can be determined on a gene-by-gene basis using microarrays. Tissue microarrays are an efficient method to extend and validate the findings obtained from the initial 'discovery' phase of the research, done using cDNA microarrays. In addition, tissue microarrays can be used for quality assurance for immunohistochemical and in situ hybridization procedures. In this review we give a brief overview of microarray technology and research uses, and discuss potential applications of microarrays in the practice of diagnostic histopathology.

    View details for Web of Science ID 000188821600001

    View details for PubMedID 14764053

  • Gene expression profiling identifies clinically relevant subtypes of prostate cancer PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lapointe, J., Li, C., Higgins, J. P., van de Rijn, M., Bair, E., Montgomery, K., Ferrari, M., Egevad, L., Rayford, W., Bergerheim, U., Ekman, P., DeMarzo, A. M., Tibshirani, R., Botstein, D., Brown, P. O., Brooks, J. D., Pollack, J. R. 2004; 101 (3): 811-816


    Prostate cancer, a leading cause of cancer death, displays a broad range of clinical behavior from relatively indolent to aggressive metastatic disease. To explore potential molecular variation underlying this clinical heterogeneity, we profiled gene expression in 62 primary prostate tumors, as well as 41 normal prostate specimens and nine lymph node metastases, using cDNA microarrays containing approximately 26,000 genes. Unsupervised hierarchical clustering readily distinguished tumors from normal samples, and further identified three subclasses of prostate tumors based on distinct patterns of gene expression. High-grade and advanced stage tumors, as well as tumors associated with recurrence, were disproportionately represented among two of the three subtypes, one of which also included most lymph node metastases. To further characterize the clinical relevance of tumor subtypes, we evaluated as surrogate markers two genes differentially expressed among tumor subgroups by using immunohistochemistry on tissue microarrays representing an independent set of 225 prostate tumors. Positive staining for MUC1, a gene highly expressed in the subgroups with "aggressive" clinicopathological features, was associated with an elevated risk of recurrence (P = 0.003), whereas strong staining for AZGP1, a gene highly expressed in the other subgroup, was associated with a decreased risk of recurrence (P = 0.0008). In multivariate analysis, MUC1 and AZGP1 staining were strong predictors of tumor recurrence independent of tumor grade, stage, and preoperative prostate-specific antigen levels. Our results suggest that prostate tumors can be usefully classified according to their gene expression patterns, and these tumor subtypes may provide a basis for improved prognostication and treatment stratification.

    View details for DOI 10.1073/pnas.0304146101

    View details for Web of Science ID 000188555400023

    View details for PubMedID 14711987

    View details for PubMedCentralID PMC321763

  • Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans AMERICAN JOURNAL OF PATHOLOGY Linn, S. C., West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., Gilks, C. B., van de Rijn, M. 2003; 163 (6): 2383-2395


    Dermatofibrosarcoma protuberans (DFSP) is an aggressive spindle cell neoplasm. It is associated with the chromosomal translocation, t(17:22), which fuses the COL1A1 and PDGFbeta genes. We determined the characteristic gene expression profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative genomic hybridization (array CGH). Fresh frozen and formalin-fixed, paraffin-embedded samples of DFSP were analyzed by array CGH (four cases) and DNA microarray analysis of global gene expression (nine cases). The nine DFSPs were readily distinguished from 27 other diverse soft tissue tumors based on their gene expression patterns. Genes characteristically expressed in the DFSPs included PDGF beta and its receptor, PDGFRB, APOD, MEOX1, PLA2R, and PRKCA. Array CGH of DNA extracted either from frozen tumor samples or from paraffin blocks yielded equivalent results. Large areas of chromosomes 17q and 22q, bounded by COL1A1 and PDGF beta, respectively, were amplified in DFSP. Expression of genes in the amplified regions was significantly elevated. Our data shows that: 1) DFSP has a distinctive gene expression profile; 2) array CGH can be applied successfully to frozen or formalin-fixed, paraffin-embedded tumor samples; 3) a characteristic amplification of sequences from chromosomes 17q and 22q, demarcated by the COL1A1 and PDGF beta genes, respectively, was associated with elevated expression of the amplified genes.

    View details for Web of Science ID 000186769800024

    View details for PubMedID 14633610

    View details for PubMedCentralID PMC1892373

  • Gene expression patterns in ovarian carcinomas MOLECULAR BIOLOGY OF THE CELL Schaner, M. E., Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., Sikic, B. I. 2003; 14 (11): 4376-4386


    We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly serous papillary) based on their gene expression patterns. The differences may yield insights into the worse prognosis and therapeutic resistance associated with clear cell carcinomas. A comparison of the gene expression patterns in the ovarian cancers to published data of gene expression in breast cancers revealed a large number of differentially expressed genes. We identified a group of 62 genes that correctly classified all 125 breast and ovarian cancer specimens. Among the best discriminators more highly expressed in the ovarian carcinomas were PAX8 (paired box gene 8), mesothelin, and ephrin-B1 (EFNB1). Although estrogen receptor was expressed in both the ovarian and breast cancers, genes that are coregulated with the estrogen receptor in breast cancers, including GATA-3, LIV-1, and X-box binding protein 1, did not show a similar pattern of coexpression in the ovarian cancers.

    View details for Web of Science ID 000186738300005

    View details for PubMedID 12960427

    View details for PubMedCentralID PMC266758

  • Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology AMERICAN JOURNAL OF PATHOLOGY Nielsen, T. O., Hsu, F. D., O'Connell, J. X., Gilks, C. B., Sorensen, P. H., Linn, S., West, R. B., Liu, C. L., Botstein, D., Brown, P. O., van de Rijn, M. 2003; 163 (4): 1449-1456


    Histological diagnosis of synovial sarcoma can be difficult. Genome-wide expression profiling has identified a number of genes expressed at higher levels in synovial sarcoma than in other soft tissue tumors, representing excellent candidates for diagnostic immunohistochemical markers. A tissue microarray comprising 77 sarcomas, including 46 synovial sarcomas, was constructed to validate identified markers and investigate their expression in tumors in the differential diagnosis of synovial sarcoma. Immunostaining was performed for two such markers, epidermal growth factor receptor and SAL (drosophila)-like 2 (SALL2), and for fifteen established markers used in the differential diagnosis of sarcomas. As predicted by expression profiling, epidermal growth factor receptor (a potential therapeutic target) and SALL2 stained most cases of synovial sarcoma; staining was significantly less common among other tested sarcomas. Hierarchical clustering analysis applied to immunostaining results for all 18 antibodies showed that synovial sarcomas, leiomyosarcomas, hemangiopericytomas, and solitary fibrous tumors cluster distinctly, and assigned one case with indeterminate histology as a Ewing sarcoma. Digital images from over 2500 immunostained cores analyzed in this study were captured and are made accessible through the accompanying website:

    View details for Web of Science ID 000185517500022

    View details for PubMedID 14507652

    View details for PubMedCentralID PMC1868308

  • Endothelial cell diversity revealed by global expression profiling PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Chi, J. T., Chang, H. Y., Haraldsen, G., Jahnsen, F. L., Troyanskaya, O. G., Chang, D. S., Wang, Z., Rockson, S. G., van de Rijn, M., Botstein, D., Brown, P. O. 2003; 100 (19): 10623-10628


    The vascular system is locally specialized to accommodate widely varying blood flow and pressure and the distinct needs of individual tissues. The endothelial cells (ECs) that line the lumens of blood and lymphatic vessels play an integral role in the regional specialization of vascular structure and physiology. However, our understanding of EC diversity is limited. To explore EC specialization on a global scale, we used DNA microarrays to determine the expression profile of 53 cultured ECs. We found that ECs from different blood vessels and microvascular ECs from different tissues have distinct and characteristic gene expression profiles. Pervasive differences in gene expression patterns distinguish the ECs of large vessels from microvascular ECs. We identified groups of genes characteristic of arterial and venous endothelium. Hey2, the human homologue of the zebrafish gene gridlock, was selectively expressed in arterial ECs and induced the expression of several arterial-specific genes. Several genes critical in the establishment of left/right asymmetry were expressed preferentially in venous ECs, suggesting coordination between vascular differentiation and body plan development. Tissue-specific expression patterns in different tissue microvascular ECs suggest they are distinct differentiated cell types that play roles in the local physiology of their respective organs and tissues.

    View details for DOI 10.1073/pnas.1434429100

    View details for Web of Science ID 000185415300012

    View details for PubMedID 12963823

  • Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray AMERICAN JOURNAL OF PATHOLOGY Higgins, J. P., Shinghal, R., Gill, H., Reese, J. H., Terris, M., Cohen, R. J., Fero, M., Pollack, J. R., van de Rijn, M., Brooks, J. D. 2003; 162 (3): 925-932


    Renal cell carcinoma comprises several histological types with different clinical behavior. Accurate pathological characterization is important in the clinical management of these tumors. We describe gene expression profiles in 41 renal tumors determined by using DNA microarrays containing 22,648 unique cDNAs representing 17,083 different UniGene Clusters, including 7230 characterized human genes. Differences in the patterns of gene expression among the different tumor types were readily apparent; hierarchical cluster analysis of the tumor samples segregated histologically distinct tumor types solely based on their gene expression patterns. Conventional renal cell carcinomas with clear cells showed a highly distinctive pattern of gene expression. Papillary carcinomas formed a tightly clustered group, as did tumors arising from the distal nephron and the normal kidney samples. Surprisingly, conventional renal cell carcinomas with granular cytoplasm were heterogeneous, and did not resemble any of the conventional carcinomas with clear cytoplasm in their pattern of gene expression. Characterization of renal cell carcinomas based on gene expression patterns provides a revised classification of these tumors and has the potential to supply significant biological and clinical insights.

    View details for Web of Science ID 000181215000023

    View details for PubMedID 12598325

    View details for PubMedCentralID PMC1868114

  • Hep par 1 antibody stain for the differential diagnosis of hepatocellular carcinoma: 676 tumors tested using tissue microarrays and conventional tissue sections. Modern pathology Fan, Z., van de Rijn, M., Montgomery, K., Rouse, R. V. 2003; 16 (2): 137-144


    A well-characterized positive marker for hepatocellular differentiation would be a useful tool for the diagnosis of hepatocellular carcinoma (HCC). The recently commercially available Hep Par 1 antibody (clone OCH1E5.2.10) has been reported to be a sensitive marker for HCC in paraffin embedded sections. Of non-hepatocellular tumors, occasional carcinomas have been reported to stain, most frequently gastric adenocarcinomas. This study further evaluated the staining of this antibody on a large number of neoplasms using tissue microarray technology as well as conventional tissue sections. Six hundred seventy-six tumors, including 19 cases of HCC, were tested. Eighteen of 19 cases of HCC were positive, 3 showing <5% staining. Two cases negative on the array showed focal staining when whole tissue sections from the same tumors were used. 16 of 34 cases of gastric carcinomas gave positive reactions, 4 of these showed less than 5% staining. Staining of gastric carcinomas was not limited to signet ring-type carcinomas or to areas of hepatoid differentiation. Only 1 of 11 cases of cholangiocarcinoma showed focal staining. We also noted several other tumors to stain occasionally, including adrenal cortical carcinoma (3/13), yolk sac tumor (2/9), colonic adenocarcinoma (8/106), lung carcinoma (3/52), ovarian carcinoma (5/48), and endocervical adenocarcinoma (1/5). We did not observe staining in pancreatic carcinoma (11), renal cell carcinoma (36), breast carcinoma (85), melanoma (25), or mesothelioma (5). This study supports Hep Par 1 as a useful marker in the differential diagnosis of HCC, but with significant limitations. Cautious use of this antibody in a panel with other positive (alpha fetoprotein, CD10, polyclonal carcinoembryonic antigen) and negative (epithelial membrane antigen, monoclonal carcinoembryonic antigen, CD15) markers of hepatocellular differentiation may aid in the accurate diagnosis of HCC.

    View details for PubMedID 12591966

  • Expression of FKBP12 in benign and malignant vascular endothelium - An immunohistochemical study on conventional sections and tissue microarrays AMERICAN JOURNAL OF SURGICAL PATHOLOGY Higgins, J. P., Montgomery, K., Wang, L. L., Domanay, E., Warnke, R. A., Brooks, J. D., van de Rijn, M. 2003; 27 (1): 58-64


    FKBP12 is a cytosolic FK506 binding protein that interacts with calcineurin and thereby mediates the immunosuppressive effects of FK506. Because initial immunohistochemical staining showed abundant expression of FKBP12 in vascular endothelial cells, we evaluated whether it could serve as a marker for vascular neoplasms. We performed immunohistochemical staining of conventional sections from formalin-fixed, paraffin-embedded tissue from 59 benign and malignant vascular neoplasms using a polyclonal rabbit antiserum against FKBP12. Western blot analysis of tissue from 6 angiosarcomas showed a single band at 12 kD, consistent with the published molecular weight for the FKBP12 protein. Together, CD31, CD34, and FKBP12 identified all 59 vascular neoplasms in this study. Specificity of immunohistochemical staining was assessed on 1,321 tissues represented on 7 tissue microarrays. All proteins were occasionally expressed in non-vascular tissue. Six of 8 vascular neoplasms represented on the arrays stained for FKBP12, as did normal vessels in numerous cores. The polyclonal antiserum shows comparable sensitivity (94.9%) and specificity (96.5%) to CD34 and CD31 and may be a useful additional marker for vascular differentiation. Because we have evaluated a large number of tissues by tissue microarray, we anticipate that our estimate of the specificity of immunostaining for FKBP12 as a marker for vascular endothelium will be accurate. In addition, our findings may explain the toxic effects of FK506 on vascular endothelium of the kidney.

    View details for Web of Science ID 000180144000007

    View details for PubMedID 12502928

  • Gene expression in the normal adult human kidney assessed by complementary DNA microarray 92nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Higgins, J. P., Wang, L., Kambham, N., Montgomery, K., Vogelmann, S., Lemley, K., Pollack, J. R., van de Rijn, M., Brooks, J. D. NATURE PUBLISHING GROUP. 2003: 266A–266A
  • Novel gene FLJ10261 in gastrointestinal stromal tumors 92nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology West, R. B., Linn, S. C., Nielsen, T. O., Montgomery, K., Goldblum, J. R., Patel, R., Rubin, B. P., BROWN, P., Botstein, D., van de Rijn, M. NATURE PUBLISHING GROUP. 2003: 20A–20A
  • Array-based comparative genomic hybridization (ACGH) of dermatofibrosarcoma protuberans (DFSP) on cDNA micorarrays using DNA isolated from fresh frozen and paraffin embedded tissue 92nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Jensen, K., West, R. B., Zhu, S. X., Linn, S. C., Nielsen, T. O., Goldblum, J. R., Patel, R., Rubin, B. P., Botstein, D., BROWN, P., Pollack, J., Gilks, B., van de Rijn, M. NATURE PUBLISHING GROUP. 2003: 15A–15A
  • Expression profiling of fibromatosis by cDNA gene array analysis 92nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Cheng, L., West, R. B., Zhu, S., Linn, S. C., Nielsen, T. O., Goldblum, J. R., Patel, R., Rubin, B. P., BROWN, P., Botstein, D., van de Rijn, M. NATURE PUBLISHING GROUP. 2003: 10A–10A
  • Array-based comparative genomic hybridization (ACGH) of dermatofibrosarconta protuberans (DFSP) on cDNA micorarrays using DNA isolated from fresh frozen and paraffin embedded tissue 92nd Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Jensen, K., West, R. B., Zhu, S. X., Linn, S. C., Nielsen, T. O., Goldblum, J. R., Patel, R., Rubin, B. P., Botstein, D., BROWN, P., Pollack, J., Gilks, B., van de Rijn, M. NATURE PUBLISHING GROUP. 2003: 15A–15A
  • Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome AMERICAN JOURNAL OF PATHOLOGY van de Rijn, M., Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, C., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Kochli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., BROWN, P. 2002; 161 (6): 1991-1996


    While several prognostic factors have been identified in breast carcinoma, the clinical outcome remains hard to predict for individual patients. Better predictive markers are needed to help guide difficult treatment decisions. In a previous study of 78 breast carcinoma specimens, we noted an association between poor clinical outcome and the expression of cytokeratin 17 and/or cytokeratin 5 mRNAs. Here we describe the results of immunohistochemistry studies using monoclonal antibodies against these markers to analyze more than 600 paraffin-embedded breast tumors in tissue microarrays. We found that expression of cytokeratin 17 and/or cytokeratin 5/6 in tumor cells was associated with a poor clinical outcome. Moreover, multivariate analysis showed that in node-negative breast carcinoma, expression of these cytokeratins was a prognostic factor independent of tumor size and tumor grade.

    View details for Web of Science ID 000179663400005

    View details for PubMedID 12466114

  • Tissue microarrays are an effective quality assurance tool for diagnostic immunohistochemistry MODERN PATHOLOGY Hsu, F. D., Nielsen, T. O., Alkushi, A., Dupuis, B., Huntsman, D., Liu, C. L., van de Rijn, M., Gilks, C. B. 2002; 15 (12): 1374-1380


    There has been considerable variability in the reported results of immunohistochemical staining for some diagnostically relevant antigens. Our objectives in this study were to (1) use a multitumor tissue microarray with tissue from 351 cases received in our department, representing 16 normal tissues and 47 different tumor types, to compare immunohistochemical staining results in our laboratory with published data, using a panel of 22 antibodies; (2) assess interlaboratory variability of immunohistochemical staining for S-100 using this microarray; and (3) test the ability of hierarchical clustering analysis to group tumors by primary site, based on their immunostaining profile. Tissue microarrays consisting of duplicate 0.6-mm cores from blocks identified in the hospital archives were constructed and stained according to our usual protocols. Antibodies directed against the following antigens were used: B72.3, bcl-2, carcinoembryonic antigen, c-kit, pankeratin, CD 68, CD 99, CK 5/6, CK 7, CK 8/18, CK19, CK 20, CK 22, epithelial membrane antigen, estrogen receptor, melan-A, p53, placental alkaline phosphatase, S-100, synaptophysin, thyroid transcription factor-1, and vimentin. Staining results on the array cases were compared with published results, and hierarchical clustering analysis was performed based on the immunohistochemical staining results. Unstained slides of the multitumor tissue microarray were sent to five other diagnostic immunohistochemistry laboratories and stained for S-100 protein. The staining results from the different laboratories were compared. Staining results using our current methods and samples from our laboratory were compatible with those described in the literature for most antigens. Placental alkaline phosphatase staining was not specific with our protocol, showing staining of a broad spectrum of different tumors; this finding initiated a review of our recent requests for placental alkaline phosphatase immunostaining and revealed two instances in which placental alkaline phosphatase positivity was incorrectly interpreted as evidence of a germ cell tumor. S-100 staining was less sensitive but more specific for the diagnosis of melanoma or neural tumor in our laboratory, compared to some published reports. Assessment of interlaboratory variability of S-100 immunostaining showed that there was more frequent staining of carcinomas in some laboratories, resulting in decreased specificity of S-100 staining in distinguishing melanoma from carcinoma. Hierarchical clustering analysis showed a strong trend for tumors to cluster by tissue of origin, but there were significant exceptions. We conclude that multiple-tumor microarrays are an efficient method for assessing the sensitivity and specificity of staining with any antibody used diagnostically. As a tool for quality assurance, they offer the advantage of taking into account local differences in tissue fixation, processing, and staining. They also allow cost-effective assessment of interlaboratory variability in immunohistochemical staining. Results of hierarchical clustering analysis show the potential for panels of immunohistochemical stains to identify the primary site of metastatic carcinomas but also confirm the limitations of currently available antibodies in giving unequivocal tissue-specific staining patterns.

    View details for DOI 10.1097/01.MP.0000039571.02827.CE

    View details for Web of Science ID 000180034300018

    View details for PubMedID 12481020

  • Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays AMERICAN JOURNAL OF PATHOLOGY Liu, C. L., Prapong, W., Natkunam, Y., Alizadeh, A., Montgomery, K., Gilks, C. B., van de Rijn, M. 2002; 161 (5): 1557-1565


    The creation of tissue microarrays (TMAs) allows for the rapid immunohistochemical analysis of thousands of tissue samples, with numerous different antibodies per sample. This technical development has created a need for tools to aid in the analysis and archival storage of the large amounts of data generated. We have developed a comprehensive system for high-throughput analysis and storage of TMA immunostaining data, using a combination of commercially available systems and novel software applications developed in our laboratory specifically for this purpose. Staining results are recorded directly into an Excel worksheet and are reformatted by a novel program (TMA-Deconvoluter) into a format suitable for hierarchical clustering analysis or other statistical analysis. Hierarchical clustering analysis is a powerful means of assessing relatedness within groups of tumors, based on their immunostaining with a panel of antibodies. Other analyses, such as generation of survival curves, construction of Cox regression models, or assessment of intra- or interobserver variation, can also be done readily on the reformatted data. Finally, the immunoprofile of a specific case can be rapidly retrieved from the archives and reviewed through the use of Stainfinder, a novel web-based program that creates a direct link between the clustered data and a digital image database. An on-line demonstration of this system is available at

    View details for Web of Science ID 000179197000006

    View details for PubMedID 12414504

    View details for PubMedCentralID PMC1850765

  • Gene expression studies on soft tissue tumors AMERICAN JOURNAL OF PATHOLOGY van de Rijn, M., Rubin, B. P. 2002; 161 (5): 1531-1534

    View details for Web of Science ID 000179197000002

    View details for PubMedID 12414500

  • Diversity, topographic differentiation, and positional memory in human fibroblasts PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Chang, H. Y., Chi, J. T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., Brown, P. O. 2002; 99 (20): 12877-12882


    A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and conduit for blood and lymphatic vessels, nerves, and leukocytes. Reciprocal interactions between mesenchymal and epithelial cells are known to play a critical role in orchestrating the development and morphogenesis of tissues and organs, but the roles played by specific stromal cells in controlling the design and function of tissues remain poorly understood. The principal cells of stromal tissue are called fibroblasts, a catch-all designation that belies their diversity. We characterized genome-wide patterns of gene expression in cultured fetal and adult human fibroblasts derived from skin at different anatomical sites. Fibroblasts from each site displayed distinct and characteristic transcriptional patterns, suggesting that fibroblasts at different locations in the body should be considered distinct differentiated cell types. Notable groups of differentially expressed genes included some implicated in extracellular matrix synthesis, lipid metabolism, and cell signaling pathways that control proliferation, cell migration, and fate determination. Several genes implicated in genetic diseases were found to be expressed in fibroblasts in an anatomic pattern that paralleled the phenotypic defects. Finally, adult fibroblasts maintained key features of HOX gene expression patterns established during embryogenesis, suggesting that HOX genes may direct topographic differentiation and underlie the detailed positional memory in fibroblasts.

    View details for DOI 10.1073/pnas.162488599

    View details for Web of Science ID 000178391700069

    View details for PubMedID 12297622

  • Gene expression patterns in human liver cancers MOLECULAR BIOLOGY OF THE CELL Chen, X., Cheung, S. T., So, S., Fan, S. T., Barry, C., Higgins, J., Lai, K. M., Ji, J. F., Dudoit, S., Ng, I. O., van de Rijn, M., Botstein, D., Brown, P. O. 2002; 13 (6): 1929-1939


    Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Using cDNA microarrays to characterize patterns of gene expression in HCC, we found consistent differences between the expression patterns in HCC compared with those seen in nontumor liver tissues. The expression patterns in HCC were also readily distinguished from those associated with tumors metastatic to liver. The global gene expression patterns intrinsic to each tumor were sufficiently distinctive that multiple tumor nodules from the same patient could usually be recognized and distinguished from all the others in the large sample set on the basis of their gene expression patterns alone. The distinctive gene expression patterns are characteristic of the tumors and not the patient; the expression programs seen in clonally independent tumor nodules in the same patient were no more similar than those in tumors from different patients. Moreover, clonally related tumor masses that showed distinct expression profiles were also distinguished by genotypic differences. Some features of the gene expression patterns were associated with specific phenotypic and genotypic characteristics of the tumors, including growth rate, vascular invasion, and p53 overexpression.

    View details for DOI 10.1091/mbc.02-02-0023

    View details for Web of Science ID 000176418800012

    View details for PubMedID 12058060

    View details for PubMedCentralID PMC117615

  • Challenges in developing a molecular characterization of cancer SEMINARS IN ONCOLOGY Pollack, J. R., van de Rijn, M., Botstein, D. 2002; 29 (3): 280-285


    DNA microarrays are widely used to measure gene expression across thousands of genes in parallel. Recently, considerable efforts have been made to utilize this technology to improve our understanding of cancer and to identify novel diagnostic markers and therapeutic targets. Here, we detail some of the challenges in developing a molecular characterization of cancer and in translating these new discoveries towards clinical utility.

    View details for DOI 10.1053/sonc.2002.32903

    View details for Web of Science ID 000176156500009

    View details for PubMedID 12063681

  • Molecular characterisation of soft tissue tumours: a gene expression study LANCET Nielsen, T. O., West, R. B., Linn, S. C., Alter, O., Knowling, M. A., O'Connell, J. X., Zhu, S., Fero, M., Sherlock, G., Pollack, J. R., Brown, P. O., Botstein, D., van de Rijn, M. 2002; 359 (9314): 1301-1307


    Soft-tissue tumours are derived from mesenchymal cells such as fibroblasts, muscle cells, or adipocytes, but for many such tumours the histogenesis is controversial. We aimed to start molecular characterisation of these rare neoplasms and to do a genome-wide search for new diagnostic markers.We analysed gene-expression patterns of 41 soft-tissue tumours with spotted cDNA microarrays. After removal of errors introduced by use of different microarray batches, the expression patterns of 5520 genes that were well defined were used to separate tumours into discrete groups by hierarchical clustering and singular value decomposition.Synovial sarcomas, gastrointestinal stromal tumours, neural tumours, and a subset of the leiomyosarcomas, showed strikingly distinct gene-expression patterns. Other tumour categories--malignant fibrous histiocytoma, liposarcoma, and the remaining leiomyosarcomas--shared molecular profiles that were not predicted by histological features or immunohistochemistry. Strong expression of known genes, such as KIT in gastrointestinal stromal tumours, was noted within gene sets that distinguished the different sarcomas. However, many uncharacterised genes also contributed to the distinction between tumour types.These results suggest a new method for classification of soft-tissue tumours, which could improve on the method based on histological findings. Large numbers of uncharacterised genes contributed to distinctions between the tumours, and some of these could be useful markers for diagnosis, have prognostic significance, or prove possible targets for treatment.

    View details for Web of Science ID 000174989700013

    View details for PubMedID 11965276

  • Software tools for high-throughput analysis and image retrieval of immunohistochemistry stains obtained on tissue microarrays Lui, C. L., Natkunam, Y., Prapong, W., Montgomery, K., Botstein, D., Brown, P. O., van de Rijn, M. NATURE PUBLISHING GROUP. 2002: 341A–341A
  • Tissue microarray analysis of CD44, p53, Ki-67 and bcl-2 as prognostic markers in rhabdomyosarcoma Linn, S. C., West, R. B., Wijnaendts, L. C., Montgomery, K., Mitchell, J., van de Rijn, M. NATURE PUBLISHING GROUP. 2002: 312A–313A
  • The mRNA expression signature of solitary fibrous tumors West, R. B., Linn, S. C., Foxman, E., Neilson, T., Zhu, S., Alter, O., Goldblum, J. R., Patel, R., Rubin, B. P., Brown, P. O., Botstein, D., van de Rijn, M. NATURE PUBLISHING GROUP. 2002: 24A–24A
  • Expression of FKBP12 in benign and malignant vascular endothelium: An immunohistochemical study using conventional sections and tissue microarrays Higgins, J. P., Montgomery, K., Wang, L., Brooks, J. D., van de Rijn, M. NATURE PUBLISHING GROUP. 2002: 16A–16A
  • Distinction between low grade endometrial stromal sarcoma and smooth muscle tumors by cDNA gene array analysis West, R. B., Linn, S. C., Nielsen, T., Zhu, S., Longacre, T., Husain, A., Alter, O., Patel, R., Brown, P. O., Botstein, D., Rubin, B. P., Goldblum, J. R., van de Rijn, M. NATURE PUBLISHING GROUP. 2002: 213A–214A
  • Genome-wide mRNA expression profiling of dermatofibrosarcoma protuberans using cDNA microarrays Linn, S. C., West, R. B., Zhu, S., Nielsen, T., Goldblum, J. R., Patel, R., Rubin, B. P., Alter, O., Brown, P. O., Botstein, D., van de Rijn, M. NATURE PUBLISHING GROUP. 2002: 18A–18A
  • Tissue Microarray analysis of known and novel synovial sarcoma markers Nielsen, T. O., O'Connell, J. X., Hsu, F. D., West, R. B., Linn, S. C., van de Rijn, M. NATURE PUBLISHING GROUP. 2002: 20A–20A
  • Diversity of gene expression in adenocarcinoma of the lung PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Garber, M. E., Troyanskaya, O. G., Schluens, K., Petersen, S., Thaesler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen, G. D., Perou, C. M., Whyte, R. I., Altman, R. B., Brown, P. O., Botstein, D., Petersen, I. 2001; 98 (24): 13784-13789


    The global gene expression profiles for 67 human lung tumors representing 56 patients were examined by using 24,000-element cDNA microarrays. Subdivision of the tumors based on gene expression patterns faithfully recapitulated morphological classification of the tumors into squamous, large cell, small cell, and adenocarcinoma. The gene expression patterns made possible the subclassification of adenocarcinoma into subgroups that correlated with the degree of tumor differentiation as well as patient survival. Gene expression analysis thus promises to extend and refine standard pathologic analysis.

    View details for Web of Science ID 000172328100058

    View details for PubMedID 11707590

    View details for PubMedCentralID PMC61119

  • Orbital hemangiopericytoma and solitary fibrous tumor: A morphologic continuum 88th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Goldsmith, J. D., van de Rijn, M., Syed, N. SAGE PUBLICATIONS INC. 2001: 295–302


    Solitary fibrous tumors (SFT) and hemangiopericytomas (HPC) are soft tissue tumors with known histologic and immunohistochemical overlap. A series of these tumors located in the orbit were analyzed in order to determine whether they could be re-classified based on currently recognized histologic criteria. Ten orbital spindle cell lesions, all of which were positive for CD34 antigen, were examined. Diagnostic criteria for SFT included a cytologically bland spindle cell lesion with variable cellularity and focal dense collagenization with diffuse, strong CD34 reactivity, while the criteria for HPC required a more monotonous cellular proliferation without significant variability in cellularity, a "staghorn" vascular pattern, minimal collagenization, and focal or absent CD34 staining. Tumors with typical histologic and immunohistochemical features of HPC or SFT were diagnosed as HPC and SFT, respectively. Those tumors with histologic or antigenic profiles not classic for HPC or SFT were defined as 'indeterminate.' Three lesions were classified as SFT and 1 tumor was diagnosed as HPC through use of the above-cited histologic criteria. All lesions showed positive staining of tumor cells with CD34 antigen in varying amounts and were negative for cytokeratin AE1-3, epithelial membrane antigen, CD68, and Factor XIIIa. One solitary fibrous tumor focally stained for S-100 protein and 1 hemangiopericytoma was focally positive for HHF-35. Of the 10 analyzed tumors, 6 were classified as 'indeterminate.' Furthermore, 1 lesion whose primary histology was that of an SFT recurred 9 years later with an appearance consistent with an 'indeterminate' lesion. Our results call into question the present histologic separation of HPC and SFT in the orbit. As in other sites, including deep soft tissue, these data suggest that SFT and HPC are 2 lesions whose morphologic features are best interpreted to exist along a continuum, rather than 2 lesions with distinctly defined histopathology.

    View details for Web of Science ID 000173413500006

    View details for PubMedID 12574845

  • Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Sorlie, T., Perou, C. M., Tibshirani, R., Aas, T., Geisler, S., Johnsen, H., Hastie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., Thorsen, T., Quist, H., Matese, J. C., Brown, P. O., Botstein, D., Lonning, P. E., Borresen-Dale, A. L. 2001; 98 (19): 10869-10874


    The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A total of 85 cDNA microarray experiments representing 78 cancers, three fibroadenomas, and four normal breast tissues were analyzed by hierarchical clustering. As reported previously, the cancers could be classified into a basal epithelial-like group, an ERBB2-overexpressing group and a normal breast-like group based on variations in gene expression. A novel finding was that the previously characterized luminal epithelial/estrogen receptor-positive group could be divided into at least two subgroups, each with a distinctive expression profile. These subtypes proved to be reasonably robust by clustering using two different gene sets: first, a set of 456 cDNA clones previously selected to reflect intrinsic properties of the tumors and, second, a gene set that highly correlated with patient outcome. Survival analyses on a subcohort of patients with locally advanced breast cancer uniformly treated in a prospective study showed significantly different outcomes for the patients belonging to the various groups, including a poor prognosis for the basal-like subtype and a significant difference in outcome for the two estrogen receptor-positive groups.

    View details for Web of Science ID 000170966800067

    View details for PubMedID 11553815

    View details for PubMedCentralID PMC58566

  • Towards a novel classification of human malignancies based on gene expression patterns JOURNAL OF PATHOLOGY Alizadeh, A. A., Ross, D. T., Perou, C. M., van de Rijn, M. 2001; 195 (1): 41-52


    As a result of progress on the human genome project, approximately 19 000 genes have been identified and tens of thousands more tentatively identified as partial fragments of genes termed expressed sequence tags (ESTs). Most of these genes are only partially characterized and the functions of the vast majority are as yet unknown. It is likely that many genes that might be useful for diagnosis and/or prognostication of human malignancies have yet to be recognized. The advent of cDNA microarray technology now allows the efficient measurement of expression for almost every gene in the human genome in a single overnight hybridization experiment. This genomic scale approach has begun to reveal novel molecular-based sub-classes of tumours in breast carcinoma, colon carcinoma, lymphoma, leukaemia, and melanoma. In several instances, gene microarray analysis has already identified genes that appear to be useful for predicting clinical behaviour. This review discusses some recent findings using gene microarray technology and describes how this and related technologies are likely to contribute to the emergence of novel molecular classifications of human malignancies.

    View details for Web of Science ID 000171160100006

    View details for PubMedID 11568890

  • Analysis of MUM1/IRF4 protein expression using tissue microarrays and immunohistochemistry MODERN PATHOLOGY Natkunam, Y., Warnke, R. A., Montgomery, K., Falini, B., van de Rijn, M. 2001; 14 (7): 686-694


    The gene encoding MUM1 was characterized as a possible translocation partner in chromosomal abnormalities involving a significant number of multiple myelomas. The overexpression of the MUM1 protein as a result of translocation t(6;14) (p25;q32) identified MUM1 as a putative regulatory molecule involved in B-cell differentiation and tumorigenesis. The expression of MUM1 protein in multiple myelomas supports this hypothesis. In the current study, using tissue microarray technology, we have tested the expression of the MUM1 protein in 1335 human malignancies and normal tissues. Our data show that the MUM1 protein is expressed in a wide spectrum of hematolymphoid neoplasms and in malignant melanomas but is absent in other human tumors. In addition, in tissue microarrays as well as in conventional paraffin sections, MUM1 staining was found to lack specificity in detecting plasmacytic differentiation as compared with two markers, CD138/Syndecan and VS38, commonly used in paraffin immunohistochemistry for detection of plasma cells.

    View details for Web of Science ID 000169927200008

    View details for PubMedID 11455001

  • Tissue microarray analysis of normal human CNS/PNS structures and tumors. Harris, B. T., Montgomery, K., van de Rijn, M. LIPPINCOTT WILLIAMS & WILKINS. 2001: 531–31
  • CD40L, but not CD40, is required for allergen-induced bronchial hyperresponsiveness in mice AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY Mehlhop, P. D., van de Rijn, M., Brewer, J. P., Kisselgof, A. B., Geha, R. S., Oettgen, H. C., Martin, T. R. 2000; 23 (5): 646-651


    Asthma is characterized by immunoglobulin (Ig) E production, infiltration of the respiratory mucosa by eosinophils (EOSs) and mononuclear cells, and bronchial hyperresponsiveness (BHR). Interaction of CD40 on B cells and antigen presenting cells, with its ligand (CD40L) expressed transiently on activated T cells, is known to augment both T cell-driven inflammation and humoral immune responses, especially IgE production. Considering both the prominent role of inflammation in asthma and the association of the disease with IgE, we hypothesized that CD40-CD40L interactions would be important in pathogenesis. To test this hypothesis, we subjected wild-type (WT) mice and animals lacking either CD40 or CD40L to repeated inhalation of Aspergillus fumigatus (Af ) antigen. Af-treated WT mice displayed elevated IgE levels, bronchoalveolar lavage and pulmonary tissue eosinophilic inflammation, and BHR. IgE production was markedly suppressed in both the CD40 -/- and CD40L -/- strains. However, pulmonary inflammation did not appear to be inhibited by either of these mutations. Paradoxically, development of BHR was prevented by the lack of CD40L but not by the absence of CD40. We conclude that CD40/CD40L interactions, although critical in the induction of IgE responses to inhaled allergen, are not required for the induction of EOS-predominant inflammation. CD40L, but not CD40, is necessary for the development of allergen-induced BHR.

    View details for Web of Science ID 000165276700009

    View details for PubMedID 11062143

  • Molecular portraits of human breast tumours NATURE Perou, C. M., Sorlie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., Rees, C. A., Pollack, J. R., Ross, D. T., Johnsen, H., Akslen, L. A., Fluge, O., Pergamenschikov, A., Williams, C., Zhu, S. X., Lonning, P. E., Borresen-Dale, A. L., Brown, P. O., Botstein, D. 2000; 406 (6797): 747-752


    Human breast tumours are diverse in their natural history and in their responsiveness to treatments. Variation in transcriptional programs accounts for much of the biological diversity of human cells and tumours. In each cell, signal transduction and regulatory systems transduce information from the cell's identity to its environmental status, thereby controlling the level of expression of every gene in the genome. Here we have characterized variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. These patterns provided a distinctive molecular portrait of each tumour. Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample. Sets of co-expressed genes were identified for which variation in messenger RNA levels could be related to specific features of physiological variation. The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns.

    View details for Web of Science ID 000088767700049

    View details for PubMedID 10963602

  • Peripheral T-cell lymphoma complicated by a proliferation of large B cells 88th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Higgins, J. P., van de Rijn, M., Jones, C. D., Zehnder, J. L., Warnke, R. A. AMER SOC CLINICAL PATHOLOGY. 2000: 236–47


    We studied 14 cases that showed a morphologic appearance of peripheral T-cell lymphoma and contained substantial numbers of CD20+ large B cells. In all but 2 cases, the CD20+ large cells showed a mix of kappa and lambda light chain expression. Two cases showed a focal predominance of kappa expression. In situ hybridization using the EBER1 probe for detection of Epstein-Barr virus (EBV) RNA was performed on every case. EBV RNA was present in 10 cases. Of 8 cases with EBV RNA stained by immunohistochemistry for the latent membrane protein of EBV, 6 were positive. Double-labeling immunohistochemistry and in situ hybridization confirmed that EBV was present in the large B cells. Polymerase chain reaction (PCR) analysis showed a clonal rearrangement of the T-cell receptor (TCR)-gamma chain gene in 12 of 13 cases tested. One additional case showed a clonal rearrangement of the TCR-beta chain gene by Southern blot hybridization. PCR analysis showed a clonal immunoglobulin gene rearrangement in 5 cases, a suggestion of a clonal rearrangement in 1, an oligoclonal pattern in 4, and a polyclonal pattern in 4. The finding of large B and T cells may result in a misdiagnosis of a reactive process or of T-cell-rich B-cell lymphoma. The presence of EBV in some cases could cause further confusion with the reactive T- and B-immunoblastic proliferation of infectious mononucleosis.

    View details for Web of Science ID 000088460700010

    View details for PubMedID 10941339

  • Systematic variation in gene expression patterns in human cancer cell lines NATURE GENETICS Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D., Brown, P. O. 2000; 24 (3): 227-235


    We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumours from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumour specimens revealed features of the expression patterns in the tumours that had recognizable counterparts in specific cell lines, reflecting the tumour, stromal and inflammatory components of the tumour tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumours in vivo.

    View details for Web of Science ID 000085590600011

    View details for PubMedID 10700174

  • Immunoblot analysis of CD34 expression in histologically diverse neoplasms AMERICAN JOURNAL OF PATHOLOGY Natkunam, Y., Rouse, R. V., Zhu, S., Fisher, C., van de Rijn, M. 2000; 156 (1): 21-27


    CD34 is a heavily glycosylated transmembrane protein of approximately 110 kd whose function is essentially uncharacterized. First identified in a myeloid leukemia cell line, immunohistological reactivity with anti-CD34 antibodies is also encountered in a histologically diverse subset of nonhematolymphoid neoplasms including angiosarcoma, solitary fibrous tumors, epithelioid sarcomas, spindle cell lipomas, dermatofibrosarcoma protuberans, and myofibroblastomas. Immunohistological reactivity for CD34 in hematopoietic stem cells and endothelial cells has been shown to correspond to the expression of the CD34 protein. With the exception of gastrointestinal stromal tumors, CD34 protein expression has not been investigated in other CD34 immunohistologically reactive nonhematolymphoid neoplasms. We undertook this study to examine whether the observed reactivity for anti-CD34 antibodies in apparently unrelated tumors is due to the expression of the same protein or whether shared epitopes elaborated by other proteins could account for this reactivity. Immunoblot analyses with anti-CD34 antibodies of six different CD34 immunohistologically reactive lesions show the same approximately 110-kd molecular weight protein. In addition, two cases of dermatofibrosarcoma protuberans show double bands at approximately 110 kd. Laser-capture microdissection of CD34 immunohistologically reactive epithelioid sarcoma and nonreactive epidermal cells illustrates that this reactivity is specific to tumor cells. These results show that the observed immunohistological reactivity with anti-CD34 antibodies is due to the expression of the CD34 protein and not to shared epitopes on unrelated proteins.

    View details for Web of Science ID 000084773300005

    View details for PubMedID 10623649

    View details for PubMedCentralID PMC1868614

  • Distinctive gene expression patterns in human mammary epithelial cells and breast cancers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Perou, C. M., Jeffrey, S. S., van de Rijn, M., Rees, C. A., Eisen, M. B., Ross, D. T., Pergamenschikov, A., Williams, C. F., Zhu, S. X., Lee, J. C., Lashkari, D., Shalon, D., Brown, P. O., Botstein, D. 1999; 96 (16): 9212-9217


    cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of coexpressed genes identified through manipulations of mammary epithelial cells in vitro also showed consistent patterns of variation in expression among breast tumor samples. By using immunohistochemistry with antibodies against proteins encoded by a particular gene in a cluster, the identity of the cell type within the tumor specimen that contributed the observed gene expression pattern could be determined. Clusters of genes with coherent expression patterns in cultured cells and in the breast tumors samples could be related to specific features of biological variation among the samples. Two such clusters were found to have patterns that correlated with variation in cell proliferation rates and with activation of the IFN-regulated signal transduction pathway, respectively. Clusters of genes expressed by stromal cells and lymphocytes in the breast tumors also were identified in this analysis. These results support the feasibility and usefulness of this systematic approach to studying variation in gene expression patterns in human cancers as a means to dissect and classify solid tumors.

    View details for Web of Science ID 000081835500080

    View details for PubMedID 10430922

    View details for PubMedCentralID PMC17759

  • A population based, case control study of non-Hodgkin's lymphoma in patients with rheumatoid arthritis JOURNAL OF RHEUMATOLOGY Kamel, O. W., Holly, E. A., van de Rijn, M., Lele, C., Sah, A. 1999; 26 (8): 1676-1680


    Epstein-Barr virus (EBV) associated lymphoproliferative disorders (LPD) similar to those that occur in immunosuppressed solid organ recipients have been reported in patients with rheumatoid arthritis (RA). These LPD cause significant morbidity and/or mortality in a state of sustained immunosuppression, but may spontaneously regress if immunocompetence is restored. We determined the population based frequency of EBV associated LPD relative to all non-Hodgkin's lymphomas (NHL) that occur in the general population of patients with RA.Forty-two case patients with NHL and RA and 49 control patients with NHL and no RA were identified in a population based, case control study of NHL that occurred in a 6 county Northern California area during the years 1988-94. The lymphoma tissue specimens were reviewed and the diagnosis of NHL was confirmed. In addition, the specimens were analyzed for NHL grade, histologic subtype, histopathologic features associated with immunosuppression, immunophenotype, and the presence of EBV genome in the tumor cells.No significant differences were identified between NHL in the RA case group and the control group (no RA) with respect to any variables investigated. One patient (2%) in the case group and one (2%) in the control group developed LPD containing EBV.Our findings reveal that EBV associated lymphomas represent only a small fraction of all NHL in the general RA patient population. EBV associated LPD should be recognized when they occur because they require a special approach to patient management. However, these data indicate that the majority of NHL that occurs in patients with RA is probably coincidental with RA and not the result of significant immunosuppression.

    View details for Web of Science ID 000081725000007

    View details for PubMedID 10451061

  • Absence of SYT-SSX fusion products in soft tissue tumors other than synovial sarcoma AMERICAN JOURNAL OF CLINICAL PATHOLOGY van de Rijn, M., Barr, F. G., Collins, M. H., Xiong, Q. B., Fisher, C. 1999; 112 (1): 43-49


    The chromosomal translocation t(X;18), which generates SYT-SSX1 and SYT-SSX2 fusion products, is a sensitive marker for synovial sarcoma; most synovial sarcomas test positive for this marker. However, few studies have addressed the presence of t(X;18) or its fusion products in spindle cell sarcomas in the differential diagnosis of synovial sarcoma. We studied the presence of the SYT-SSX fusion products with reverse transcriptase polymerase chain reaction on frozen tissue samples of 24 synovial sarcomas and 24 other spindle cell sarcomas, including 12 malignant peripheral nerve sheath tumors. In cases histopathologically diagnosed as synovial sarcoma, SYT-SSX fusion products were detected in 21 of 24 (87%) lesions. No evidence of these fusions was found in 12 malignant peripheral nerve sheath tumors, 2 hemangiopericytomas, 3 leiomyosarcomas, 2 fibrosarcomas, 1 poorly differentiated sarcoma (malignant fibrous histiocytoma), 1 sarcoma with rhabdoid features, and 2 sarcomas not otherwise specified. One lesion with histologic, immunohistologic, and ultrastructural features indeterminate for a diagnosis of synovial sarcoma or malignant peripheral nerve sheath tumor was studied and was positive for SYT-SSX1. The SYT-SSX fusion products appear specific for synovial sarcoma and are not seen in other spindle cell lesions in its differential diagnosis.

    View details for Web of Science ID 000081088000005

    View details for PubMedID 10396284

  • Detection of a variant SYT-SSX1 fusion in a case of predominantly epithelioid synovial sarcoma MOLECULAR DIAGNOSIS Sanders, M. E., van de Rijn, M., Barr, F. G. 1999; 4 (1): 65-70


    The translocation t(X;18)(p11.2;q11.2) characterizes synovial sarcoma, fusing the SYT gene at 18q11.2 to either SSX1 or SSX2 at Xp11.2. The usual chimeric product fuses SYT codon 379 to SSX1 or SSX2 codon 111. To date only three variant fusions have been identified. A predominantly epithelioid synovial sarcoma that expressed a novel variant of the SYT-SSX1 fusion is described.The current case was tested for the SYT-SSX fusion by reverse transcriptase polymerase chain reaction (PCR) followed by sequencing of the PCR product. Analysis revealed a 673 bp SYT-SSX1 chimeric product characterized by a novel junction of SYT codon 379 to SSX1 codon 83 with a 6 bp insertion at the fusion junction.As the number of reported variations of the SYT-SSX chimeric fusion increases in synovial sarcoma, the mechanics of the translocation machinery and the functional significance of these chimeric fusions will be better understood.

    View details for Web of Science ID 000080348100009

    View details for PubMedID 10229776

  • Colonic adenocarcinoma presenting as supraclavicular lymphadenopathy in a 26-yr-old man: A case report AMERICAN JOURNAL OF GASTROENTEROLOGY Krasinskas, A. M., Rosato, E. F., Partington, M. T., Whalen, C. J., Reynolds, C., van de Rijn, M., Montone, K. T. 1999; 94 (1): 282-283

    View details for Web of Science ID 000082426600062

    View details for PubMedID 9934779

  • Desmoplastic fibroblastoma (collagenous fibroma) - Case report and review of the literature INTERNATIONAL JOURNAL OF SURGICAL PATHOLOGY Li, S. Y., Junkins-Hopkins, J. M., FRAKER, D. L., van de Rijn, M. 1999; 7 (1): 33-38
  • Poorly differentiated synovial sarcoma - An analysis of clinical, pathologic, and molecular genetic features AMERICAN JOURNAL OF SURGICAL PATHOLOGY van de Rijn, M., Barr, F. G., Xiong, Q. B., Hedges, M., Shipley, J., Fisher, C. 1999; 23 (1): 106-112


    Poorly differentiated synovial sarcoma is a variant of synovial sarcoma in which the tumor cells lack the bland spindle cell appearance of the usual type monophasic synovial sarcoma. Although poorly differentiated synovial sarcoma has been recognized as an entity for many years, no series addressing the clinicopathologic features of this variant have appeared. We describe the histologic, immunohistologic, and molecular findings of a series of 20 poorly differentiated synovial sarcomas. Three types of poorly differentiated synovial sarcoma can be recognized: a large cell epithelioid variant, a small cell variant, and a high-grade spindle cell variant. Epithelial membrane antigen reactivity was seen in 95% of cases, and reactivity for cytokeratin was seen in 42%. The S100 antigen was expressed in 63% of cases. Electron microscopic findings in poorly differentiated synovial sarcoma parallel those found in usual type synovial sarcoma. In 10 cases, material was available for molecular studies; 9 of 10 cases showed the presence of t(X;18) or the associated fusion gene product. These data indicate that poorly differentiated synovial sarcoma is a lesion that shares immunologic, ultrastructural, and molecular characteristics with the usual synovial sarcoma. Follow-up data were available in 16 patients with a mean follow-up of 39 months. Eight patients died with a mean survival time of 33 months. Poorly differentiated synovial sarcoma is a variant of synovial sarcoma that may be associated with a poor prognosis.

    View details for Web of Science ID 000077886000012

    View details for PubMedID 9888710

  • Sensitivity and specificity of antibodies on necrotic tumor tissue USCAP Annual Meeting Judkins, A. R., Montone, K. T., LiVolsi, V. A., van de Rijn, M. AMER SOC CLINICAL PATHOLOGY. 1998: 641–46


    Immunohistochemistry occasionally is used to determine the lineage of entirely necrotic tumors. However, the sensitivity and specificity of antibodies on necrotic tissue are unknown. To determine the usefulness of immunohistochemistry with necrotic lesions, a series of 24 known tumors consisting of 14 carcinomas, 2 lymphomas, 2 melanomas, and 6 sarcomas (all with extensive necrosis) was examined for reactivity with 6 cytokeratin antibodies, S100, and LCA. Carcinomas stained positively with at least 1 cytokeratin antibody in 78% of the cases. The cytokeratin antibodies with the highest sensitivity were AE1, AE1/3, S903, and PANCK. These antibodies also retained specificity for epithelial differentiation; no reactivity was observed in the 10 necrotic nonepithelial tumors. LCA retained its reactivity with necrotic lymphoma, but S100 reacted with only one third of the necrotic lesions. Unexpectedly, reactivity for LCA and S100 occurred in some necrotic carcinomas. Keratin markers can be used on necrotic tissue to determine epithelial differentiation, but the results obtained with S100 and LCA on necrotic tissue should be interpreted with caution.

    View details for Web of Science ID 000076601000011

    View details for PubMedID 9802350

  • Interleukin-9 promotes allergen-induced eosinophilic inflammation and airway hyperresponsiveness in transgenic mice AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY McLane, M. P., Haczku, A., van de Rijn, M., Weiss, C., Ferrante, V., MacDonald, D., Renauld, J. C., Nicolaides, N. C., Holroyd, K. J., Levitt, R. C. 1998; 19 (5): 713-720


    Human atopic asthma is a complex heritable inflammatory disorder of the airways associated with clinical signs of allergic inflammation and airway hyperresponsiveness. Recent studies demonstrate that the degree of airway responsiveness is strongly associated with interleukin (IL)-9 expression in murine lung. To investigate the contribution of IL-9 to airway hyperresponsiveness, and to explore directly its relationship to airway inflammation, we studied transgenic mice overexpressing IL-9. In this report we show that IL-9 transgenic mice (FVB/N-TG5), in comparison with FVB/NJ mice, display significantly enhanced eosinophilic airway inflammation, elevated serum total immunoglobulin E, and airway hyperresponsiveness following lung challenge with a natural antigen (Aspergillus fumigatus). These data support a central role for IL-9 in the complex pathogenesis of allergic inflammation.

    View details for Web of Science ID 000079084500001

    View details for PubMedID 9806735

  • A murine model of allergic rhinitis: Studies on the role of IgE in pathogenesis and analysis of the eosinophil influx elicited by allergen and eotaxin JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY van de Rijn, M., Mehlhop, P. D., Judkins, A., Rothenberg, M. E., Luster, A. D., Oettgen, H. C. 1998; 102 (1): 65-74


    Allergic rhinitis is a prevalent disease with significant morbidity. Studies of its pathophysiology in human subjects have been limited. Nasal biopsy specimens are difficult to obtain, and nasal secretions incompletely reflect the cellular and molecular events in the mucosa. IgE-mediated mast cell activation and the elaboration of factors promoting eosinophil development and chemotaxis are likely to participate in pathogenesis.We sought to develop a murine model of allergic rhinitis, to use it to assess the role of IgE in pathogenesis, and to study the effects of IL-5 and eotaxin in the nasal mucosa.A protein extract of Aspergillus fumigatus (Af) was instilled intranasally in mice. Histologic changes were examined in wild-type and IgE-deficient (IgE-/-) animals. The effect of eotaxin administration was assessed in wild-type and IL-5 transgenic mice.Af-treated mice developed a nasal mucosal eosinophil influx comparable to that described for humans. This histology was distinct from that observed in a murine model of Af-induced asthma. The pathology appeared over a time course similar to that reported for human subjects. There was no difference in the intensity of the mucosal inflammatory infiltrate of Af-treated IgE-/- mice compared with wild-type mice. Eotaxin was able to recruit eosinophils to the mucosa but only in IL-5 transgenic animals.We describe a murine model for allergic rhinitis with an eosinophilic infiltrate comparable to that found in human disease and have demonstrated that rhinitis can arise in the absence of IgE. We have shown that the eosinophil influx can be induced by eotaxin in the presence of IL-5.

    View details for Web of Science ID 000074909500011

    View details for PubMedID 9679849

  • Immunohistochemical analysis of gel-transferred cells in cytologic preparations following smear division DIAGNOSTIC CYTOPATHOLOGY Hunt, J. L., van de Rijn, M., Gupta, P. K. 1998; 18 (5): 377-380


    Fine-needle aspirations on solid tumors are used increasingly as a means of obtaining a primary diagnosis. In many cases, a panel of immunostains performed on these aspirates is necessary to further characterize the cytologic interpretation. The amount of material obtained through aspiration, however, is often quite limited and is present on few glass slides. Previous studies have demonstrated the success of dividing cytologic smear preparations into smaller parts that could then be used for a panel of immunohistochemical stains. These results, however, did not compare the immunoreactivities of various antibodies before and after tissue transfer on cytologic preparations. In the present study, 41 immunohistochemical stains that employed 16 antibodies on 15 tumor preparations were performed following smear partition using the tissue-transfer technique. The percentage of cells that stained positive after transfer was determined and was correlated quantitatively to the untransferred controls. Specific immunoreactivity was demonstrated in 30 of 38 cases (79%) but was significantly decreased or lost in 8 of 38 cases (21%), which included antibodies for S-100, estrogen and progesterone receptors, chromogranin, neuron-specific enolase, and cytokeratin. Morphology was well preserved following tissue transfer, although limited cytoplasmic damage was seen in up to 25% of tumor cells. Immunopositive samples were found to be easily interpretable. Because sporadic cases fail to show immunohistochemical staining reactions following cytologic smear division and transfer, negative immunohistochemical stains in such preparations should be approached with caution.

    View details for Web of Science ID 000073296400016

    View details for PubMedID 9582578

  • Radiation-associated synovial sarcoma HUMAN PATHOLOGY VANDERIJN, M., Barr, F. G., Xiong, Q. B., Salhany, K. E., FRAKER, D. L., Fisher, C. 1997; 28 (11): 1325-1328


    We describe a case of synovial sarcoma occurring in a 36 year-old woman, 8 years after radiation therapy for Hodgkin's disease. The tumor showed histological, immunohistochemical, ultrastructural, and molecular features diagnostic of synovial sarcoma. To our knowledge, this is the first report of a fully documented case of radiation associated synovial sarcoma.

    View details for Web of Science ID A1997YH03400021

    View details for PubMedID 9385945

  • Extranodal head and neck lymphomas in guatemala: High frequency of Epstein-Barr virus-associated sinonasal lymphomas Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology VANDERIJN, M., Bhargava, V., MolinaKirsch, H., CarlosBregni, R., Warnke, R. A., Cleary, M. L., Kamel, O. W. W B SAUNDERS CO-ELSEVIER INC. 1997: 834–39


    Sinonasal lymphomas of T cell or natural killer cell (T/NK cell) phenotype represent a subset of extranodal head and neck lymphomas. T/NK cell sinonasal lymphomas have been described in diverse geographic settings, including China, Japan, Peru, Northern Europe, and North America. The frequency of these lymphomas is highly dependent on the geographic location in which they occur, their incidence being low in Europe and North America and relatively high in Asian countries and in Peru. Regardless of their geographic location, they are typically associated with the Epstein-Barr virus (EBV). Few studies have addressed the relative frequency of sinonasal lymphoma within the group of extranodal head and neck lymphomas. We investigated the anatomic distribution, immunophenotypical profile, and EBV status of 33 cases of extranodal head and neck lymphoma from patients in Guatemala. The anatomic distribution of these lymphomas is similar to that seen in Asian countries: 17 (52%) in the sinonasal area, five (15%) in the palate, and 11 (33%) in other locations. Fifteen (88%) of the 17 sinonasal lymphomas showed a T or null cell phenotype with a strong association with EBV by in situ hybridization. Most Guatemalan patients with these lymphomas were of Mayan descent. In Guatemala, the relative frequency of sinonasal lymphomas within the group of head and neck lymphomas is significantly higher than that reported for Western countries. In addition, the relative frequency of T/NK versus B cell sinonasal lymphomas is higher than that described in North America and similar to that observed in Asian countries and Peru.

    View details for Web of Science ID A1997XL66100014

    View details for PubMedID 9224753

  • CD5 immunostaining of lymphoid neoplasms in paraffin sections AMERICAN JOURNAL OF CLINICAL PATHOLOGY Salhany, K. E., VANDERIJN, M., Montone, K. T., Tomaszewski, J. E. 1997; 107 (4): 496-496

    View details for Web of Science ID A1997WP86600020

    View details for PubMedID 9124220

  • Allergen-induced bronchial hyperreactivity and eosinophilic inflammation occur in the absence of IgE in a mouse model of asthma PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Mehlhop, P. D., VANDERIJN, M., Goldberg, A. B., Brewer, J. P., Kurup, V. P., Martin, T. R., Oettgen, H. C. 1997; 94 (4): 1344-1349


    In patients with asthma, elevations of IgE correlate both with allergic inflammation of the airways and with bronchial hyperreactivity (BHR). Several investigations, using mouse models of this disease, have indicated a central role for IgE in the pathogenesis of the eosinophilic inflammation as well as in the obstructive airway physiology of BHR. Some diagnostic studies and therapeutic strategies for asthma are based on the putative role of IgE in asthma pathogenesis. Here, we use mice with a null mutation of the C epsilon locus to show that bronchial inflammation and BHR in response to allergen inhalation both can occur in the absence of IgE. We demonstrate that the eosinophilic bronchial inflammation elicited in an established mouse model of hypersensitivity to Aspergillus fumigatus (Af) is accompanied by the asthmatic physiology of BHR. Wild-type and IgE-deficient mice were sensitized intranasally with Af extract. Both groups of animals developed bronchoalveolar lavage eosinophilia and pulmonary parenchymal eosinophilia. This was accompanied by increased serum levels of total and Af-specific IgE in the wild-type animals only. This Af-sensitization protocol resulted in significant BHR in both wild-type mice and IgE-deficient mice. Interestingly, unsensitized IgE-deficient mice had increased bronchial responsiveness compared with unsensitized wild-type controls. We conclude that BHR and airways inflammation can be fully expressed via IgE-independent mechanisms. These may involve the activation of mast cells by factors other than IgE as well as a mucosal lymphocyte-mediated immune response to allergen.

    View details for Web of Science ID A1997WJ62100053

    View details for PubMedID 9037055

  • Primary low-grade endometrial B-cell lymphoma 85th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology VANDERIJN, M., Kamel, O. W., Chang, P. P., Lee, A., Warnke, R. A., Salhany, K. E. LIPPINCOTT WILLIAMS & WILKINS. 1997: 187–94


    We describe three cases of primary low-grade B-cell lymphoma of the endometrium and contrast the histological, immunohistochemical, and molecular features with two examples of benign endometrial lymphoid infiltrates. The first case was an incidental finding in a curettage specimen, confirmed on a subsequent hysterectomy. The other two cases of lymphoma were incidental findings on hysterectomy procedures performed for prolapse and cervical dysplasia, respectively. All three lymphomas occurred in patients in their sixties; none formed gross tumors. Histologic examination revealed lymphoid nodules adjacent to endometrial glands. The lymphoid cells showed mild nuclear enlargement and slight irregularities of the nuclear contour. None of the three patients had evidence of disease outside the endometrium by physical examination, bone marrow biopsy, or sampling of pelvic lymph nodes. Immunohistochemistry demonstrated a B-cell phenotype of the lymphoid cells (CD20 positive, CD79a positive) with aberrant coexpression of the T-cell-associated marker CD43. Polymerase chain reaction (PCR) amplification of the VDJ region of the immunoglobulin heavy-chain was performed on DNA isolated from paraffin sections. These studies demonstrated a clonal proliferation of B-lymphocytes in two cases. In the third case, a faint band was found superimposed on a background smear, suggesting the presence of a B-cell clone. In contrast, the two examples of histologically benign lymphoid aggregates of the endometrium consisted predominantly of T cells with rare B-lymphocytes; there was no evidence of coexpression of CD43 by B-cells. The PCR amplification from the benign lymphoid aggregates did not support a clonal process. Primary lymphoid neoplasms of the endometrium are rare, and all cases described so far have been high-stage, high-grade neoplasms. To our knowledge, this is the first report of primary low-grade B-cell lymphoma of the endometrium, presumably arising from endometrial lymphoid tissue.

    View details for Web of Science ID A1997WH87300008

    View details for PubMedID 9042285

  • Clonality of Epstein-Barr virus in lymphoproliferative disorders in patients treated with immunosuppressive therapy for rheumatoid arthritis JOURNAL OF CLINICAL ONCOLOGY VANDERIJN, M., Kamel, O. W. 1996; 14 (11): 3050-3051

    View details for Web of Science ID A1996VU59100023

    View details for PubMedID 8918505

  • Hodgkin's disease and lymphoproliferations resembling Hodgkin's disease in patients receiving long-term low-dose methotrexate therapy AMERICAN JOURNAL OF SURGICAL PATHOLOGY Kamel, O. W., Weiss, L. M., VANDERIJN, M., Colby, T. V., Kingma, D. W., Jaffe, E. S. 1996; 20 (10): 1279-1287


    Recently, it has been shown that patients with rheumatologic diseases who are treated with methotrexate can develop immunosuppression-associated lymphoproliferative disorders. Although a variety of lymphoproliferations have been described in the setting of methotrexate therapy, only rare cases of Hodgkin's disease (HD) have been reported. In this study, we provide a more complete characterization of the spectrum of lymphoproliferations that resemble HD or show features diagnostic of HD that occur in patients receiving long-term low-dose methotrexate therapy. Eight patients were receiving methotrexate for various disorders. Four cases were considered to represent lymphoproliferations resembling HD; the other four cases were diagnosed as HD because they showed diagnostic morphologic and immunophenotypic features. All three patients with lymphoproliferations resembling HD on whom follow-up was available experienced tumor regression with methotrexate withdrawal or with methotrexate withdrawal and steroids; none of these three patients required further therapy. All three patients with HD on whom follow-up was available are alive and free of disease following chemotherapy or radiation therapy. In two of these patients, the tumor persisted or progressed despite discontinuation of methotrexate with observation; the third patient received chemotherapy at the same time methotrexate was stopped. Our findings indicate that a spectrum of lymphoproliferations resembling HD or diagnostic of HD can occur in patients receiving long-term low-dose methotrexate therapy. Recognition of these lymphoproliferative disorders is clinically important because a subset of these neoplasms will completely resolve with discontinuation of methotrexate, thereby obviating the need for chemotherapy or radiation therapy.

    View details for Web of Science ID A1996VJ66800015

    View details for PubMedID 8827036

  • Pregnancy-associated lymphomas - A clinicopathologic study CANCER Gelb, A. B., VANDERIJN, M., Warnke, R. A., Kamel, O. W. 1996; 78 (2): 304-310


    The natural histories of Hodgkin's disease (HD) and non-Hodgkin's lymphomas (NHL) during pregnancy are not well understood.All cases of HD and NHL diagnosed during pregnancy at Stanford University Medical Center since 1987 were reviewed and clinical follow-up was obtained. Various immunohistochemical studies and in situ hybridization for Epstein-Barr virus (EBV) encoded RNA were performed in a subset of cases.Seventeen cases of HD and 12 cases of NHL were accessioned (median age; 27 yrs). The HD cases were classified as 13 nodular sclerosis type, 3 mixed cellularity type, and 1 unclassified. Clinical follow-up revealed most of the patients had Stage II to III disease and were diagnosed on average at 22 weeks gestation. Most of the patients deferred therapy until after delivery and had no evidence of disease at the last follow-up except for one death with disease but not from it. NHL were classified according to the working formulation as high or intermediate grade lymphomas of various types, including both nodal and extranodal sites. Clinical follow-up revealed most had Stage II to IV disease and were diagnosed on average at 23 weeks gestation. Patients with HD tended to survive longer than those with NHL (raw mortality, P = 0.04). In situ hybridization failed to provide support for the presence of EBV in a subset of patients with NHL.The clinical behavior of these neoplasms during pregnancy does not appear to be significantly different from that outside of the setting of pregnancy. Treatment of selected HD patients apparently may be safely deferred until after delivery. Patients with NHL present with higher stage disease and have a poorer prognosis than those with HD.

    View details for Web of Science ID A1996UV02200018

    View details for PubMedID 8674008

  • Eotaxin triggers eosinophil-selective chemotaxis and calcium flux via a distinct receptor and induces pulmonary eosinophilia in the presence of interleukin 5 in mice MOLECULAR MEDICINE Rothenberg, M. E., Ownbey, R., Mehlhop, P. D., Loiselle, P. M., VANDERIJN, M., Bonventre, J. V., Oettgen, H. C., Leder, P., Luster, A. D. 1996; 2 (3): 334-348


    Understanding the processes that control selective eosinophilia is of fundamental importance in a variety of human diseases (e.g., allergies, parasitic infections, malignancy). Interleukin 5, an eosinophil-specific growth and activating factor, and eotaxin appear to collaborate in this process. Eotaxin is a recently described chemotactic factor that belongs to the C-C (or beta) chemokine family and has been implicated in animal and human eosinophilic inflammatory states. We have recently reported the molecular characterization of murine eotaxin and now report the biological properties of purified recombinant murine eotaxin in vitro and in vivo in the presence or absence of interleukin 5 (IL-5) in mice.Murine eotaxin was expressed in bacteria and purified by affinity chromatography and HPLC. Activity was tested in vitro by examining chemotactic and calcium flux responses of purified murine leukocytes. Additionally, desensitization of calcium flux responses to other chemokines, eosinophil survival assays, and basophil histamine release were examined. Finally, eotaxin was delivered to wild-type or IL-5 transgenic mice and the host response was examined.Eotaxin had activity only when the recombinant molecule had the native mature amino terminus and contained the first 25 amino acids of the mature protein. It was active in vitro at an effective concentration between 10 and 100 ng/ml in both chemotaxis and calcium flux assays toward eosinophils, but not macrophages or neutrophils. Furthermore, intranasal or subcutaneous application of eotaxin selectively recruited large numbers of eosinophils into the mouse lung and skin, respectively, only in the presence of interleukin 5. Macrophage inflammatory protein-1 alpha, a related C-C chemokine active on eosinophils, and eotaxin were not able to cross-desensitize. Eotaxin had no affect on the in vitro survival of eosinophils and did not induce basophil histamine release.Mouse eotaxin is an eosinophil specific chemoattractant that has a markedly enhanced effect in vivo in the presence of another eosinophil selective cytokine IL-5, and utilizes a signal transduction receptor pathway that is distinct from that utilized by macrophage inflammatory protein-1 alpha. This data suggests that the development of tissue eosinophilia in vivo involves a two-step mechanism elicited by interleukin 5 and eotaxin.

    View details for Web of Science ID A1996UQ24300009

    View details for PubMedID 8784786

  • Epstein-Barr virus clonality in lymphomas occurring in patients with rheumatoid arthritis ARTHRITIS AND RHEUMATISM VANDERIJN, M., Cleary, M. L., Variakojis, D., Warnke, R. A., Chang, P. P., Kamel, O. W. 1996; 39 (4): 638-642


    A causative role for Epstein-Barr virus (EBV) in the development of lymphoma in patients with rheumatoid arthritis (RA) has been proposed. We investigated the molecular features of EBV-positive diffuse large cell lymphomas in 2 patients with RA.Southern blot analysis for immunoglobulin gene rearrangements, terminal repeat analysis for clonality of the EBV genome, and double-labeling of the lymphoma cells by in situ hybridization and immunoperoxidase staining were performed.In both cases, double-labeling studies localized the EBV genome to the malignant B cells. Both neoplasms contained clonal immunoglobulin gene rearrangements and clonal EBV genomes.Our data indicate that EBV infection was an early step in the development of these neoplasms. The findings further extend knowledge on the similarity of this subset of lymphomas to posttransplantation lymphomas and emphasize the role of immunosuppression in their genesis.

    View details for Web of Science ID A1996UD63800014

    View details for PubMedID 8630114

  • RANTES chemokine expression in diseased and normal human tissues CYTOKINE VONLUETTICHAU, I., Nelson, P. J., Pattison, J. M., VANDERIJN, M., Huie, P., Warnke, R., Wiedermann, C. J., Stahl, R. A., Sibley, R. K., KRENSKY, A. M. 1996; 8 (1): 89-98


    RANTES is a member of a large family of cytokines, called chemokines, which are thought to play a regulatory role in inflammatory processes. We have made recombinant human RANTES protein which was used to generate a panel of anti-RANTES monoclonal antibodies. Following characterization, select anti-RANTES monoclonal antibodies were used for immunohistologic staining of a large panel of normal, diseased and fetal tissue sections. Diseased tissues included eleven lymphomas and eight renal tumors. Most tissues were also tested in parallel for RANTES mRNA by in situ hybridization using RANTES mRNA specific oligomeric probes. As expected, most normal adult tissues contain few, if any, RANTES positive cells. In contrast, RANTES expression dramatically increases in inflammatory sites. In addition, megakaryocytes, some tumours, and select fetal tissues express high levels of RANTES message and protein. These results indicate a wider expression of RANTES than previously appreciated and suggest multiple physiologic roles for this soluble factor.

    View details for Web of Science ID A1996TT98200012

    View details for PubMedID 8742071

  • Hodgkin's disease and Hodgkin's disease-like large cell lymphomas in patients receiving long-term low-dose methotrexate therapy Kamel, O. W., Weiss, L. M., VANDERIJN, M., Kingma, D. W., Jaffe, E. S. NATURE PUBLISHING GROUP. 1996: 662–62

    View details for Web of Science ID A1995TH15700017

    View details for PubMedID 7477181

  • FREQUENT PRESENCE OF THE EPSTEIN-BARR-VIRUS IN INFLAMMATORY PSEUDOTUMOR HUMAN PATHOLOGY Arber, D. A., Kamel, O. W., VANDERIJN, M., Davis, R. E., Medeiros, L. J., Jaffe, E. S., Weiss, L. M. 1995; 26 (10): 1093-1098


    Inflammatory pseudotumor is a presumably nonneoplastic, hematopoietic, and spindled fibrous proliferation that may occur at a variety of anatomic sites. The origin of these proliferations is generally unknown. To evaluate the role of the Epstein-Barr virus (EBV) in inflammatory pseudotumor, 18 specimens from 17 patients were studied by in situ hybridization for EBV ribonucleic acid (RNA), and the morphological and immunologic characteristics of the infected cells were evaluated. These specimens included 10 lymph nodes, six splenic masses, and two hepatic masses. Overall, EBV RNA was detected in 41.2% (seven of 18) of the cases. These included two of 10 (20%) lymph nodes, four of six (66.7%) splenic pseudotumors, and one of two (50%) hepatic lesions. The degree of EBV infection was significantly greater within the tumors in comparison with the surrounding, uninvolved tissue. Two morphologically different EBV-positive cell types, spindled and round cells, were evident, and the infected cell type differed significantly when the nodal and extranodal cases were compared. All of the positive extranodal cases shown, numerous EBV-positive spindled cells, whereas no positive spindle cells (only positive round cells, morphologically consistent with lymphocytes) were noted in the two EBV-positive lymph node pseudotumors. Double-labeling immunohistochemical and in situ hybridization studies in some cases identified rare EBV-positive B cells and rare EBV positive T cells in four and three cases, respectively. Most EBV-positive cells in all cases failed to immunoreact with any B- or T-cell markers. Three of five cases studied, however, did show a subpopulation of smooth muscle actin/EBV-positive spindled cells, five of seven cases showed vimentin/EBV-positive spindled cells, and one of four cases had EBV-positive spindled cells that immunoreacted as follicular dendritic cells. These results suggest that EBV plays a role in a significant number of cases of inflammatory pseudotumor with differences in the incidence of EBV infection and the cell type (spindled vs round cell) infected when extranodal and nodal cases are compared, suggesting a difference in pathogenesis. The cell type infected in extranodal cases seemed to be of mesenchymal origin but could not be clearly defined.

    View details for Web of Science ID A1995RZ22000007

    View details for PubMedID 7557942



    Although Hodgkin's disease (HD) has been a subject of much investigation, fundamental questions remain unanswered regarding its lineage and clonality. The authors used a polymerase chain reaction (PCR) technique to investigate whether clonal Variable-Diversity-Joining recombination of the immunoglobulin heavy (IgH) chain gene, a phenomenon that characterizes clonal B-cell proliferations, exists in nodular sclerosing (NSHD) and mixed cellularity (MCHD) Hodgkin's disease (so-called "classical" Hodgkin's disease). The isolation of DNA from paraffin-embedded tissue sections allowed for direct correlation of PCR results with the cell populations that were analyzed. Thirty-two cases were studied. These included 12 cases in which the Reed-Sternberg (RS) cells expressed the B-cell antigen, CD20, and 10 cases that were classified as syncytial variant of NSHD (3 CD20+, 7 B-cell antigen negative). Overall, clonal patterns of VDJ PCR products were found in 14 of 32 (44%) cases. These clonal patterns were identified in 7 of 12 (58%) cases of CD20+ classical HD and in 7 of 20 (35%) cases of B-antigen-negative classical HD. Clonal patterns were found in 3 of 10 cases of syncytial variant of NSHD, including 2 of 3 (67%) CD20+ cases and 1 of 7 (14%) B-cell antigen-negative cases. The results of this study provide support that a subset of HD represents a clonal B-cell neoplasm, and indicate that clonal IgH VDJ sequences are more frequently found in CD20+ HD.

    View details for Web of Science ID A1995RZ47500011

    View details for PubMedID 7572792



    We investigated whether in situ hybridization for EBV RNA on routine cardiac biopsies could be used as a predictive test for the development of posttransplant lymphoproliferative disorder (PTLD) in cardiac transplant recipients. We examined the sensitivity of the test by determining the frequency of EBV-positive cells in cardiac biopsy specimens from patients with a known history of PTLD. Biopsy specimens obtained during routine monitoring for rejection before or shortly after the diagnosis of PTLD from 10 pediatric heart transplant patients were examined. Four of 74 specimens (5.4%) demonstrated EBV-positive lymphocytes in the cardiac biopsy rejection infiltrates. The four positive specimens were obtained from 3 different patients, all before the diagnosis of PTLD. Given the low number of cardiac biopsy specimens with EBV-positive lymphocytes, as well as the low incidence of PTLD in cardiac transplant patients, we conclude that a routine screening of all cardiac biopsy specimens using in situ hybridization for EBV with the intention of predicting PTLD is not warranted. However, in situ hybridization for EBV might be used in selected cases, such as those in which the transplant patient does not respond to immunosuppressive therapy for rejection. In these patients, the presence of EBV-positive lymphocytes in biopsy specimens initially interpreted as showing rejection might instead raise the suspicion of incipient PTLD.

    View details for Web of Science ID A1995RV75200012

    View details for PubMedID 7676496



    Basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and malignant melanoma (MM) are the three most common malignant neoplasms that arise in the skin. Deregulation of oncogene function not infrequently leads to an increased rate of cellular proliferation. However, the expansion of malignant cells can also occur if programmed cell death is inhibited. The oncogene bcl-2 participates in the regulation of apoptosis (programmed cell death). In view of this, we determined the presence and possible role of bcl-2 in primary cutaneous malignancies. Routine paraffin sections of formalin-fixed BCCs, SCCs, MMs (primary and metastatic), actinic keratoses, and SCCs in situ were labeled with anti-bcl-2 monoclonal antibody using a biotin-avidin-immunoperoxidase procedure.Twenty-three BCCs were examined and all expressed cytoplasmic bcl-2. Two of 20 SCCs were positive. One of these had patchy, diffuse staining, and the other stained in only small foci. None of eight SCCs in situ and none of eight actinic keratoses expressed bcl-2. Sixteen of 18 MMs expressed bcl-2.The bcl-2 gene product has been found to inhibit apoptosis. Our preliminary results suggest that the expression of bcl-2 is present quite consistently in BCCs and MMs, but not in SCCs or precursor lesions. The expression (or lack thereof) of bcl-2 may reflect the difference in the regulation of cell turnover between these tumors, or histogenetic differences.

    View details for Web of Science ID A1995RN89700006

    View details for PubMedID 7632062



    Recently, a new category of oncogenes has been discovered that regulate programmed cell death. The bcl-2 oncogene has been found to inhibit cellular death without affecting cellular proliferation. In the skin, bcl-2 expression is limited to cells along the basal cell layer. However, we also noticed that resting melanocytes appeared to express bcl-2. We examined the expression of bcl-2 and its possible role in the biology of benign melanocytic proliferations. Routine paraffin sections of formalin-fixed tissue were labeled with anti-bcl-2 monoclonal antibody, and expression of bcl-2 was detected by a biotin-avidin-immunoperoxidase procedure.We examined 13 congenital, 11 acquired, and six atypical or dysplastic nevi for expression of bcl-2. Expression of bcl-2 was observed in 11 of 13 congenital nevi. All 11 acquired nevi and 6 nevi with architectural disarray and cytologic atypia expressed bcl-2. Both junctional and intradermal melanocytes expressed bcl-2 in a perinuclear and cytoplasmic pattern. Within neurotized areas, bcl-2 became significantly weaker and totally absent.In mature tissues, bcl-2 expression is quite limited. It appears to be restricted to pluripotential stem cells that serve as a reservoir for tissue that is constantly undergoing renewal, such as the hematopoietic cells and the intestinal mucosa. In the skin, bcl-2 expression has been previously reported to be limited to the epidermal basal cell layer and proliferation zones. Our results indicate that resting melanocytes and melanocytic nevi regularly express bcl-2.

    View details for Web of Science ID A1995RN89700007

    View details for PubMedID 7632063



    Virus-associated hemophagocytic syndromes are a heterogeneous group of disorders in which viral infection is associated with a proliferation of hemophagocytic histiocytes throughout the reticuloendothelial system. The authors report the case of a 24-year-old Vietnamese male who developed a hemophagocytic syndrome associated with Epstein-Barr virus (EBV) and who died following a rapidly progressive course. A proliferation of reactive-appearing lymphoid cells was associated with an extensive proliferation of erythrophagocytic histiocytes. Immunophenotypically, the lymphoid infiltrate consisted of CD56+ natural killer cells, predominantly CD8+ T-cells and rare B-cells (CD20+). Double-label immunohistochemical studies showed CD3+ T-cells and CD56+ natural killer cells to be distinct cell populations. Combined immunohistochemical-in situ hybridization studies localized EBV to CD43+, CD3-, CD68-, lymphoid-appearing cells, indicating the presence of EBV within natural killer cells. Southern hybridization analysis of EBV genomic termini revealed clonal EBV genome. However, there was no detectable immunoglobulin or T-cell receptor gene rearrangements. The findings indicate that this case of hemophagocytic syndrome represents a clonal proliferation of natural killer cells containing EBV and highlights the importance of the analysis of EBV genomic termini for determination of clonality in EBV-associated proliferations. It is possible that other cases of fulminant EBV-associated hemophagocytic syndromes represent clonal natural killer cell proliferations.

    View details for Web of Science ID A1995QF55100015

    View details for PubMedID 7856561



    The association between rheumatic disease and the occurrence of hematolymphoid neoplasms has been a subject of investigation for many years. Recently, we and others have reported the development in rheumatic patients of lymphoproliferative disorders that are similar to those occurring in patients with known immunocompromised states. The lymphoid neoplasms that develop in patients with immunosuppression are characterized by several features including the presence of EBV genome in the neoplastic cells. The fact that lymphomas with features of those occurring in immunosuppressed patients can occur in patients with rheumatic disease suggests that immune system impairment secondary to the rheumatic disease, the treatment given for the rheumatic disease, or to a combination of these factors, might play a role in the development of lymphoma in these patients. This review will first describe the characteristics of lymphoproliferative disorders that occur in patients with known immunocompromised states. It will then review general aspects of lymphomas in rheumatic patients with a focus on more recent reports that have described the development of immunosuppression-associated lymphoproliferative disorders in rheumatic patients. Studies that investigate the relative contribution of the rheumatic disease versus therapy for rheumatic disease in the development of lymphoma in this patient group are still needed.

    View details for Web of Science ID A1995QJ55000001

    View details for PubMedID 7787745



    We describe the first case of an Epstein-Barr virus (EBV)-associated natural killer-large granular lymphocyte (NK-LGL) leukemia in the United States to the best of our knowledge. A 29-year-old woman of Japanese descent developed EBV infection after a blood transfusion as indicated by a rise in serum antibody titers. Peripheral blood and bone marrow aspirate smears demonstrated increased LGLs. Flow cytometry showed that these cells expressed NK-associated surface antigens. Cytogenetic analysis of the bone marrow aspirate showed two distinct but related clones with multiple copies of a modified 7 marker chromosome. Death followed colonic perforation. Findings at necropsy included bone marrow lymphocytosis and erythrophagocytosis, a mononucleosis-like lymphadenitis, atypical hepatitis with a mixed, predominantly T-cell infiltrate, interstitial pneumonitis, and multiorgan system vasculitis with perforation of the transverse colon. Epstein-Barr virus transcripts were identified in lymphocytes infiltrating liver and peripheral nerve by in situ hybridization. In addition, Southern blot analyses showed monoclonal bands superimposed on oligoclonal ladders of EBV termini in liver and lymph node. The identical episomal form of EBV was found in the bone marrow, lymph node, and liver. No immunoglobulin (Ig), T-cell receptor beta, or T-cell receptor gamma chain gene rearrangements were identified. These studies support the hypothesis that the LGL population was a neoplastic EBV-related clonal proliferation of NK cells.

    View details for Web of Science ID A1994PG35800018

    View details for PubMedID 8088773



    The protein encoded by the Bcl-2 proto-oncogene has been shown to inhibit programmed cell death and has been primarily studied in hematolymphoid malignancies. Recent work ahs elucidated Bcl-2 expression in nonhematolymphoid malignancies of the lung, prostate, and nasopharynx. Studies of Bcl-2 expression in prostate carcinoma have suggested that its expression may be related to hormonal control. To determine its presence and possible significance in breast carcinoma, a malignancy in which therapy is influenced by hormone receptor status, we used a monoclonal antibody directed against the Bcl-2 gene product to examine Bcl-2 immunoreactivity in a series of paraffin-embedded primary breast tumors. Benign breast tissue showed Bcl-2 positivity in the basal layer and in superficial cells. Twenty-four of 41 (58%) carcinomas were Bcl-2 positive. Staining for Bcl-2 was equivocal in two cases. We identified a strong correlation between Bcl-2 expression and hormone receptor positivity as 23 of 24 (96%) cases that were Bcl-2 positive were estrogen receptor (ER) positive (P = 0.0001) and 21 of 24 (87.5%) were positive for progesterone receptor PR (P = 0.0001). Of 15 Bcl-2-negative cases, 14 (93%) were ER negative and all were PR negative. One case of mucinous carcinoma was ER positive and Bcl-2 negative. Grade 1 and 2 tumors (Scarff-Bloom-Richardson scale) were almost three times as likely to be Bcl-2 positive (90%) as grade 3 tumors (33%) (P = 0.0057). Bcl-2 reactivity appears to be more prevalent in well-differentiated tumors, suggesting that its presence may diminish with loss of differentiation, a hypothesis that is further supported by a subset of cases that were ER negative, Bcl-2 negative, and of poor histological grade. These may be tumors that do not require Bcl-2 inhibition of apoptosis and respond to hormonally independent proliferation factors. Our findings support the hypothesis that Bcl-2 expression may be related to hormonal regulation in breast carcinoma.

    View details for Web of Science ID A1994PG11000007

    View details for PubMedID 8080038



    Solitary fibrous tumors are rare neoplasms that most commonly involve the pleura, mediastinum, and lung. Because they lack distinctive histologic features, immunologic staining has frequently been employed to exclude other neoplasms in the differential diagnosis. Their reported phenotype to date is generally negative, notably for muscle-type actins, desmin, keratin, and S-100 protein. Although this testing is of some help, it does not serve to distinguish all processes in the differential diagnosis, and when it does, it places too great an emphasis on a negative finding to make a diagnosis. We report here that CD34 monoclonal antibodies reacted with 11 of 14 solitary fibrous tumors in paraffin sections. Thus, they provide a positive marker that distinguishes the solitary fibrous tumor from most elements in the differential diagnosis.

    View details for Web of Science ID A1994NZ05000008

    View details for PubMedID 7518652



    Gastrointestinal stromal tumors (GISTs) are neoplasms arising in the wall of the gastrointestinal tract that frequently show evidence of smooth muscle differentiation, either by their appearance alone or by immunohistology. A significant number of these neoplasms fail to react with any markers of muscle differentiation, however. A subset of these neoplasms have epithelioid features, and the presence of these features can give rise to confusion with other neoplasms, such as carcinomas and melanomas. Here we show that the CD34 monoclonal antibody My10 reacts with 19 of 23 (83%) of these lesions, including both those with and without epithelioid features. Five of 10 epithelioid and one of 13 spindled neoplasms lacked detectable muscle-specific actin (MSA), smooth muscle actin (SMA), and desmin; all six were CD34 reactive. Immunoblotting experiments show that the antigen on these stromal neoplasms has a molecular weight identical to that found on hematopoietic cells. The frequency and intensity of the reactivity of GISTs with anti-CD34 antibodies are distinctly higher than those reported for smooth muscle neoplasms of soft tissue and myometrium. This reactivity can be a useful adjunct in the diagnosis of difficult cases, especially in those exhibiting epithelioid morphology.

    View details for Web of Science ID A1994PC66300007

    View details for PubMedID 7520017



    We recently reported two cases of reversible Epstein-Barr virus (EBV)-associated lymphomas in patients undergoing methotrexate therapy for rheumatic disease. The current study was undertaken to investigate how frequently lymphoid neoplasms in patients with rheumatic disease show features of lymphoproliferations occurring in immunocompromised patients. Eighteen patients (including the two previously reported patients) with rheumatoid arthritis or dermatomyositis who developed lymphoproliferative lesions and on whom detailed clinical information was available were studied. As a group these patients developed a spectrum of lymphoproliferative lesions; however, a subset of patients developed neoplasms with features associated with immunosuppression. The neoplasms occurred in extranodal sites in 10 (56%) patients, showed a diffuse large-cell histology in nine (50%) patients, and contained EBV (EBER1) transcripts and EBV latent membrane protein in six (33%) patients. In three (17%) patients the neoplasms showed the entire constellation of features typical of immunosuppression-associated lymphoproliferations, including extranodal location, large-cell or polymorphous histology, geographic areas of necrosis, and the presence of EBV. These three patients were receiving both steroids and methotrexate at the time they developed their neoplasms. The findings of this study support the hypothesis that a subset of lymphoid neoplasms in rheumatic patients occurs in an immunocompromised setting and suggest that therapeutic immunosuppression may contribute, at least in part, to the development of these lymphoid neoplasms.

    View details for Web of Science ID A1994NX22700003

    View details for PubMedID 8026822



    We evaluated the immunophenotypes of 22 spindled and 36 epithelioid uterine smooth muscle neoplasms (SMNs) and 16 extrauterine nongastrointestinal spindled smooth-muscle neoplasms for various markers. The epithelioid neoplasms were subdivided into two histological groups designated true and intermediate, the former showing typical epithelioid features and the latter showing epithelioid features that could be explained by cross-sectioning of blunt spindled cells. Desmin, muscle-specific actin, and smooth muscle actin were equally sensitive in detecting muscle differentiation in all these neoplasms. The true epithelioid variants were more frequently keratin positive but less frequently positive for vimentin, CD34 or the muscle markers, compared with their spindled counterparts. The intermediate epithelioid variants more closely resembled the spindled neoplasms in their immunostaining for muscle markers, vimentin, and CD34 but like the true epithelioid variants were relatively frequently positive for keratin. CD34 was positive in 36% of the spindled and 6% of the true epithelioid uterine SMNs, in most cases faintly. Antikeratin AE1 was positive more frequently than CAM5.2, with 18% of the spindled and 35% of the true epithelioid neoplasms being AE1 positive. The immunophenotype of uterine SMNs, including the epithelioid variant, permits their distinction from carcinomas based on their frequent reactivity for muscle markers in spite of their high rate of keratin positivity. They show sufficient overlap in immunoreactivity with endometrial stromal sarcomas to preclude definitive differentiation from them on immunohistochemical features alone.

    View details for Web of Science ID A1994NX22700008

    View details for PubMedID 7517911



    Trichoepitheliomas (TE) are benign follicular neoplasms which are frequently confused with basal cell carcinomas (BCC). It is important to distinguish these entities precisely, as the treatments and prognoses are different. To this end, we stained a series of formalin-fixed, paraffin-embedded specimens of unequivocal TE and BCC with antibodies directed against bcl-2, an oncogene associated with programmed cell death, and known to be overexpressed in some malignant tumours. The TE showed staining of tumour cells limited to the outermost layer of the proliferation. The BCC tumour cells demonstrated diffuse staining throughout the tumour nodules. This difference in staining pattern was then applied to more equivocal cases, and seemed clearly to separate the entities. The observed findings may prove to be of diagnostic help in distinguishing borderline cases, and also offer some possible explanations for the biological differences between these neoplasms.

    View details for Web of Science ID A1994NW74700004

    View details for PubMedID 8043419

  • Brief report: reversible lymphomas associated with Epstein-Barr virus occurring during methotrexate therapy for rheumatoid arthritis and dermatomyositis. New England journal of medicine Kamel, O. W., van de Rijn, M., Weiss, L. M., Del Zoppo, G. J., HENCH, P. K., Robbins, B. A., Montgomery, P. G., Warnke, R. A., Dorfman, R. F. 1993; 328 (18): 1317-1321

    View details for PubMedID 8385742



    The mouse lymph node specific homing receptor gp90MEL-14 is a 95-kDa molecular mass ubiquitinated cell surface molecule involved in the binding of lymphocytes to high endothelial venules in peripheral lymph nodes. The molecule is thought to consist of a core protein to which ubiquitin side chains are covalently bound. Recently we cloned the cDNA encoding the core protein; this cDNA clone encodes for a polypeptide with an estimated molecular mass of 37 kDa. We have studied the biosynthesis of gp90MEL-14 in an effort to explain the difference in molecular mass between the core protein and the 95-kDa mature molecule. Pulse labeling experiments show a rapid synthesis of a 70-kDa precursor form that contains high-mannose N-linked oligosaccharides. On processing of the high-mannose oligosaccharides into complex N-linked oligosaccharides, the precursor matures in a single step into the 95-kDa form. Experiments using deglycosylating enzymes and inhibitors of N-linked glycosylation demonstrate that the molecular mass of deglycosylated gp90MEL-14 is 45 kDa; extensive N-linked glycosylation is responsible for the difference in molecular mass with the mature 95-kDa form. The core protein molecular weight of in vitro transcribed and translated gp90MEL-14 cDNA is consistent with the estimated molecular mass of 37 kDa, calculated from the cDNA sequence of the core protein, and 8 to 10 kDa less than the protein molecular mass of gp90MEL-14 translated in vivo in the presence of tunicamycin (45 kDa). Inasmuch as we have ruled out glycosylation as accounting for this discrepancy, this is consistent with the addition of one ubiquitin moiety to the core protein during biosynthesis. Limited proteolysis confirms the similarity between in vitro transcribed gp90MEL-14 cDNA and the tunicamycin form of gp90MEL-14.

    View details for Web of Science ID A1990DV27900028

    View details for PubMedID 2166761

  • Autopsy findings after coronary rotational atherectomy. The American journal of cardiovascular pathology van de Rijn, M., Regula, D. P., Billingham, M. 1990; 3 (4): 301-304


    We describe the findings at autopsy in a patient who underwent Rotablator atherectomy of the right coronary artery. During the procedure, the artery became occluded. Despite attempts to reopen the vessel with balloon angioplasty and emergency coronary artery bypass grafting, the patient developed irreversible cardiac failure and expired 2 days after the Rotablator procedure. At autopsy, the right coronary artery was found to be occluded by thrombus. No evidence of dissection or perforation of the vessel wall was seen. Small intramyocardial arteries and arterioles, downstream from the treated vessel, were embolized by pulverized atheroma.

    View details for PubMedID 2129571



    Recently, hematopoietic stem cells were purified to homogeneity from mouse bone marrow. The protein structure of Sca-1, the cell surface antigen used in the isolation of hematopoietic stem cells, is described here. It is shown that the Sca-1 antigen is a member of the Ly-6 antigen family. The anti-Sca-1 antibody was used in immunohistochemistry experiments to define the structures in several tissues that had previously been shown to contain Ly-6 antigens. In thymus, spleen, and kidney, specific staining of parenchymal cells can be demonstrated, whereas only vasculature reacts with anti-Sca-1 in brain, heart, and liver and possibly in lung.

    View details for Web of Science ID A1989AB24900063

    View details for PubMedID 2660142



    Isolation of a clone encoding the mouse lymph node homing receptor reveals a deduced protein with an unusual protein mosaic architecture, containing a separate carbohydrate-binding (lectin) domain, an epidermal growth factor-like (EGF) domain, and an extracellular precisely duplicated repeat unit, which preserves the motif seen in the homologous repeat structure of complement regulatory proteins and other proteins. The receptor molecule is potentially highly glycosylated, and contains an apparent transmembrane region. Analysis of messenger RNA transcripts reveals a predominantly lymphoid distribution in direct relation to the cell surface expression of the MEL-14 determinant, and the cDNA clone is shown to confer the MEL-14 epitope in heterologous cells. The many novel features, including ubiquitination, embodied in this single receptor molecule form the basis for numerous approaches to the study of cell-cell interactions.

    View details for Web of Science ID A1989T473200027

    View details for PubMedID 2646713



    T-cell receptors bind antigens only when the antigens are exposed on the cell surface. This can be studied best in the interaction of cytolytic T lymphocytes (CTL) with target cells because the recognition and binding event can be separated from the lytic phase. Studies with CTL clones specific for HLA-A2 and HLA-B7 demonstrated that conjugates of CTL's and target cells can be formed in the absence of specific antigen recognition. Furthermore, T-cell receptor and target antigen cannot interact unless there is conjugate formation. This indicates that nonspecific conjugate formation between CTL's and target cells precedes the recognition of specific antigen by the T-cell receptor.

    View details for Web of Science ID A1986A802000038

    View details for PubMedID 3485822



    T6 and M241 antigens are products of the Class I major histocompatibility complex. The T6 and M241 antigens can be detected on human cortical thymocytes and on dendritic cells in the skin by monoclonal antibodies. Here we report a method of purification of the T6 and M241 antigens. Amino acid sequence data of purified antigens indicate that the heavy chains are blocked at their N-termini, whereas the partial N-terminal amino acid sequence of the light chains is identical to that of the human beta 2-microglobulin. In order to obtain sequence data from the heavy chains a method is described for isolation of purified cyanogen bromide fragments by electrophoretic methods.

    View details for Web of Science ID A1986A015000005

    View details for PubMedID 3084948



    The human T lymphocyte cell surface antigen T8 has been found to be associated on thymocytes with a protein of 46 kDa through disulfide bridges. Analysis by isoelectric focusing, and of peptides obtained by limited proteolysis and chemical cleavage demonstrated that this 46-kDa protein was the cell surface antigen T6, which is expressed on cortical thymocytes. The findings are discussed in the context of the importance of the T8 and T6 molecules in thymic differentiation.

    View details for Web of Science ID A1985AKM6200019

    View details for PubMedID 3922774



    Monoclonal antibodies anti-T6 and anti-M241 define unique cell populations within different lineages: cortical thymocytes and dendritic cells in the skin. T6 positive cutaneous dendritic cells are located predominantly in the epidermis and belong to the Langerhans/indeterminate lineage, whereas, most of the M241 positive cells are located in the perivascular regions of the dermis. Biochemical analysis of thymocytes and cutaneous dendritic cells was performed in order to determine whether the reactivity of these antibodies with these cell types is due to sharing of antigenic determinants by two unrelated proteins, or whether similar proteins are present on cells of different lineages. Our results indicate that T6 antigens are borne by the same glycoprotein (49K) on cortical thymocytes and Langerhans/indeterminate cells. Similarly, M241 antigens isolated from thymocytes and cutaneous dendritic cells are found on the same glycoprotein (43K).

    View details for Web of Science ID A1984SK25000002

    View details for PubMedID 6425248



    Beta 2-microglobulin (beta 2-m) is a highly conserved polypeptide (12,000 molecular weight; 12K) noncovalently associated with the heavy chain (45-48K) of the major histocompatibility complex (MHC) class I antigens. Its synthesis is required for expression of the HLA-A/B and H-2K/D heavy chains at the cell surface; beta 2-m is also associated with the human cell-surface antigens T6 and M241 isolated from thymocytes. However, on the T leukaemic cell line MOLT-4 some of the T6 antigens contain a different 12K subunit, termed beta t (refs 3, 7, 8). Purified human beta 2-m can exchange partially both with human beta 2-m associated with HLA-antigens, and with mouse beta 2-m associated with murine alloantigens. As MOLT-4 cells were grown in the presence of fetal calf serum (FCS) and as serum is known to contain some free beta 2-m, we examined whether beta t was bovine beta 2-m which had replaced endogenous beta 2-m on the surface of the cell. Here we show both that beta 2-m from FCS or human serum (HuS) used in cell culture can exchange with beta 2-m on the cell surface, and that beta t is in fact bovine beta 2-m.

    View details for Web of Science ID A1984SM02100066

    View details for PubMedID 6369147



    A gene coding for the major histocompatibility antigen HLA-A2 was transferred into human HLA-A2 negative M1 cells and murine L cells. Following transfection, these cells expressed molecules at the cell surface that are biochemically indistinguishable from HLA-A2 antigens on the human cell line JY from which the HLA-A2 gene was isolated. The M1A2 cells were recognized and lysed by a cytolytic T-cell clone specific for HLA-A2. The transfected L cells which express HLA-A2 in association with human beta 2-microglobulin were not lysed by this T-cell clone. The specific cytolysis of M1A2 cells could be inhibited by monoclonal antibodies to HLA-A2, and monoclonal antibodies to T3, T8, and LFA-1 on cytotoxic T lymphocytes. These results suggest that killing by allospecific T cells requires HLA-A2 antigens as well as other species-specific structures on the target cell surface.

    View details for Web of Science ID A1984TT08100028

    View details for PubMedID 6333726

  • EXPRESSION OF THE MAJOR HISTOCOMPATIBILITY ANTIGENS HLA-A2 AND HLA-B7 BY DNA-MEDIATED GENE-TRANSFER JOURNAL OF IMMUNOLOGY Bernabeu, C., Finlay, D., VANDERIJN, M., Maziarz, R. T., Biro, P. A., Spits, H., Devries, J., Terhorst, C. P. 1983; 131 (4): 2032-2037


    Genes coding for the heavy chain of the class I antigens HLA-A2 or HLA-B7 of the human major histocompatibility complex have been introduced into mouse LtK- cells by cotransfection with the herpes simplex virus thymidine kinase gene. HAT-resistant colonies were isolated expressing either HLA-A2 or HLA-B7 as monitored by indirect immunofluorescence. Immunoprecipitation analysis of both antigens by either sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) or isoelectric focusing (IEF) showed that they were identical to the HLA-A2 and HLA-B7 expressed in the human lymphoblastoid cell line JY (homozygous HLA-A2, HLA-B7). However, human cytotoxic T lymphocytes (CTL) generated against JY and CTL clones specific for HLA-A2 or HLA-B7 were unable to recognize the transfectants as targets. These results indicate that the human HLA-A2 (or B7) complexed with the murine beta 2-microglobulin could be an inappropriate target structure for the CTL. However, because the transfectants are not killed by human CTL even in the presence of lectins, it is suggested that other molecules that are not able to overcome the human-mouse species barrier may be involved in the killing mechanism.

    View details for Web of Science ID A1983RJ17600078

    View details for PubMedID 6352810

  • Structural and functional aspects of the T-cell differentiation antigens T3, T6, and T8. Haematology and blood transfusion TERHORST, C., Borst, J., Lerch, P., van de Rijn, M., Snow, P., Spits, H., de Vries, J. 1983; 28: 440-446

    View details for PubMedID 6602747



    A monoclonal antiserum, 66-IG10, raised against human thymocytes was found to be directed against the human transferrin receptor. A panel of human X Chinese hamster somatic cell hybrids, in conjunction with the 66-IG10 reagent, was used to assign the gene(s) coding for the transferrin receptor to the q12 leads to qter region of human chromosome 3.

    View details for Web of Science ID A1983RT50600002



    The human thymic differentiation antigen T6, which was found to be associated with beta 2-microglobulin, was compared to the HLA-A,B antigens. Using a heteroantiserum prepared against denatured heavy chains of HLA-A,B antigens, no cross-reactivity with denatured T6 could be detected. The molecular weight of the protein backbone of T6 was found to be 34,000 as compared to 40,000 for the HLA-A,B antigens. Also, not only was the percentage of carbohydrate of T6 (25-35%) different from the HLA-A,B antigens (10%), but lectin binding studies showed that their sugar composition may differ. The two forms of T6, which previously had been found on MOLT-4 cells, appeared to have different levels of glycosylation, but apparently had the same protein backbone. T6, like HLA, has a hydrophobic domain, since it could be labeled with [125I]iodonaphthylazide. We conclude from these studies that T6 may be a class I MHC antigen which is different from the classical HLA-A,B antigens.

    View details for Web of Science ID A1983QB62200002

    View details for PubMedID 6187718



    The human beta 2-microglobulin (beta-2m)-associated human thymocyte differentiation antigens T6 and M241 were compared using biochemical techniques. T6 and M241 antigens reside on different molecules with apparent m.w. of 49,000 and 43,000, respectively. Here we show that both proteins have a protein backbone m.w. of 33,000. In addition, T6 and M241 have a large portion of their peptides in common. When we compared the protein backbone m.w. of T6 and M241 with the murine beta-2m-associated thymus leukemia (TL) antigens, we found a considerable difference in size, suggesting that T6 and M241 may not be human homologues of TL antigens and constitute a novel type of major histocompatibility (MHC) class I antigens.

    View details for Web of Science ID A1983QZ47000058

    View details for PubMedID 6190941