Sabine Kohler, MD, Professor of Pathology

Publications

  • Best clinical management of tenosynovial giant cell tumour (TGCT): A consensus paper from the community of experts. Cancer treatment reviews Silvia, S., Hans Roland, D., Inga-Marie, S., Klaus, W., Rick, H., Annalisa, T., Augusto, C., Jyoti, B., Giacomo Giulio, B., Nicholas, B., Jean-Yves, B., Kjetil, B., Javier-Martin, B., Wei-Wu Tom, C., Tos Paolo Angelo, D., Jayesh, D., Stephan, E., Mikael, E., Alessandro, G., Hans, G., Jendrik, H., Wolfgang, H., John, H., Antoine, I., Jones Robin, L., Akira, K., Andreas, L., Herbert, L., Eric, M., Carlo, M., Nadine, O., Emanuela, P., Shreyaskumar R, P., Peter, R., Brian, R., Piotr, R., Claudia, S., Kathrin, S., Seddon Beatrice, M., Morena, S., Staals Eric, L., William, T., Vanhoenacker Filip, M. M., Andrew, W., Lisette, W., Sydney, S., de Sande Michiel, V., Sebastian, B. 2022; 112: 102491

    Abstract

    Tenosynovial giant cell tumour (TGCT) is a rare, locally aggressive, mesenchymal tumor arising from the joints, bursa and tendon sheaths. TGCT comprises a nodular- and a diffuse-type, with the former exhibiting mostly indolent course and the latter a locally aggressive behavior. Although usually not life-threatening, TGCT may cause chronic pain and adversely impact function and quality of life (QoL). CSFR1 inhibitors are effective with benefit on symptoms and QoL but are not available in most countries. The degree of uncertainty in selecting the most appropriate therapy and the lack of guidelines on the clinical management of TGCT make the adoption of new treatments inconsistent across the world, with suboptimal outcomes for patients. A global consensus meeting was organized in June 2022, involving experts from several disciplines and patient representatives from SPAGN to define the best evidence-based practice for the optimal approach to TGCT and generate the recommendations presented herein.

    View details for DOI 10.1016/j.ctrv.2022.102491

    View details for PubMedID 36502615

  • Interactions in CSF1-driven Tenosynovial Giant Cell Tumors. Clinical cancer research : an official journal of the American Association for Cancer Research van IJzendoorn, D. G., Matusiak, M., Charville, G. W., Spierenburg, G., Varma, S., Colburg, D. R., van de Sande, M. A., van Langevelde, K., Mohler, D. G., Ganjoo, K. N., Bui, N. Q., Avedian, R. S., Bovee, J. V., Steffner, R., West, R. B., van de Rijn, M. 2022

    Abstract

    A major component of cells in Tenosynovial Giant Cell Tumor (TGCT) consists of bystander macrophages responding to CSF1 that is overproduced by a small number of neoplastic cells with a chromosomal translocation involving the CSF1 gene. An autocrine loop was postulated where the neoplastic cells would be stimulated through CSF1R expressed on their surface. Here we use single cell RNA sequencing to investigate cellular interactions in TGCT.A total of 18,788 single cells from three TGCT and two Giant Cell Tumor of Bone (GCTB) samples underwent singe cell RNAseq. The three TGCTs were additionally analyzed using long read RNA sequencing. Immunofluorescence and immunohistochemistry for a range of markers was used to validate and extend the scRNAseq findings.Two recurrent neoplastic cell populations were identified in TGCT that are highly similar to non-neoplastic synoviocytes. We identified GFPT2 as a marker that highlights the neoplastic cells in TCGT. We show that the neoplastic cells themselves do not express CSF1R. We identified overlapping features between the giant cells in TGCT and GCTB.The neoplastic cells in TGCT are highly similar non-neoplastic synoviocytes. The lack of CSF1R on the neoplastic cells indicates they may be unaffected by current therapies. High expression of GFPT2 in the neoplastic cells is associated with activation of the YAP1/TAZ pathway. In addition, we identified expression of the PDGF receptor in the neoplastic cells. These findings suggest two additional pathways to target in this tumor.

    View details for DOI 10.1158/1078-0432.CCR-22-1898

    View details for PubMedID 36007098

  • Identifying and characterizing EZH2 as a druggable dependency factor for desmoid tumors in a genetic Xenopus tropicalis model for Gardner's Syndrome Naert, T., Tulkens, D., Van Nieuwenhuysen, T., Przybyl, J., Demuynck, S., Al-Jazrawe, M., Van De Rijn, M., Alman, B., De Leenheer, K., Coucke, P., Creytens, D., Vleminckx, K. SPRINGERNATURE. 2022: 71-72
  • Reproducible, high-dimensional imaging in archival human tissue by multiplexed ion beam imaging by time-of-flight (MIBI-TOF). Laboratory investigation; a journal of technical methods and pathology Liu, C. C., Bosse, M., Kong, A., Kagel, A., Kinders, R., Hewitt, S. M., Varma, S., van de Rijn, M., Nowak, S. H., Bendall, S. C., Angelo, M. 2022

    Abstract

    Multiplexed ion beam imaging by time-of-flight (MIBI-TOF) is a form of mass spectrometry imaging that uses metal labeled antibodies and secondary ion mass spectrometry to image dozens of proteins simultaneously in the same tissue section. Working with the National Cancer Institute's (NCI) Cancer Immune Monitoring and Analysis Centers (CIMAC), we undertook a validation study, assessing concordance across a dozen serial sections of a tissue microarray of 21 samples that were independently processed and imaged by MIBI-TOF or single-plex immunohistochemistry (IHC) over 12 days. Pixel-level features were highly concordant across all 16 targets assessed in both staining intensity (R2=0.94±0.04) and frequency (R2=0.95±0.04). Comparison to digitized, single-plex IHC on adjacent serial sections revealed similar concordance (R2=0.85±0.08) as well. Lastly, automated segmentation and clustering of eight cell populations found that cell frequencies between serial sections yielded an average correlation of R2=0.94±0.05. Taken together, we demonstrate that MIBI-TOF, with well-vetted reagents and automated analysis, can generate consistent and quantitative annotations of clinically relevant cell states in archival human tissue, and more broadly, present a scalable framework for benchmarking multiplexed IHC approaches.

    View details for DOI 10.1038/s41374-022-00778-8

    View details for PubMedID 35351966

  • Author Correction: The immunoregulatory landscape of human tuberculosis granulomas. Nature immunology McCaffrey, E. F., Donato, M., Keren, L., Chen, Z., Delmastro, A., Fitzpatrick, M. B., Gupta, S., Greenwald, N. F., Baranski, A., Graf, W., Kumar, R., Bosse, M., Fullaway, C. C., Ramdial, P. K., Forgo, E., Jojic, V., Van Valen, D., Mehra, S., Khader, S. A., Bendall, S. C., van de Rijn, M., Kalman, D., Kaushal, D., Hunter, R. L., Banaei, N., Steyn, A. J., Khatri, P., Angelo, M. 2022

    View details for DOI 10.1038/s41590-022-01178-2

    View details for PubMedID 35277696

  • Detection of MDM2 amplification by shallow whole genome sequencing of cell-free DNA of patients with dedifferentiated liposarcoma. PloS one Przybyl, J., Spans, L., Ganjoo, K., Bui, N., Mohler, D., Norton, J., Poultsides, G., Debiec-Rychter, M., van de Rijn, M. 2022; 17 (1): e0262272

    Abstract

    High-level amplification of MDM2 and other genes in the 12q13-15 locus is a hallmark genetic feature of well-differentiated and dedifferentiated liposarcomas (WDLPS and DDLPS, respectively). Detection of this genomic aberration in plasma cell-free DNA may be a clinically useful assay for non-invasive distinction between these liposarcomas and other retroperitoneal tumors in differential diagnosis, and might be useful for the early detection of disease recurrence. In this study, we performed shallow whole genome sequencing of cell-free DNA extracted from 10 plasma samples from 3 patients with DDLPS and 1 patient with WDLPS. In addition, we studied 31 plasma samples from 11 patients with other types of soft tissue tumors. We detected MDM2 amplification in cell-free DNA of 2 of 3 patients with DDLPS. By applying a genome-wide approach to the analysis of cell-free DNA, we also detected amplification of other genes that are known to be recurrently affected in DDLPS. Based on the analysis of one patient with DDLPS with longitudinal plasma samples available, we show that tracking MDM2 amplification in cell-free DNA may be potentially useful for evaluation of response to treatment. The patient with WDLPS and patients with other soft tissue tumors in differential diagnosis were negative for the MDM2 amplification in cell-free DNA. In summary, we demonstrate the feasibility of detecting amplification of MDM2 and other DDLPS-associated genes in plasma cell-free DNA using technology that is already routinely applied for other clinical indications. Our results may have clinical implications for improved diagnosis and surveillance of patients with retroperitoneal tumors.

    View details for DOI 10.1371/journal.pone.0262272

    View details for PubMedID 34986184

  • The immunoregulatory landscape of human tuberculosis granulomas. Nature immunology McCaffrey, E. F., Donato, M., Keren, L., Chen, Z., Delmastro, A., Fitzpatrick, M. B., Gupta, S., Greenwald, N. F., Baranski, A., Graf, W., Kumar, R., Bosse, M., Fullaway, C. C., Ramdial, P. K., Forgó, E., Jojic, V., Van Valen, D., Mehra, S., Khader, S. A., Bendall, S. C., van de Rijn, M., Kalman, D., Kaushal, D., Hunter, R. L., Banaei, N., Steyn, A. J., Khatri, P., Angelo, M. 2022

    Abstract

    Tuberculosis (TB) in humans is characterized by formation of immune-rich granulomas in infected tissues, the architecture and composition of which are thought to affect disease outcome. However, our understanding of the spatial relationships that control human granulomas is limited. Here, we used multiplexed ion beam imaging by time of flight (MIBI-TOF) to image 37 proteins in tissues from patients with active TB. We constructed a comprehensive atlas that maps 19 cell subsets across 8 spatial microenvironments. This atlas shows an IFN-γ-depleted microenvironment enriched for TGF-β, regulatory T cells and IDO1+ PD-L1+ myeloid cells. In a further transcriptomic meta-analysis of peripheral blood from patients with TB, immunoregulatory trends mirror those identified by granuloma imaging. Notably, PD-L1 expression is associated with progression to active TB and treatment response. These data indicate that in TB granulomas, there are local spatially coordinated immunoregulatory programs with systemic manifestations that define active TB.

    View details for DOI 10.1038/s41590-021-01121-x

    View details for PubMedID 35058616

  • CRISPR-SID: Identifying EZH2 as a druggable target for desmoid tumors via invivo dependency mapping. Proceedings of the National Academy of Sciences of the United States of America Naert, T., Tulkens, D., Van Nieuwenhuysen, T., Przybyl, J., Demuynck, S., van de Rijn, M., Al-Jazrawe, M., Alman, B. A., Coucke, P. J., De Leeneer, K., Vanhove, C., Savvides, S. N., Creytens, D., Vleminckx, K. 2021; 118 (47)

    Abstract

    Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/beta-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast, efficient, and penetrant genetic Xenopus tropicalis desmoid tumor models to identify and characterize drug targets. We used multiplexed CRISPR/Cas9 genome editing in these models to simultaneously target a tumor suppressor gene (apc) and candidate dependency genes. Our methodology CRISPR/Cas9 selection-mediated identification of dependencies (CRISPR-SID) uses calculated deviations between experimentally observed gene editing outcomes and deep-learning-predicted double-strand break repair patterns to identify genes under negative selection during tumorigenesis. This revealed EZH2 and SUZ12, both encoding polycomb repressive complex 2 components, and the transcription factor CREB3L1 as genetic dependencies for desmoid tumors. In vivo EZH2 inhibition by Tazemetostat induced partial regression of established autochthonous tumors. In vitro models of patient desmoid tumor cells revealed a direct effect of Tazemetostat on Wnt pathway activity. CRISPR-SID represents a potent approach for invivo mapping of tumor vulnerabilities and drug target identification.

    View details for DOI 10.1073/pnas.2115116118

    View details for PubMedID 34789568

  • Prognostic relevance of the hexosamine biosynthesis pathway activation in leiomyosarcoma. NPJ genomic medicine Tolwani, A., Matusiak, M., Bui, N., Forgo, E., Varma, S., Baratto, L., Iagaru, A., Lazar, A. J., van de Rijn, M., Przybyl, J. 2021; 6 (1): 30

    Abstract

    Metabolic reprogramming of tumor cells and the increase of glucose uptake is one of the hallmarks of cancer. In order to identify metabolic pathways activated in leiomyosarcoma (LMS), we analyzed transcriptomic profiles of distinct subtypes of LMS in several datasets. Primary, recurrent and metastatic tumors in the subtype 2 of LMS showed consistent enrichment of genes involved in hexosamine biosynthesis pathway (HBP). We demonstrated that glutamine-fructose-6-phosphate transaminase 2 (GFPT2), the rate-limiting enzyme in HBP, is expressed on protein level in a subset of LMS and the expression of this enzyme is frequently retained in patient-matched primary and metastatic tumors. In a new independent cohort of 327 patients, we showed that GFPT2 is associated with poor outcome of uterine LMS but not extra-uterine LMS. Based on the analysis of a small group of patients studied by 18F-FDG-PET imaging, we propose that strong expression of GFPT2 in primary LMS may be associated with high metabolic activity. Our data suggest that HBP is a potential new therapeutic target in one of the subtypes of LMS.

    View details for DOI 10.1038/s41525-021-00193-w

    View details for PubMedID 33941787

  • Relationships between highly recurrent tumor suppressor alterations in 489 leiomyosarcomas. Cancer Schaefer, I., Lundberg, M. Z., Demicco, E. G., Przybyl, J., Matusiak, M., Chibon, F., Ingram, D. R., Hornick, J. L., Wang, W., Bauer, S., Baker, L. H., Lazar, A. J., van de Rijn, M., Marino-Enriquez, A., Fletcher, J. A. 2021

    Abstract

    BACKGROUND: Leiomyosarcoma (LMS) is the most common soft tissue and uterine sarcoma, but no standard therapy is available for recurrent or metastatic LMS. TP53, p16/RB1, and PI3K/mTOR pathway dysregulations are recurrent events, and some LMS express estrogen receptor (ER) and/or progesterone receptor (PR). To characterize relationships between these pathway perturbations, the authors evaluated protein expression in soft tissue and uterine nonprimary leiomyosarcoma (np-LMS), including local recurrences and distant metastases.METHODS: TP53, RB1, p16, and PTEN expression aberrations were determined by immunohistochemistry (IHC) in tissue microarrays (TMAs) from 227 np-LMS and a comparison group of 262 primary leiomyosarcomas (p-LMS). Thirty-five of the np-LMS had a matched p-LMS specimen in the TMAs. Correlative studies included differentiation scoring, ER and PR IHC, and CDKN2A/p16 fluorescence in situ hybridization.RESULTS: Dysregulation of TP53, p16/RB1, and PTEN was demonstrated in 90%, 95%, and 41% of np-LMS, respectively. PTEN inactivation was more common in soft tissue np-LMS than uterine np-LMS (55% vs 31%; P = .0005). Moderate-strong ER expression was more common in uterine np-LMS than soft tissue np-LMS (50% vs 7%; P < .0001). Co-inactivation of TP53 and RB1 was found in 81% of np-LMS and was common in both soft tissue and uterine np-LMS (90% and 74%, respectively). RB1, p16, and PTEN aberrations were nearly always conserved in p-LMS and np-LMS from the same patients.CONCLUSIONS: These studies show that nearly all np-LMS have TP53 and/or RB1 aberrations. Therefore, therapies targeting cell cycle and DNA damage checkpoint vulnerabilities should be prioritized for evaluations in LMS.

    View details for DOI 10.1002/cncr.33542

    View details for PubMedID 33788262

  • HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor. Clinical cancer research : an official journal of the American Association for Cancer Research Hemming, M. L., Coy, S. n., Lin, J. R., Andersen, J. L., Przybyl, J. n., Mazzola, E. n., Abdelhamid Ahmed, A. H., van de Rijn, M. n., Sorger, P. K., Armstrong, S. A., Demetri, G. D., Santagata, S. n. 2021

    Abstract

    Purpose: Gastrointestinal stromal tumor (GIST) arises from interstitial cells of Cajal (ICC) or their precursors, which are present throughout the gastrointestinal tract. While gastric GIST is commonly indolent and small intestine GIST more aggressive, a molecular understanding of disease behavior would inform therapy decisions in GIST. Although a core transcription factor (TF) network is conserved across GIST, accessory TFs HAND1 and BARX1 are expressed in a disease state-specific pattern. Here, we characterize two divergent transcriptional programs maintained by HAND1 and BARX1, and evaluate their association with clinical outcomes. Experimental Design: We evaluated RNA-seq and TF chromatin immunoprecipitation with sequencing (ChIP-seq) in GIST samples and cultured cells for transcriptional programs associated with HAND1 and BARX1. Multiplexed tissue-based cyclic immunofluorescence (CyCIF) and immunohistochemistry evaluated tissue and cell-level expression of TFs and their association with clinical factors. Results: We show that HAND1 is expressed in aggressive GIST, modulating KIT and core TF expression and supporting proliferative cellular programs. In contrast, BARX1 is expressed in indolent and micro-GISTs. HAND1 and BARX1 expression were superior predictors of relapse-free survival, as compared to standard risk stratification, and they predict progression-free survival on imatinib. Reflecting the developmental origins of accessory TF programs, HAND1 was expressed solely in small intestine ICCs, while BARX1 expression was restricted to gastric ICCs. Conclusions: Our results define anatomic and transcriptional determinants of GIST and molecular origins of clinical phenotypes. Assessment of HAND1 and BARX1 expression in GIST may provide prognostic information and improve clinical decisions on the administration of adjuvant therapy.

    View details for DOI 10.1158/1078-0432.CCR-20-3538

    View details for PubMedID 33451979

  • Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell Luca, B. A., Steen, C. B., Matusiak, M., Azizi, A., Varma, S., Zhu, C., Przybyl, J., Espín-Pérez, A., Diehn, M., Alizadeh, A. A., van de Rijn, M., Gentles, A. J., Newman, A. M. 2021

    Abstract

    Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale identification and validation of cell states and multicellular communities from bulk, single-cell, and spatially resolved gene expression data. When applied to 12 major cell lineages across 16 types of human carcinoma, EcoTyper identified 69 transcriptionally defined cell states. Most states were specific to neoplastic tissue, ubiquitous across tumor types, and significantly prognostic. By analyzing cell-state co-occurrence patterns, we discovered ten clinically distinct multicellular communities with unexpectedly strong conservation, including three with myeloid and stromal elements linked to adverse survival, one enriched in normal tissue, and two associated with early cancer development. This study elucidates fundamental units of cellular organization in human carcinoma and provides a framework for large-scale profiling of cellular ecosystems in any tissue.

    View details for DOI 10.1016/j.cell.2021.09.014

    View details for PubMedID 34597583

  • Atlas of clinically-distinct cell states and cellular ecosystems across human solid tumors Luca, B. A., Steen, C. B., Azizi, A., Matusiak, M., Przybyl, J., Neishaboori, N., Perez, A., Diehn, M., Alizadeh, A. A., van de Rijn, M., Gentles, A. J., Newman, A. M. AMER ASSOC CANCER RESEARCH. 2020
  • A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk. Genome biology Gentles, A. J., Hui, A. B., Feng, W. n., Azizi, A. n., Nair, R. V., Bouchard, G. n., Knowles, D. A., Yu, A. n., Jeong, Y. n., Bejnood, A. n., Forgó, E. n., Varma, S. n., Xu, Y. n., Kuong, A. n., Nair, V. S., West, R. n., van de Rijn, M. n., Hoang, C. D., Diehn, M. n., Plevritis, S. K. 2020; 21 (1): 107

    Abstract

    Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway.To develop a deeper understanding of the interactions between cells within human lung tumors, we perform RNA-seq profiling of flow-sorted malignant cells, endothelial cells, immune cells, fibroblasts, and bulk cells from freshly resected human primary non-small-cell lung tumors. We map the cell-specific differential expression of prognostically associated secreted factors and cell surface genes, and computationally reconstruct cross-talk between these cell types to generate a novel resource called the Lung Tumor Microenvironment Interactome (LTMI). Using this resource, we identify and validate a prognostically unfavorable influence of Gremlin-1 production by fibroblasts on proliferation of malignant lung adenocarcinoma cells. We also find a prognostically favorable association between infiltration of mast cells and less aggressive tumor cell behavior.These results illustrate the utility of the LTMI as a resource for generating hypotheses concerning tumor-microenvironment interactions that may have prognostic and therapeutic relevance.

    View details for DOI 10.1186/s13059-020-02019-x

    View details for PubMedID 32381040

  • Detection of Circulating Tumor DNA in Patients With Uterine Leiomyomas. JCO precision oncology Przybyl, J., Spans, L., Lum, D. A., Zhu, S., Vennam, S., Forgó, E., Varma, S., Ganjoo, K., Hastie, T., Bowen, R., Debiec-Rychter, M., van de Rijn, M. 2019; 3

    Abstract

    The preoperative distinction between uterine leiomyoma (LM) and leiomyosarcoma (LMS) is difficult, which may result in dissemination of an unexpected malignancy during surgery for a presumed benign lesion. An assay based on circulating tumor DNA (ctDNA) could help in the preoperative distinction between LM and LMS. This study addresses the feasibility of applying the two most frequently used approaches for detection of ctDNA: profiling of copy number alterations (CNAs) and point mutations in the plasma of patients with LM.By shallow whole-genome sequencing, we prospectively examined whether LM-derived ctDNA could be detected in plasma specimens of 12 patients. Plasma levels of lactate dehydrogenase, a marker suggested for the distinction between LM and LMS by prior studies, were also determined. We also profiled 36 LM tumor specimens by exome sequencing to develop a panel for targeted detection of point mutations in ctDNA of patients with LM.We identified tumor-derived CNAs in the plasma DNA of 50% (six of 12) of patients with LM. The lactate dehydrogenase levels did not allow for an accurate distinction between patients with LM and patients with LMS. We identified only two recurrently mutated genes in LM tumors (MED12 and ACLY).Our results show that LMs do shed DNA into the circulation, which provides an opportunity for the development of ctDNA-based testing to distinguish LM from LMS. Although we could not design an LM-specific panel for ctDNA profiling, we propose that the detection of CNAs or point mutations in selected tumor suppressor genes in ctDNA may favor a diagnosis of LMS, since these genes are not affected in LM.

    View details for DOI 10.1200/po.18.00409

    View details for PubMedID 32232185

    View details for PubMedCentralID PMC7105159

  • Detection of Circulating Tumor DNA in Patients With Uterine Leiomyomas JCO PRECISION ONCOLOGY Przybyl, J., Spans, L., Lum, D. A., Zhu, S., Vennam, S., Forgo, E., Varma, S., Ganjoo, K., Hastie, T., Bowen, R., Debiec-Rychter, M., van de Rijn, M. 2019; 3
  • Detection of SS18-SSX1/2 fusion transcripts in circulating tumor cells of patients with synovial sarcoma. Diagnostic pathology Przybyl, J., van de Rijn, M., Rutkowski, P. 2019; 14 (1): 24

    Abstract

    A recent study on 15 patients with synovial sarcoma demonstrated very low prevalence of tumor-specific fusion transcripts in peripheral blood specimens. Our results in an independent cohort of 38 patients with synovial sarcoma support these findings. Synovial sarcoma patients could greatly benefit from a non-invasive monitoring of tumor burden by liquid biopsies. However, given the low detection rate of SS18-SSX1/2 in circulation, we conclude that alternative markers other than the tumor-type specific fusion transcripts should be considered.

    View details for PubMedID 30871572

  • Detection of SS18-SSX1/2 fusion transcripts in circulating tumor cells of patients with synovial sarcoma DIAGNOSTIC PATHOLOGY Przybyl, J., van de Rijn, M., Rutkowski, P. 2019; 14
  • Genomic aberrations in cell cycle genes predict progression of KIT-mutant gastrointestinal stromal tumors (GISTs) CLINICAL SARCOMA RESEARCH Heinrich, M. C., Patterson, J., Beadling, C., Wang, Y., Debiec-Rychter, M., Dewaele, B., Corless, C. L., Duensing, A., Raut, C. P., Rubin, B., Ordog, T., van de Rijn, M., Call, J., Muehlenberg, T., Fletcher, J. A., Bauer, S. 2019; 9
  • Discovery and Characterization of Recurrent, Targetable ALK Fusions in Leiomyosarcoma MOLECULAR CANCER RESEARCH Davis, L. E., Nusser, K. D., Przybyl, J., Pittsenbarger, J., Hofmann, N. E., Varma, S., Vennam, S., Debiec-Rychter, M., van de Rijn, M., Davare, M. A. 2019; 17 (3): 676–85
  • Systematic Analysis of GATA3 Expression in 530 Primary Mesenchymal Neoplasms Wei, C., Charville, G., Bean, G., Troxell, M., Allison, K., Van de Rijn, M., West, R. NATURE PUBLISHING GROUP. 2019
  • Systematic Analysis of GATA3 Expression in 530 Primary Mesenchymal Neoplasms Wei, C., Charville, G., Bean, G., Troxell, M., Allison, K., Van de Rijn, M., West, R. NATURE PUBLISHING GROUP. 2019
  • Indolent in situ High-Grade B-cell lymphoma with a MYC Translocation and Mutations Identified by Next Generation Sequencing Kumar, J., Wu, S., Butzmann, A., Lau, J., Zehnder, J., Warnke, R., Nybakken, G., Van De Rijn, M., Ohgami, R. NATURE PUBLISHING GROUP. 2019
  • Indolent in situ High-Grade B-cell lymphoma with a MYC Translocation and Mutations Identified by Next Generation Sequencing Kumar, J., Wu, S., Butzmann, A., Lau, J., Zehnder, J., Warnke, R., Nybakken, G., Van de Rijn, M., Ohgami, R. NATURE PUBLISHING GROUP. 2019
  • Detection of Premalignant Gastrointestinal Lesions Using Surface-Enhanced Resonance Raman Scattering-Nanoparticle Endoscopy. ACS nano Harmsen, S., Rogalla, S., Huang, R., Spaliviero, M., Neuschmelting, V., Hayakawa, Y., Lee, Y., Tailor, Y., Toledo-Crow, R., Kang, J. W., Samii, J. M., Karabeber, H., Davis, R. M., White, J. R., van de Rijn, M., Gambhir, S. S., Contag, C. H., Wang, T. C., Kircher, M. F. 2019; 13 (2): 1354–64

    Abstract

    Cancers of the gastrointestinal (GI) tract are among the most frequent and most lethal cancers worldwide. An important reason for this high mortality is that early disease is typically asymptomatic, and patients often present with advanced, incurable disease. Even in high-risk patients who routinely undergo endoscopic screening, lesions can be missed due to their small size or subtle appearance. Thus, current imaging approaches lack the sensitivity and specificity to accurately detect incipient GI tract cancers. Here we report our finding that a single dose of a high-sensitivity surface-enhanced resonance Raman scattering nanoparticle (SERRS-NP) enables reliable detection of precancerous GI lesions in animal models that closely mimic disease development in humans. Some of these animal models have not been used previously to evaluate imaging probes for early cancer detection. The studies were performed using a commercial Raman imaging system, a newly developed mouse Raman endoscope, and finally a clinically applicable Raman endoscope for larger animal studies. We show that this SERRS-NP-based approach enables robust detection of small, premalignant lesions in animal models that faithfully recapitulate human esophageal, gastric, and colorectal tumorigenesis. This method holds promise for much earlier detection of GI cancers than currently possible and could lead therefore to marked reduction of morbidity and mortality of these tumor types.

    View details for PubMedID 30624916

  • The Outcome of Patients With Localized Undifferentiated Pleomorphic Sarcoma of the Lower Extremity Treated at Stanford University AMERICAN JOURNAL OF CLINICAL ONCOLOGY-CANCER CLINICAL TRIALS Kamat, N. V., Million, L., Yao, D., Donaldson, S. S., Mohler, D. G., van de Rijn, M., Avedian, R. S., Kapp, D. S., Ganjoo, K. N. 2019; 42 (2): 166–71
  • Detection of Premalignant Gastrointestinal Lesions Using Surface-Enhanced Resonance Raman Scattering-Nanoparticle Endoscopy ACS NANO Harmsen, S., Rogalla, S., Huang, R., Spaliviero, M., Neuschmelting, V., Hayakawa, Y., Lee, Y., Tailor, Y., Toledo-Crow, R., Kang, J., Samii, J. M., Karabeber, H., Davis, R. M., White, J. R., van de Rijn, M., Gambhir, S. S., Contag, C. H., Wang, T. C., Kircher, M. F. 2019; 13 (2): 1354–64
  • Genomic aberrations in cell cycle genes predict progression of KIT-mutant gastrointestinal stromal tumors (GISTs). Clinical sarcoma research Heinrich, M. C., Patterson, J., Beadling, C., Wang, Y., Debiec-Rychter, M., Dewaele, B., Corless, C. L., Duensing, A., Raut, C. P., Rubin, B., Ordog, T., van de Rijn, M., Call, J., Muhlenberg, T., Fletcher, J. A., Bauer, S. 2019; 9: 3

    Abstract

    Background: Activating mutations of the receptor tyrosine kinase KIT are early events in the development of most gastrointestinal stromal tumors (GISTs). Although GISTs generally remain dependent on oncogenic KIT during tumor progression, KIT mutations alone are insufficient to induce malignant behavior. This is evidenced by KIT-mutant micro-GISTs, which are present in up to one-third of normal individuals, but virtually never progress to malignancy.Methods: We performed whole exome sequencing on 29 tumors obtained from 21 patients with high grade or metastatic KIT-mutant GIST (discovery set). We further validated the frequency and potential prognostic significance of aberrations in CDKN2A/B, RB1, and TP53 in an independent series of 71 patients with primary GIST (validation set).Results: Using whole exome sequencing we found significant enrichment of genomic aberrations in cell cycle-associated genes (Fisher's Exact p=0.001), most commonly affecting CDKN2A/B, RB1, and TP53 in our discovery set. We found a low mutational tumor burden in these 29 advanced GIST samples, a finding with significant implications for the development of immunotherapy for GIST. In addition, we found mutation of spliceosome genes in a minority of cases, implicating dysregulation of splicing as a potential cancer promoting mechanism in GIST. We next assessed the prognostic significance of CDKN2A, RB1 or TP53 mutation/copy loss in an independent cohort of 71 patients with primary GIST. Genetic events (mutation, deletion, and/or LOH) involving at least one of the three genes examined were found in 17% of the very low-risk, 36% of the low-risk, 42% of the intermediate risk, 67% of the high-risk/low mitotic-count, and in 86% of the high-risk/high mitotic-count group. The presence of cell cycle-related events was associated with a significantly shorter relapse-free survival (median 67months versus not reached; p<0.0001) and overall survival (Log Rank, p=0.042).Conclusion: Our results demonstrate that genomic events targeting cell cycle-related genes are associated with GIST progression to malignant disease. Based on this data, we propose a model for molecular pathogenesis of malignant GIST.

    View details for PubMedID 30867899

  • A clinico-genomic analysis of soft tissue sarcoma patients reveals CDKN2A deletion as a biomarker for poor prognosis. Clinical sarcoma research Bui, N. Q., Przybyl, J., Trabucco, S. E., Frampton, G., Hastie, T., van de Rijn, M., Ganjoo, K. N. 2019; 9: 12

    Abstract

    Background: Sarcomas are a rare, heterogeneous group of tumors with variable tendencies for aggressive behavior. Molecular markers for prognosis are needed to risk stratify patients and identify those who might benefit from more intensive therapeutic strategies.Patients and methods: We analyzed somatic tumor genomic profiles and clinical outcomes of 152 soft tissue (STS) and bone sarcoma (BS) patients sequenced at Stanford Cancer Institute as well as 206 STS patients from The Cancer Genome Atlas. Genomic profiles of 7733 STS from the Foundation Medicine database were used to assess the frequency of CDKN2A alterations in histological subtypes of sarcoma.Results: Compared to all other tumor types, sarcomas were found to carry the highest relative percentage of gene amplifications/deletions/fusions and the lowest average mutation count. The most commonly altered genes in STS were TP53 (47%), CDKN2A (22%), RB1 (22%), NF1 (11%), and ATRX (11%). When all genomic alterations were tested for prognostic significance in the specific Stanford cohort of localized STS, only CDKN2A alterations correlated significantly with prognosis, with a hazard ratio (HR) of 2.83 for overall survival (p=0.017). These findings were validated in the TCGA dataset where CDKN2A altered patients had significantly worse overall survival with a HR of 2.7 (p=0.002). Analysis of 7733 STS patients from Foundation One showed high prevalence of CDKN2A alterations in malignant peripheral nerve sheath tumors, myxofibrosarcomas, and undifferentiated pleomorphic sarcomas.Conclusion: Our clinico-genomic profiling of STS shows that CDKN2A deletion was the most prevalent DNA copy number aberration and was associated with poor prognosis.

    View details for DOI 10.1186/s13569-019-0122-5

    View details for PubMedID 31528332

  • PAX7 expression in sarcomas bearing the EWSR1-NFATC2 translocation MODERN PATHOLOGY Charville, G. W., Wang, W., Ingram, D. R., Roy, A., Thomas, D., Patel, R. M., Hornick, J. L., van de Rijn, M., Lazar, A. J. 2019; 32 (1): 154–56
  • The Outcome of Patients With Localized Undifferentiated Pleomorphic Sarcoma of the Lower Extremity Treated at Stanford University. American journal of clinical oncology Kamat, N. V., Million, L., Yao, D., Donaldson, S. S., Mohler, D. G., van de Rijn, M., Avedian, R. S., Kapp, D. S., Ganjoo, K. N. 2018

    Abstract

    BACKGROUND: As a diagnosis of exclusion, Undifferentiated Pleomorphic Sarcoma (UPS) has unclear clinical characteristics. The objective of this retrospective cohort study is to investigate which clinical and prognostic factors of primary lower-extremity UPS will determine failure.METHODS: We retrospectively reviewed 55 primary lower-extremity UPS cases treated at Stanford between 1998 and 2015. Overall Survival (OS) and Disease-Free Survival (DFS) curves were calculated. Univariate Fisher's Exact Tests were used to examine relationships between disease recurrence, treatment, patient factors, tumor characteristics, and surgical margins.RESULTS: 5-year DFS and OS rates were 60% (95% CI, 45%-72%) and 68% (95% CI, 53%-79%), respectively. The 5-year DFS rate for patients with positive margins was 33.3% (95% CI, 5%-68%) compared with 63% (95% CI, 47%-76%) for patients with negative margins. (Log-rank, P=0.03). The OS rate for those with disease recurrence was 42% % (95% CI, 16%-67%) compared with 76% (95% CI, 59%-87%) for patients who did not have disease recurrence (log-rank, P=0.021). Local failure occurred more frequently with omission of radiation therapy (Fisher's exact test, P=0.009).CONCLUSIONS: Positive surgical margins are an important prognostic factor for predicting relapse in UPS. Relapse of any kind led to worse OS. Radiation therapy improved local control of disease but had no statistically significant effect on DFS, highlighting the need for improved diagnostics to identify those at highest risk for hematogenous metastasis and for selection of patients for adjuvant systemic treatment.

    View details for PubMedID 30557163

  • Discovery and characterization of recurrent, targetable ALK fusions in leiomyosarcoma. Molecular cancer research : MCR Davis, L. E., Nusser, K. D., Przybyl, J., Pittsenbarger, J., Hofmann, N. E., Varma, S., Vennam, S., Debiec-Rychter, M., van de Rijn, M., Davare, M. A. 2018

    Abstract

    Soft tissue sarcomas such as leiomyosarcoma (LMS) pose a clinical challenge because systemic treatment options show only modest therapeutic benefit. Discovery and validation of targetable vulnerabilities is essential. To discover putative kinase fusions, we analyzed existing transcriptomic data from LMS clinical samples. Potentially oncogenic ALK rearrangements were confirmed by application of multiple RNA-sequencing fusion detection algorithms and fluorescence in situ hybridization (FISH). We functionally validated the oncogenic potential and targetability of discovered kinase fusions through biochemical, cell-based (Ba/F3, NIH3T3 and murine smooth muscle cell) and in vivo tumor modelling approaches. We identified ALK rearrangements in 9 of 377 (2.4%) LMS patients, including a novel KANK2-ALK fusion and a recurrent ACTG2-ALK fusion. Functional characterization of the novel ALK fusion, KANK2-ALK, demonstrates it is a dominant oncogene in Ba/F3 or NIH3T3 model systems, and has tumorigenic potential when introduced into smooth muscle cells. Oral monotherapy with targeted ALK kinase inhibitor lorlatinib significantly inhibits tumor growth and prolongs survival in a murine model of KANK2-ALK leiomyosarcoma. These results provide the first functional validation of a targetable oncogenic kinase fusion as a driver in a subset of leiomyosarcomas. Overall, these findings suggest that some soft tissue sarcomas may harbor previously unknown kinase gene translocations, and their discovery may propel new therapeutic strategies in this treatment-refractory cancer. Implications: A subset of leiomyosarcomas harbor previously unrecognized oncogenic ALK fusions that are highly responsive to ALK inhibitors and thus these data emphasize the importance of detailed genomic investigations of leiomyosarcoma tumors.

    View details for PubMedID 30518629

  • Immune checkpoint blockade as a potential therapeutic strategy for undifferentiated malignancies. Human pathology Devereaux, K. A., Charu, V., Zhao, S., Charville, G. W., Bangs, C. D., van de Rijn, M., Cherry, A. M., Natkunam, Y. 2018; 82: 39–45

    Abstract

    Undifferentiated malignancies (UMs) encompass a diverse set of aggressive tumors that pose not only a diagnostic challenge but also a challenge for clinical management. Most tumors in this category are currently treated empirically with nonspecific chemotherapeutic agents that yield extremely poor clinical response. Given that UMs are inherently genetically unstable neoplasms with the potential for immune dysregulation and increased neoantigen production, they are likely to be particularly amenable to immune checkpoint inhibitors, which target programmed cell death protein 1 (PD-1) or its ligands, PD-L1 and PD-L2, to promote T-cell antitumor activity. Aberrant expression of PD-L1 and, more recently, chromosomal 9p24.1/CD274(PD-L1)/PDCD1LG2(PD-L2) alterations can be used as biomarkers to predict responsiveness to checkpoint inhibitors. Here we evaluated 93 cases previously diagnosed as an "undifferentiated" malignancy and found that 56% (52/93) of UMs moderately to strongly express PD-L1 by immunohistochemistry (IHC). Concurrent CD274(PD-L1) and PDCD1LG2(PD-L2) fluorescence in situ hybridization (FISH) was performed on 24 of these cases and demonstrates a genetic gain at both loci in 62.5% of UMs. Genetic alterations at the CD274(PD-L1) and PDCD1LG2(PD-L2) loci were found to be completely concordant by FISH. Overall, we found that a significant proportion of UMs express PD-L1 and provide molecular support for using checkpoint inhibitors as a treatment approach for this class of tumors.

    View details for PubMedID 30539796

  • Immunohistochemistry for PAX7 is a useful confirmatory marker for Ewing sarcoma in decalcified bone marrow core biopsy specimens VIRCHOWS ARCHIV Fernandez-Pol, S., van de Rijn, M., Natkunam, Y., Charville, G. W. 2018; 473 (6): 765–69
  • Immune checkpoint blockade as a potential therapeutic strategy for undifferentiated malignancies HUMAN PATHOLOGY Devereaux, K. A., Charu, V., Zhao, S., Charville, G. W., Bangs, C. D., van de Rijn, M., Cherry, A. M., Natkunam, Y. 2018; 82: 39–45
  • 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; 78 (13): 3445–57
  • Identifying dynamic EMT states and constructing a proteomic EMT landscape of lung cancer using single cell multidimensional analysis Karacosta, L. G., Anchang, B., Kimmey, S., van de Rijn, M., Shrager, J. B., Bendall, S. C., Plevritis, S. K. AMER ASSOC CANCER RESEARCH. 2018
  • Vangl2 regulates cancer stem cell self-renewal and growth in rhabdomyosarcoma Hayes, M., McCarthy, K., Jin, A., Iyer, S., Garcia, S., Oliveira, M. L., Sindiri, S., Gryder, B., Motala, Z., Nielsen, G., Borg, J., van de Rijn, M., Malkin, D., Khan, J., Ignatius, M., Langenau, D. M. AMER ASSOC CANCER RESEARCH. 2018
  • 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

    Abstract

    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 PubMedID 29928276

  • Combination Approach for Detecting Different Types of Alterations in Circulating Tumor DNA in Leiomyosarcoma CLINICAL CANCER RESEARCH Przybyl, J., Chabon, J. J., Spans, L., Ganjoo, K. N., Vennam, S., Newman, A. M., Forgo, E., Varma, S., Zhu, S., Debiec-Rychter, M., Alizadeh, A. A., Diehn, M., van de Rijn, M. 2018; 24 (11): 2688–99
  • 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

    Abstract

    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 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

    Abstract

    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 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-+

    Abstract

    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 PubMedID 29499154

  • 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. n., van de Rijn, M. n., Natkunam, Y. n., Charville, G. W. 2018

    Abstract

    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 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. n., Thomas, D. n., Patel, R. M., Hornick, J. L., van de Rijn, M. n., Lazar, A. J. 2018

    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. n., Chabon, J. J., Spans, L. n., Ganjoo, K. n., Vennam, S. n., Newman, A. M., Forgó, E. n., Varma, S. n., Zhu, S. n., Debiec-Rychter, M. n., Alizadeh, A. A., Diehn, M. n., van de Rijn, M. n. 2018

    Abstract

    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 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
  • 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
  • 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-+

    Abstract

    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

  • Macrophage infiltration and genetic landscape of undifferentiated uterine sarcomas. JCI insight Przybyl, J., Kowalewska, M., Quattrone, A., Dewaele, B., Vanspauwen, V., Varma, S., Vennam, S., Newman, A. M., Swierniak, M., Bakula-Zalewska, E., Siedlecki, J. A., Bidzinski, M., Cools, J., van de Rijn, M., Debiec-Rychter, M. 2017; 2 (11)

    Abstract

    Endometrial stromal tumors include translocation-associated low- and high-grade endometrial stromal sarcomas (ESS) and highly malignant undifferentiated uterine sarcomas (UUS). UUS is considered a poorly defined group of aggressive tumors and is often seen as a diagnosis of exclusion after ESS and leiomyosarcoma (LMS) have been ruled out. We performed a comprehensive analysis of gene expression, copy number variation, point mutations, and immune cell infiltrates in the largest series to date of all major types of uterine sarcomas to shed light on the biology of UUS and to identify potential novel therapeutic targets. We show that UUS tumors have a distinct molecular profile from LMS and ESS. Gene expression and immunohistochemical analyses revealed the presence of high numbers of tumor-associated macrophages (TAMs) in UUS, which makes UUS patients suitable candidates for therapies targeting TAMs. Our results show a high genomic instability of UUS and downregulation of several TP53-mediated tumor suppressor genes, such as NDN, CDH11, and NDRG4. Moreover, we demonstrate that UUS carry somatic mutations in several oncogenes and tumor suppressor genes implicated in RAS/PI3K/AKT/mTOR, ERBB3, and Hedgehog signaling.

    View details for DOI 10.1172/jci.insight.94033

    View details for PubMedID 28570276

  • MAX inactivation is an early event in GIST development that regulates p16 and cell proliferation NATURE COMMUNICATIONS Schaefer, I., Wang, Y., Liang, C., Bahri, N., Quattrone, A., Doyle, L., Marino-Enriquez, A., Lauria, A., Zhu, M., Debiec-Rychter, M., Grunewald, S., Hechtman, J. F., Dufresne, A., Antonescu, C. R., Beadling, C., Sicinska, E. T., van de Rijn, M., Demetri, G. D., Ladanyi, M., Corless, C. L., Heinrich, M. C., Raut, C. P., Bauer, S., Fletcher, J. A. 2017; 8: 14674

    Abstract

    KIT, PDGFRA, NF1 and SDH mutations are alternate initiating events, fostering hyperplasia in gastrointestinal stromal tumours (GISTs), and additional genetic alterations are required for progression to malignancy. The most frequent secondary alteration, demonstrated in ∼70% of GISTs, is chromosome 14q deletion. Here we report hemizygous or homozygous inactivating mutations of the chromosome 14q MAX gene in 16 of 76 GISTs (21%). We find MAX mutations in 17% and 50% of sporadic and NF1-syndromic GISTs, respectively, and we find loss of MAX protein expression in 48% and 90% of sporadic and NF1-syndromic GISTs, respectively, and in three of eight micro-GISTs, which are early GISTs. MAX genomic inactivation is associated with p16 silencing in the absence of p16 coding sequence deletion and MAX induction restores p16 expression and inhibits GIST proliferation. Hence, MAX inactivation is a common event in GIST progression, fostering cell cycle activity in early GISTs.

    View details for PubMedID 28270683

  • EWSR1-FLI1 Regulates PAX7 Expression in Ewing Sarcoma Charville, G., Wang, W., Hornick, J. L., van de Rijn, M., Lazar, A. J. NATURE PUBLISHING GROUP. 2017: 14A
  • Immune Check-Point Blockade as a Potential Therapeutic Strategy for Undifferentiated Malignancies Devereaux, K., Charville, G., Zhao, S., Cherry, A., van de Rijn, M., Natkunam, Y. NATURE PUBLISHING GROUP. 2017: 456A
  • EWSR1 fusion proteins mediate PAX7 expression in Ewing sarcoma. 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. n., Thomas, D. n., Patel, R. M., Hornick, J. L., van de Rijn, M. n., Lazar, A. J. 2017

    Abstract

    PAX7 is a paired-box transcription factor that is required for the developmental specification of adult skeletal muscle progenitors in mice. We previously demonstrated PAX7 expression as a marker of skeletal muscle differentiation in rhabdomyosarcoma. Here, using analyses of published whole-genome gene expression microarray data, we identify PAX7 as a gene with significantly increased expression in Ewing sarcoma in comparison to CIC-DUX4 round cell sarcoma. Analysis of PAX7 in a large cohort of 103 Ewing sarcoma cases by immunohistochemistry revealed expression in 99.0% of cases (102/103). PAX7 expression was noted in cases demonstrating three distinct Ewing sarcoma EWSR1 translocations involving FLI1, ERG, and NFATc2. No PAX7 expression was observed in any of 27 cases of CIC-DUX4 sarcoma by immunohistochemistry (0%; 0/27). Exploring the mechanism of PAX7 expression in Ewing sarcoma using curated RNA- and ChIP-sequencing data, we demonstrate that the EWSR1 fusion protein is required for PAX7 expression in Ewing sarcoma and identify a candidate EWSR1-FLI1-bound PAX7 enhancer that coincides with both a consensus GGAA repeat-containing binding site and a peak of regulatory H3K27 acetylation. Taken together, our findings provide mechanistic support for the utility of PAX7 immunohistochemistry in the diagnosis of Ewing sarcoma, while linking this sarcoma of uncertain histogenesis to a key transcriptional regulator of mammalian muscle progenitor cells.Modern Pathology advance online publication, 23 June 2017; doi:10.1038/modpathol.2017.49.

    View details for PubMedID 28643791

  • PAX7 Expression in Rhabdomyosarcoma, Related Soft Tissue Tumors, and Small Round Blue Cell Neoplasms. American journal of surgical pathology Charville, G. W., Varma, S., Forgó, E., Dumont, S. N., Zambrano, E., Trent, J. C., Lazar, A. J., van de Rijn, M. 2016; 40 (10): 1305-1315

    Abstract

    Rhabdomyosarcoma, the most common soft tissue malignancy of childhood, is a morphologically variable tumor defined by its phenotype of skeletal muscle differentiation. The diagnosis of rhabdomyosarcoma often relies in part on the identification of myogenic gene expression using immunohistochemical or molecular techniques. However, these techniques show imperfect sensitivity and specificity, particularly in scant tissue biopsies. Here, we expand the toolkit for rhabdomyosarcoma diagnosis by studying the expression of PAX7, a transcriptional regulator of mammalian muscle progenitor cells implicated in the pathogenesis of rhabdomyosarcoma. Immunohistochemical analysis of tissue microarrays using a monoclonal anti-PAX7 antibody was used to characterize PAX7 expression in 25 non-neoplastic tissues, 109 rhabdomyosarcomas, and 697 small round blue cell or other soft tissue tumors. Among non-neoplastic tissues, PAX7 was specifically expressed in adult muscle progenitor cells (satellite cells). In embryonal rhabdomyosarcoma, PAX7 expression was positive in 52 of 63 cases (83%), negative in 9 of 63 cases (14%), and focal in 2 of 63 cases (3%). PAX7-positive embryonal rhabdomyosarcoma cases included several showing focal or negative myogenin expression. PAX7 expression in alveolar rhabdomyosarcoma was positive in 6 of 31 cases (19%), negative in 14 of 31 cases (45%), and focal in 11 of 31 cases (36%). In addition, PAX7 was expressed in 5 of 7 pleomorphic rhabdomyosarcomas (71%) and 6 of 8 spindle cell rhabdomyosarcomas (75%). Among histologic mimics, only Ewing sarcoma showed PAX7 expression (7/7 cases, 100%). In contrast, expression of PAX7 was not seen in the large majority (688/690, 99.7%) of examined cases of other soft tissue tumors, small round blue cell neoplasms, and leukemias/lymphomas. In summary, immunohistochemical analysis of PAX7 expression may be a useful diagnostic tool in the assessment of skeletal muscle differentiation in human tumors.

    View details for DOI 10.1097/PAS.0000000000000717

    View details for PubMedID 27526298

  • Mapping a multiplexed zoo of mRNA expression DEVELOPMENT Choi, H. M., Calvert, C. R., Husain, N., Huss, D., Barsi, J. C., Deverman, B. E., Hunter, R. C., Kato, M., Lee, S. M., Abelin, A. C., Rosenthal, A. Z., Akbari, O. S., Li, Y., Hay, B. A., Sternberg, P. W., Patterson, P. H., Davidson, E. H., Mazmanian, S. K., Prober, D. A., van de Rijn, M., Leadbetter, J. R., Newman, D. K., Readhead, C., Bronner, M. E., Wold, B., Lansford, R., Sauka-Spengler, T., Fraser, S. E., Pierce, N. A. 2016; 143 (19): 3632-3637

    Abstract

    In situ hybridization methods are used across the biological sciences to map mRNA expression within intact specimens. Multiplexed experiments, in which multiple target mRNAs are mapped in a single sample, are essential for studying regulatory interactions, but remain cumbersome in most model organisms. Programmable in situ amplifiers based on the mechanism of hybridization chain reaction (HCR) overcome this longstanding challenge by operating independently within a sample, enabling multiplexed experiments to be performed with an experimental timeline independent of the number of target mRNAs. To assist biologists working across a broad spectrum of organisms, we demonstrate multiplexed in situ HCR in diverse imaging settings: bacteria, whole-mount nematode larvae, whole-mount fruit fly embryos, whole-mount sea urchin embryos, whole-mount zebrafish larvae, whole-mount chicken embryos, whole-mount mouse embryos and formalin-fixed paraffin-embedded human tissue sections. In addition to straightforward multiplexing, in situ HCR enables deep sample penetration, high contrast and subcellular resolution, providing an incisive tool for the study of interlaced and overlapping expression patterns, with implications for research communities across the biological sciences.

    View details for DOI 10.1242/dev.140137

    View details for PubMedID 27702788

  • CD47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer JOURNAL OF CLINICAL INVESTIGATION Weiskopf, K., Jahchan, N. S., Schnorr, P. J., Cristea, S., Ring, A. M., Maute, R. L., Volkmer, A. K., Volkmer, J., Liu, J., Lim, J. S., Yang, D., Seitz, G., Thuyen Nguyen, T., Wu, D., Jude, K., Guerston, H., Barkal, A., Trapani, F., George, J., Poirier, J. T., Gardner, E. E., Miles, L. A., de Stanchina, E., Lofgren, S. M., Vogel, H., Winslow, M. M., Dive, C., Thomas, R. K., Rudin, C. M., van de Rijn, M., Majeti, R., Garcia, K. C., Weissman, I. L., Sage, J. 2016; 126 (7): 2610-2620

    Abstract

    Small-cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer with limited treatment options. CD47 is a cell-surface molecule that promotes immune evasion by engaging signal-regulatory protein alpha (SIRPα), which serves as an inhibitory receptor on macrophages. Here, we found that CD47 is highly expressed on the surface of human SCLC cells; therefore, we investigated CD47-blocking immunotherapies as a potential approach for SCLC treatment. Disruption of the interaction of CD47 with SIRPα using anti-CD47 antibodies induced macrophage-mediated phagocytosis of human SCLC patient cells in culture. In a murine model, administration of CD47-blocking antibodies or targeted inactivation of the Cd47 gene markedly inhibited SCLC tumor growth. Furthermore, using comprehensive antibody arrays, we identified several possible therapeutic targets on the surface of SCLC cells. Antibodies to these targets, including CD56/neural cell adhesion molecule (NCAM), promoted phagocytosis in human SCLC cell lines that was enhanced when combined with CD47-blocking therapies. In light of recent clinical trials for CD47-blocking therapies in cancer treatment, these findings identify disruption of the CD47/SIRPα axis as a potential immunotherapeutic strategy for SCLC. This approach could enable personalized immunotherapeutic regimens in patients with SCLC and other cancers.

    View details for DOI 10.1172/JCI81603

    View details for Web of Science ID 000379094800024

    View details for PubMedID 27294525

    View details for PubMedCentralID PMC4922696

  • Loss of H3K27 tri-methylation is a diagnostic marker for malignant peripheral nerve sheath tumors and an indicator for an inferior survival MODERN PATHOLOGY Cleven, A. H., Al Sannaa, G. A., Briaire-de Bruijn, I., Ingram, D. R., van de Rijn, M., Rubin, B. P., de Vries, M. W., Watson, K. L., Torres, K. E., Wang, W., van Duinen, S. G., Hogendoorn, P. C., Lazar, A. J., Bovee, J. V. 2016; 29 (6): 582-590

    Abstract

    Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that can show overlapping features with benign neurofibromas as well as high-grade sarcomas. Additional diagnostic markers are needed to aid in this often challenging differential diagnosis. Recently mutations in two critical components of the polycomb repressor 2 (PRC2) complex, SUZ12 and EED, were reported to occur specifically in MPNSTs while such mutations are absent in neurofibromas, both in the setting of neurofibromatosis (NF) and sporadic cases. Furthermore, both SUZ12 and EED mutations in MPNSTs were associated with loss of H3K27 tri-methylation, a downstream target of PRC2. Therefore, we tested whether H3K27me3 immunohistochemistry is useful as a diagnostic and prognostic marker for MPNSTs. We performed H3K27me3 immunohistochemistry in 162 primary MPNSTs, 97 neurofibromas and 341 other tumors using tissue microarray. We observed loss of H3K27me3 in 34% (55/162) of all MPNSTs while expression was retained in all neurofibromas including atypical (n=8) and plexiform subtypes (n=24). Within other tumors we detected loss of H3K27me3 in only 7% (24/341). Surprisingly, 60% (9/15) of synovial sarcomas and 38% (3/8) of fibrosarcomatous dermatofibrosarcoma protuberans (DFSP) showed loss of H3K27 trimethylation. Only 1 out of 44 schwannomas showed loss of H3K27me3 and all 4 perineuriomas showed intact H3K27me3. Furthermore, MPNSTs with loss of H3K27 tri-methylation showed inferior survival compared with MPNSTs with intact H3K27 tri-methylation, which was validated in two independent cohorts. Our results indicate that H3K27me3 immunohistochemistry is useful as a diagnostic marker, in which loss of H3K27me3 favors MPNST above neurofibroma. However, H3K27me3 immunohistochemistry is not suitable to distinguish MPNST from its morphological mimicker synovial sarcoma or fibrosarcomatous DFSP. Since loss of H3K27 tri-methylation was related to poorer survival in MPNST, chromatin modification mediated by this specific histone seems to orchestrate more aggressive tumour biology.

    View details for DOI 10.1038/modpathol.2016.45

    View details for Web of Science ID 000377051600004

    View details for PubMedCentralID PMC4948583

  • Loss of H3K27 tri-methylation is a diagnostic marker for malignant peripheral nerve sheath tumors and an indicator for an inferior survival. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc Cleven, A. H., Sannaa, G. A., Briaire-de Bruijn, I., Ingram, D. R., van de Rijn, M., Rubin, B. P., de Vries, M. W., Watson, K. L., Torres, K. E., Wang, W. L., van Duinen, S. G., Hogendoorn, P. C., Lazar, A. J., Bovée, J. V. 2016; 29 (6): 582-90

    Abstract

    Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that can show overlapping features with benign neurofibromas as well as high-grade sarcomas. Additional diagnostic markers are needed to aid in this often challenging differential diagnosis. Recently mutations in two critical components of the polycomb repressor 2 (PRC2) complex, SUZ12 and EED, were reported to occur specifically in MPNSTs while such mutations are absent in neurofibromas, both in the setting of neurofibromatosis (NF) and sporadic cases. Furthermore, both SUZ12 and EED mutations in MPNSTs were associated with loss of H3K27 tri-methylation, a downstream target of PRC2. Therefore, we tested whether H3K27me3 immunohistochemistry is useful as a diagnostic and prognostic marker for MPNSTs. We performed H3K27me3 immunohistochemistry in 162 primary MPNSTs, 97 neurofibromas and 341 other tumors using tissue microarray. We observed loss of H3K27me3 in 34% (55/162) of all MPNSTs while expression was retained in all neurofibromas including atypical (n=8) and plexiform subtypes (n=24). Within other tumors we detected loss of H3K27me3 in only 7% (24/341). Surprisingly, 60% (9/15) of synovial sarcomas and 38% (3/8) of fibrosarcomatous dermatofibrosarcoma protuberans (DFSP) showed loss of H3K27 trimethylation. Only 1 out of 44 schwannomas showed loss of H3K27me3 and all 4 perineuriomas showed intact H3K27me3. Furthermore, MPNSTs with loss of H3K27 tri-methylation showed inferior survival compared with MPNSTs with intact H3K27 tri-methylation, which was validated in two independent cohorts. Our results indicate that H3K27me3 immunohistochemistry is useful as a diagnostic marker, in which loss of H3K27me3 favors MPNST above neurofibroma. However, H3K27me3 immunohistochemistry is not suitable to distinguish MPNST from its morphological mimicker synovial sarcoma or fibrosarcomatous DFSP. Since loss of H3K27 tri-methylation was related to poorer survival in MPNST, chromatin modification mediated by this specific histone seems to orchestrate more aggressive tumour biology.

    View details for DOI 10.1038/modpathol.2016.45

    View details for PubMedID 26990975

    View details for PubMedCentralID PMC4948583

  • 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

    Abstract

    Background The identification of high-risk stage II colon cancers is key to the selection of patients who require adjuvant treatment after surgery. Microarray-based multigene-expression signatures derived from stem cells and progenitor cells hold promise, but they are difficult to use in clinical practice. Methods We used a new bioinformatics approach to search for biomarkers of colon epithelial differentiation across gene-expression arrays and then ranked candidate genes according to the availability of clinical-grade diagnostic assays. With the use of subgroup analysis involving independent and retrospective cohorts of patients with stage II or stage III colon cancer, the top candidate gene was tested for its association with disease-free survival and a benefit from adjuvant chemotherapy. Results The transcription factor CDX2 ranked first in our screening test. A group of 87 of 2115 tumor samples (4.1%) lacked CDX2 expression. In the discovery data set, which included 466 patients, the rate of 5-year disease-free survival was lower among the 32 patients (6.9%) with CDX2-negative colon cancers than among the 434 (93.1%) with CDX2-positive colon cancers (hazard ratio for disease recurrence, 3.44; 95% confidence interval [CI], 1.60 to 7.38; P=0.002). In the validation data set, which included 314 patients, the rate of 5-year disease-free survival was lower among the 38 patients (12.1%) with CDX2 protein-negative colon cancers than among the 276 (87.9%) with CDX2 protein-positive colon cancers (hazard ratio, 2.42; 95% CI, 1.36 to 4.29; P=0.003). In both these groups, these findings were independent of the patient's age, sex, and tumor stage and grade. Among patients with stage II cancer, the difference in 5-year disease-free survival was significant both in the discovery data set (49% among 15 patients with CDX2-negative tumors vs. 87% among 191 patients with CDX2-positive tumors, P=0.003) and in the validation data set (51% among 15 patients with CDX2-negative tumors vs. 80% among 106 patients with CDX2-positive tumors, P=0.004). In a pooled database of all patient cohorts, the rate of 5-year disease-free survival was higher among 23 patients with stage II CDX2-negative tumors who were treated with adjuvant chemotherapy than among 25 who were not treated with adjuvant chemotherapy (91% vs. 56%, P=0.006). Conclusions Lack of CDX2 expression identified a subgroup of patients with high-risk stage II colon cancer who appeared to benefit from adjuvant chemotherapy. (Funded by the National Comprehensive Cancer Network, the National Institutes of Health, and others.).

    View details for DOI 10.1056/NEJMoa1506597

    View details for Web of Science ID 000368404800006

    View details for PubMedCentralID PMC4784450

  • CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. The New England journal of medicine Dalerba, P., Sahoo, D., Paik, S., Guo, X., Yothers, G., Song, N., Wilcox-Fogel, N., Forgó, 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): 211-22

    Abstract

    Background The identification of high-risk stage II colon cancers is key to the selection of patients who require adjuvant treatment after surgery. Microarray-based multigene-expression signatures derived from stem cells and progenitor cells hold promise, but they are difficult to use in clinical practice. Methods We used a new bioinformatics approach to search for biomarkers of colon epithelial differentiation across gene-expression arrays and then ranked candidate genes according to the availability of clinical-grade diagnostic assays. With the use of subgroup analysis involving independent and retrospective cohorts of patients with stage II or stage III colon cancer, the top candidate gene was tested for its association with disease-free survival and a benefit from adjuvant chemotherapy. Results The transcription factor CDX2 ranked first in our screening test. A group of 87 of 2115 tumor samples (4.1%) lacked CDX2 expression. In the discovery data set, which included 466 patients, the rate of 5-year disease-free survival was lower among the 32 patients (6.9%) with CDX2-negative colon cancers than among the 434 (93.1%) with CDX2-positive colon cancers (hazard ratio for disease recurrence, 3.44; 95% confidence interval [CI], 1.60 to 7.38; P=0.002). In the validation data set, which included 314 patients, the rate of 5-year disease-free survival was lower among the 38 patients (12.1%) with CDX2 protein-negative colon cancers than among the 276 (87.9%) with CDX2 protein-positive colon cancers (hazard ratio, 2.42; 95% CI, 1.36 to 4.29; P=0.003). In both these groups, these findings were independent of the patient's age, sex, and tumor stage and grade. Among patients with stage II cancer, the difference in 5-year disease-free survival was significant both in the discovery data set (49% among 15 patients with CDX2-negative tumors vs. 87% among 191 patients with CDX2-positive tumors, P=0.003) and in the validation data set (51% among 15 patients with CDX2-negative tumors vs. 80% among 106 patients with CDX2-positive tumors, P=0.004). In a pooled database of all patient cohorts, the rate of 5-year disease-free survival was higher among 23 patients with stage II CDX2-negative tumors who were treated with adjuvant chemotherapy than among 25 who were not treated with adjuvant chemotherapy (91% vs. 56%, P=0.006). Conclusions Lack of CDX2 expression identified a subgroup of patients with high-risk stage II colon cancer who appeared to benefit from adjuvant chemotherapy. (Funded by the National Comprehensive Cancer Network, the National Institutes of Health, and others.).

    View details for DOI 10.1056/NEJMoa1506597

    View details for PubMedID 26789870

    View details for PubMedCentralID PMC4784450

  • 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

    Abstract

    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

    Abstract

    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

  • 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., De Rijn, M. V., Quake, S. R., Clarke, M. F., Rothenberg, M. E. 2015; 149 (3): 705-?

    Abstract

    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 Web of Science ID 000360269800039

    View details for PubMedCentralID PMC4550533

  • 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

    Abstract

    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

  • 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

    Abstract

    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; ClinicalTrials.gov number, NCT01004861.).

    View details for DOI 10.1056/NEJMoa1411366

    View details for Web of Science ID 000358662200006

  • Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor. The 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): 428-37

    Abstract

    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; ClinicalTrials.gov number, NCT01004861.).

    View details for DOI 10.1056/NEJMoa1411366

    View details for PubMedID 26222558

  • 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

    Abstract

    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 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

    Abstract

    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

    View details for PubMedCentralID PMC4248015

  • ROR2 Is a Highly Expressed Biomarker and Potential Therapeutic Target in Wilms Tumor Hoffinann, J., Varma, S., Robison, P., Espinoza, I., Van de Rijn, M. NATURE PUBLISHING GROUP. 2015: 468A
  • ROR2 Is a Highly Expressed Biomarker and Potential Therapeutic Target in Wilms Tumor Hoffmann, J., Varma, S., Robison, P., Espinoza, I., Van de Rijn, M. NATURE PUBLISHING GROUP. 2015: 468A
  • 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

    Abstract

    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 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

    Abstract

    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

    Abstract

    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)

    Abstract

    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-?

    Abstract

    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

  • Dystrophin Is a tumor suppressor in human cancers with myogenic programs Wang, Y., Marino-Enriquez, A., Bennett, R., Zhu, M., Eilers, G., Antonescu, C., Fletche, C., Raut, C., van de Rijn, M., Kunkel, L., Demetri, G., Fletcher, J. AMER ASSOC CANCER RESEARCH. 2014
  • 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

    Abstract

    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

    View details for PubMedCentralID PMC4153008

  • 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

    Abstract

    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

    Abstract

    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 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

    Abstract

    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 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

    Abstract

    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

    Abstract

    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

    Abstract

    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 Web of Science ID 000321291700055

  • 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

    Abstract

    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. P., Mühlenberg, T., Weissman, I. L., van de Rijn, M. 2013; 2 (6): e24452

    Abstract

    Acquired resistance to imatinib is a significant problem for the clinical management of gastrointestinal stromal tumor (GIST) patients, and second-line small molecules have shown limited efficacy in this setting. We have recently demonstrated that a monoclonal antibody targeting KIT could potentially bypass imatinib resistance in preclinical models of GIST.

    View details for DOI 10.4161/onci.24452

    View details for PubMedID 23894705

    View details for PubMedCentralID PMC3716740

  • 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)

    Abstract

    Acquired resistance to imatinib is a significant problem for the clinical management of gastrointestinal stromal tumor (GIST) patients, and second-line small molecules have shown limited efficacy in this setting. We have recently demonstrated that a monoclonal antibody targeting KIT could potentially bypass imatinib resistance in preclinical models of GIST.

    View details for DOI 10.4161/onci.24452

    View details for Web of Science ID 000322060900007

    View details for PubMedCentralID PMC3716740

  • 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)

    Abstract

    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

    View details for PubMedCentralID PMC3663836

  • 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)

    Abstract

    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

  • 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

    Abstract

    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 PubMedID 23382202

  • 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

    Abstract

    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

  • 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
  • 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
  • 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)

    Abstract

    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

    Abstract

    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 PubMedID 23112155

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

    Abstract

    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

    View details for PubMedCentralID PMC3494646

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

    Abstract

    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 PubMedID 23170280

    View details for PubMedCentralID PMC3494646

Publications

2018

Fernandez-Pol S, van de Rijn M, Natkunam Y, Charville GW. Immunohistochemistry for PAX7 is a useful confirmatory marker for Ewing sarcoma in decalcified bone marrow core biopsy specimens. Virchows Arch. 2018 Jul 17. doi: 10.1007/s00428-018-2410-5. PubMed PDF

Zhang W, Bouchard G , Yu A, Shafiq M, Jamali M, Shrager JB, Ayers K, Bakr S, Gentles AJ, Diehn M, Quon A, West RB, Nair V, van de Rijn , Napel S, Plevritis SK. GFPT2-expressing cancer-associated fibroblasts mediate metabolic reprogramming in human lung adenocarcinoma.Cancer Res. 2018 May 14. pii: canres.2928.2017. doi: 10.1158/0008-5472.CAN-17-2928. PubMed PDF

Afghahi A, Purington N, Han SS, Desai M, Pierson E, Mathur MB, Seto T, Thompson CA, Rigdon J, Telli ML, Badve SS, Curtis C, West RB, Horst K, Gomez SL, Ford JM, Sledge GW, Kurian AW. Higher Absolute Lymphocyte Counts Predict Lower Mortality from Early-Stage Triple-Negative Breast Cancer. Clin Cancer Res. 2018 Mar 26. pii: clincanres.1323.2017. doi: 10.1158/1078-0432.CCR-17-1323. PubMed PDF

Przybyl J, Kidzinski L, Hastie T, Debiec-Rychter M, Nusse R, van de Rijn M. Gene expression profiling of low-grade endometrial stromal sarcoma indicates fusion protein-mediated activation of the Wnt signaling pathway. Gynecol Oncol. 2018 Mar 12. pii: S0090-8258(18)30177-X. doi: 10.1016/j.ygyno.2018.03.007. PubMed PDF

Hayes MN, McCarthy K, Jin A, Oliveira ML, Iyer S, Garcia SP, Sindiri S, Gryder B, Motala Z, Nielsen GP, Borg JP, van de Rijn M, Malkin D, Khan J, Ignatius MS, Langenau DM. Vangl2/RhoA Signaling Pathway Regulates Stem Cell Self-Renewal Programs and Growth in Rhabdomyosarcoma. Cell Stem Cell. 2018 Mar 1;22(3):414-427.e6. doi: 10.1016/j.stem.2018.02.002. PubMed PDF

Joanna Przybyl, Jacob J. Chabon, Lien Spans, Kristen N. Ganjoo, Sujay Vennam, Aaron M. Newman, Erna Forgó, Sushama Varma, Shirley Zhu , Maria Debiec-Rychter, Ash A. Alizadeh, Maximilian Diehn, Matt van de Rijn. Combination approach for detecting different types of alterations in circulating tumor DNA in leiomyosarcoma. Clin Cancer Res. 2018 Feb 20. pii: clincanres.3704.2017. doi: 10.1158/1078-0432.CCR-17-3704. PubMed PDF

2017

Cancer Genome Atlas Research Network. National Cancer Institute at NIH.Collaborators (264) Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell. 2017 Nov 2;171(4):950-965.e28. doi: 10.1016/j PubMed PDF

Amanatullah DF, Tamaresis JS, Chu P, Bachmann MH, Hoang NM, Collyar D, Mayer AT, West RB, Maloney WJ, Contag CH, King BL. Local estrogen axis in the human bone microenvironment regulates estrogen receptor-positive breast cancer cells. Breast Cancer Res. 2017 Nov 15;19(1):121. doi: 10.1186/s13058-017-0910-x. PubMed PDF

Y.C.KO, C.ZHU, S.ZHU, S.VENNAMR, C.JORDANJ, POLLACK, R.WEST GENE EXPRESSION PROFILE OF AMELOBLASTOMA Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology. Volume 124, Issue 3, September 2017, Page e204. PDF

Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS3, Liu CL, Zhou L, Scherer F, Kurtz DM, Say C, Carter JN, Merriott DJ, Dudley JC, Binkley MS, Modlin L, Padda SK, Gensheimer MF, West RB, Shrager JB, Neal JW, Wakelee HA, Loo BW, Alizadeh A4, Diehn M. Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling. Cancer Discov. 2017 Sep 12. pii: CD-17-0716. doi: 10.1158/2159-8290.CD-17-0716. PubMed PDF

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou 4, Sidow A. Genome-wide reconstruction of complex structural variants using read clouds. Nat Methods. 2017 Jul 17. doi: 10.1038/nmeth.4366. PubMed PDF

Charville GW, Wang WL, Ingram DR, Roy A, Thomas D, Patel RM, Hornick JL, van de Rijn M, Lazar AJ. EWSR1 fusion proteins mediate PAX7 expression in Ewing sarcoma. Mod Pathol. 2017 Jun 23. doi: 10.1038/modpathol.2017.49. PubMed PDF

Przybyl J, Kowalewska M, Quattrone A, Dewaele B, Vanspauwen V, Varma S, Vennam , Newman AM, Swierniak M, Bakuła-Zalewska E, Siedlecki JA, Bidzinski M, Cools J, van de Rijn M, Debiec-Rychter M. Macrophage infiltration and genetic landscape of undifferentiated uterine sarcomas. JCI Insight. 2017 Jun 2;2(11). pii: 94033. doi: 10.1172/jci.insight.94033. PubMed PDF

Schaefer IM, Wang Y, Liang CW, Bahri N, Quattrone A, Doyle L, Mariño-Enríquez A, Lauria A, Zhu M, Debiec-Rychter M, Grunewald S, Hechtman JF, Dufresne A, Antonescu CR, Beadling C, Sicinska ET, van de Rijn M, Demetri GD, Ladanyi M, Corless CL, Heinrich MC, Raut CP, Bauer S, Fletcher JA. MAX inactivation is an early event in GIST development that regulates p16 and cell proliferation. Nat Commun. 2017 Mar 8;8:14674. doi: 10.1038/ncomms14674.  PubMed   PDF

Ballard M, Jalikis F, Krings G, Schmidt RA, Chen YY, Rendi MH, Dintzis SM, Jensen KC,, West RB, Sibley RK, Troxell ML, Allison KH. 'Non-classical' HER2 FISH results in breast cancer: a multi-institutional study.  Mod Pathol. 2017 Feb;30(2):227-235. doi: 10.1038/modpathol.2016.175.  PubMed   PDF

Barasch N, Gong X, Kwei KA, Varma S, Biscocho J, Qu K, Xiao N, Lipsick JS, Pelham RJ, West RB, Pollack JR.. Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma.   PLoS One. 2017 Feb 17; 12(2): e0171265.  PubMed   PDF

Jeong Y, Hoang NT, Lovejoy A, Stehr H, Newman AM, Gentles AJ, Kong W, Truong D, Martin S, Chaudhuri A, Heiser D, Zhou L, Say C, Carter JN, Hiniker SM, Loo BW Jr, West RB, Beachy P, Alizadeh AA, Diehn M. . Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance.   Cancer Discov. 2017 Jan;7(1):86-101. doi: 10.1158/2159-8290.CD-16-0127. PubMed   PDF

2016

Brooks JD, Wei W, Pollack JR, West RB, Shin JH, Sunwoo JB, Hawley SJ, Auman H, Newcomb LF, Simko J, Hurtado-Coll A, Troyer DA, Carroll PR, Gleave ME, Lin DW, Nelson PS, Thompson IM, True LD, McKenney JK, Feng Z, Fazli L. Loss of Expression of AZGP1 Is Associated With Worse Clinical Outcomes in a Multi-Institutional Radical Prostatectomy Cohort. Prostate. 2016 Nov;76(15):1409-19. doi: 10.1002/pros.23225. Epub 2016 Jun 21. PubMed  PDF

Choi HM, Calvert CR, Husain N, Huss D, Barsi JC, Deverman BE, Hunter RC, Kato M, Lee SM, Abelin AC, Rosenthal AZ, Akbari OS, Li Y, Hay BA, Sternberg PW, Patterson PH1, Davidson EH, Mazmanian SK, Prober DA, van de Rijn M, Leadbetter JR, Newman DK1, Readhead C, Bronner ME, Wold B, Lansford R, Sauka-Spengler T, Fraser SE, Pierce NA. Mapping a multiplexed zoo of mRNA expression.   Development. 2016 Oct 1;143(19):3632-3637. PubMed   PDF

Charville GW, Varma S, Forgó E, Dumont SN, Zambrano E, Trent JC, Lazar AJ, van de Rijn M. PAX7 Expression in Rhabdomyosarcoma, Related Soft Tissue Tumors, and Small Round Blue Cell Neoplasms. Am J Surg Pathol. 2016 Oct;40(10):1305-15. doi: 10.109  PubMed   PDF

Tan S, Pollack JR, Kaplan MJ, Colevas AD, West RB. BRAF inhibitor therapy of primary ameloblastoma.   Oral Surg Oral Med Oral Pathol Oral Radiol. 2016 Oct;122(4):518-9. doi: 10.1016/j.oooo.2016.05.017.  PubMed PDF

Weiskopf K, Jahchan NS, Schnorr PJ, Cristea S, Ring AM, Maute RL, Volkmer AK, Volkmer JP, Liu J, Lim JS, Yang D, Seitz G, Nguyen T, Wu D, Jude K, Guerston H, Barkal A, Trapani F, George J, Poirier JT, Gardner EE, Miles LA, de Stanchina E, Lofgren SM, Vogel H, Winslow MM, Dive C, Thomas RK, Rudin CM, van de Rijn M, Majeti R, Garcia KC, Weissman IL, Sage J.  CD47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer. J Clin Invest. 2016 Jun 13. pii: 81603. doi: 10.1172/JCI81603 PubMed   PDF 

Newman AM, Lovejoy AF, Klass DM, Kurtz DM, Chabon JJ, Scherer F, Stehr H, Liu CL, Bratman SV, Say C, Zhou L, Carter JN, West RB, Sledge GW Jr, Shrager JB, Loo BW Jr, Neal JW, Wakelee HA, Diehn M, Alizadeh AA.  Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol. 2016 May;34(5):547-55. doi: 10.1038/nbt.3520. Epub 2016 Mar 28. PubMed   PDF

Cleven AH, Sannaa GA, Briaire-de Bruijn I, Ingram DR, van de Rijn M, Rubin BP, de Vries MW, Watson KL, Torres KE, Wang WL, van Duinen SG, Hogendoorn PC, Lazar AJ, Bovée JV. Loss of H3K27 tri-methylation is a diagnostic marker for malignant peripheral nerve sheath tumors and an indicator for an inferior survival. Mod Pathol. 2016 Mar 18. doi: 10.1038/modpathol.2016.45. PubMed   PDF 

Tan S, Pollack JR, Kaplan MJ, Colevas AD, West RB. BRAF inhibitor treatment of primary BRAF-mutant ameloblastoma with pathologic assessment of response.   Oral Surg Oral Med Oral Pathol Oral Radiol. 2016 Feb 23. pii: S2212-4403(16)00064-X.  PubMed    PDF 

Dalerba P, Sahoo D, Paik S, Guo X, Yothers G, Song N, Wilcox-Fogel N, Forgó E, Rajendran PS, Miranda SP, Hisamori S, Hutchison J, Kalisky T, Qian D, Wolmark N, Fisher GA, van de Rijn M, Clarke MF. CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer.   N Engl J Med. 2016 Jan 21;374(3):211-22. doi: 10.1056/NEJMoa1506597.  PubMed.   PDF

2015

Bishara A, Liu Y, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S. Read clouds uncover variation in complex regions of the human genome. Genome Res. 2015 Oct;25(10):1570-80. doi: 10.1101/gr.191189.115. Epub 2015 Aug 18. PubMed PDF 

Gentles AJ, Bratman SV, Lee LJ, Harris JP, Feng W, Nair RV, Shultz DB, Nair VS, Hoang CD, West RB, Plevritis SK, Alizadeh AA, Diehn M.Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer.  J Natl Cancer Inst. 2015 Aug 18;107(10). pii: djv211. doi: 10.1093/jnci/djv211. PubMed   PDF 

Afghahi A, Forgó E, Mitani AA, Desai M, Varma S, Seto T, Rigdon J, Jensen KC, Troxell ML, Gomez SL, Das AK, Beck AH, Kurian AW, West RB.  Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer. Breast Cancer Res. 2015 Aug 13;17:108. doi: 10.1186/s13058-015-0623-y.  PubMed   PDF 

Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, Nair VS, Xu Y, Khuong A, Hoang CD, Diehn M, West RB, Plevritis SK, Alizadeh AA. The prognostic landscape of genes and infiltrating immune cells across human cancers.  Nat Med. 2015 Aug;21(8):938-45. doi: 10.1038/nm.3909. PubMed   PDF 

Tap WD, Wainberg ZA, Anthony SP, Ibrahim PN, Zhang C, Healey JH, Chmielowski B, Staddon AP, Cohn AL, Shapiro GI, Keedy VL, Singh AS, Puzanov I, Kwak EL, Wagner AJ, Von Hoff DD, Weiss GJ, Ramanathan RK, Zhang J, Habets G, Zhang Y, Burton EA, Visor G, Sanftner L, Severson P, Nguyen H, Kim MJ, Marimuthu A, Tsang G, Shellooe R, Gee C, West BL, Hirth P, Nolop K, van de Rijn M, Hsu HH, Peterfy C, Lin PS, Tong-Starksen S, Bollag G. Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor.   N Engl J Med. 2015 Jul 30;373(5):428-37. doi: 10.1056/NEJMoa1411366. PubMed .  PDF

Riordan DP, Varma S, West RB, Brown PO. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling. 
PLoS One. 2015 Jul 15;10(7):e0128975. doi: 10.1371/journal.pone.0128975.  PubMed . PDF  

Chen EC, Karl TA, Kalisky T, Gupta SK, O'Brien CA, Longacre TA, van de Rijn M, Quake SR, Clarke MF, Rothenberg ME.  KIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and is Upregulated in a Subset of Human Colon Cancers.  Gastroenterology. 2015 May 27. pii: S0016-5085(15)00769-6. doi: 10.1053/j.gastro.2015.05.042. [Epub ahead of print]  PubMed   PDF

Popic V, Salari R, Hajirasouliha I, Kashef-Haghighi D, West RB, Batzoglou S. Fast and scalable inference of multi-sample cancer lineagesGenome Biol. 2015 May 6;16:91. doi: 10.1186/s13059-015-0647-8. PubMed   PDF 

McClary AC1, West RB, McClary AC, Pollack JR, Fischbein NJ, Holsinger CF, Sunwoo J, Colevas AD, Sirjani D. Ameloblastoma: a clinical review and trends in management.  Eur Arch Otorhinolaryngol. 2015 Apr 30. [Epub ahead of print]  PubMed  PDF

Weng Z, Spies N, Zhu SX, Newburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB. Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia. Genome Med. 2015 Apr 9;7(1):28. doi: 10.1186/s13073-015-0146-2. eCollection 2015.  PubMed PDF

Guo X, Jo VY, Mills A, Zhu S, Lee CH, Espinosa I, Nucci MR, Varma S, Forgo E, Hastie T, Anderson S, Ganjoo K, Beck AH, West R, Fletcher C, van de Rijn M.  Clinically relevant molecular subtypes in leiomyosarcoma.  Clin Cancer Res. 2015 Apr 20. pii: clincanres.3141.2014. [Epub ahead of print]  PubMed   PDF

Ang D, Ballard M, Beadling C, Warrick A, Schilling A, O'Gara R, Pukay M, Neff TL, West RB, Corless CL, Troxell ML. Novel mutations in neuroendocrine carcinoma of the breast: possible therapeutic targets.   Appl Immunohistochem Mol Morphol. 2015 Feb;23(2):97-103. doi: 10.1097/PDM.0b013e3182a40fd1. PubMed   PDF

Riess JW, West R, Dean M, Klimowicz AC, Neal JW, Hoang C, Wakelee HA  GLI1, CTNNB1 and NOTCH1 protein expression in a thymic epithelial malignancy tissue microarray. Anticancer Res. 2015 Feb;35(2):669-76.  PubMed   PDF

Liang Y, Padda SK, Riess JW, West RB, Neal JW, Wakelee HA.  Pemetrexed in patients with thymic malignancies previously treated with chemotherapy. Lung Cancer. 2015 Jan;87(1):34-8. doi: 10.1016/j.lungcan.2014.11.006. Epub 2014 Nov 15.  PubMed   PDF

2014

Marques Howarth M, Simpson D, Ngok SP, Nieves B, Chen R, Siprashvili Z, Vaka D, Breese MR, Crompton BD, Alexe G, Hawkins DS, Jacobson D, Brunner AL, West R, Mora J, Stegmaier K, Khavari P, Sweet-Cordero EA. Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis.  J Clin Invest. 2014 Nov 17. pii: 72124. doi: 10.1172/JCI72124  PubMed   PDF

Padda SK, Riess JW, Schwartz EJ, Tian L, Kohrt HE, Neal JW, West RB, Wakelee HA. Diffuse High Intensity PD-L1 Staining in Thymic Epithelial Tumors.  J Thorac Oncol. 2014 Nov 14.  PubMed   PDF

Scheeren FA, Kuo AH, van Weele LJ, Cai S, Glykofridis I, Sikandar SS, Zabala M, Qian D, Lam JS, Johnston D, Volkmer JP, Sahoo D, van de Rijn M, Dirbas FM, Somlo G6, Kalisky T, Rothenberg ME, Quake SR, Clarke MF.  A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis.  Nat Cell Biol. 2014 Nov 2. doi: 10.1038/ncb3058  PubMed   PDF

Pan Y, Volkmer JP, Mach KE, Rouse RV, Liu JJ, Sahoo D, Chang TC, Metzner TJ, Kang L, van de Rijn M, Skinner EC, Gambhir SS, Weissman IL, Liao JC.  Endoscopic molecular imaging of human bladder cancer using a CD47 antibody. Sci Transl Med. 2014 Oct 29;6(260):260ra148. doi: 10.1126/scitranslmed.3009457. Epub 2014 Oct 29.  PubMed   PDF

Keire PA, Bressler SL, Lemire JM, Edris B, Rubin BP, Rahmani M, McManus BM, van de Rijn M, Wight TN. A role for versican in the development of leiomyosarcoma. J Biol Chem. 2014 Oct 15. pii: jbc.M114.607168  PubMed   PDF

Carvalho FM, Bacchi LM, Pincerato KM, Van de Rijn M, Bacchi CE. Geographic differences in the distribution of molecular subtypes of breast cancer in Brazil. BMC Womens Health. 2014 Aug 29;14:102. doi: 10.1186/1472-6874-14-102. PubMed  PDF

Demicco EG, Boland GM, Brewer Savannah KJ, Lusby K, Young ED, Ingram D, Watson KL, Bailey M, Guo X, Hornick JL, van de Rijn M, Wang WL, Torres KE, Lev D, Lazar AJ. Progressive Loss Of Myogenic Differentiation In Leiomyosarcoma Has Prognostic Value. Histopathology. 2014 May 30. doi: 10.1111/his.12466. [Epub ahead of print]  PubMed  PDF

Brunner AL, Li J, Guo X, Sweeney RT, Varma S, Zhu SX, Li R, Tibshirani R, West RB.A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions. Genome Biol. 2014 May 23;15(5):R71. PubMed  PDF

Sweeney RT, McClary AC, Myers BR, Biscocho J, Neahring L, Kwei KA, Qu K, Gong X, Ng T, Jones CD, Varma S, Odegaard JI, Sugiyama T, Koyota S, Rubin BP, Troxell ML, Pelham RJ, Zehnder JL, Beachy PA, Pollack JR, West RB. Identification of recurrent SMO and BRAF mutations in ameloblastomas.  Nat Genet. 2014 May 25. doi: 10.1038/ng.2986. PubMed   PDF

Wang Y, Marino-Enriquez A, Bennett RR, Zhu M, Shen Y, Eilers G, Lee JC, Henze J, Fletcher BS, Gu Z, Fox EA, Antonescu CR, Fletcher CD, Guo X, Raut CP, Demetri GD, van de Rijn M, Ordog T, Kunkel LM, Fletcher JA. Dystrophin is a tumor suppressor in human cancers with myogenic programs.  Nat Genet. 2014 Jun;46(6):601-6. doi: 10.1038/ng.2974. Epub 2014 May 4. PubMed  PDF

Nair VS, Gevaert O, Davidzon G, Plevritis SK, West R.  NF-κB protein expression associates with 18F-FDG PET tumor uptake in non-small cell lung cancer: A radiogenomics validation study to understand tumor metabolism.  Lung Cancer.   2014 Feb;83(2):189-96. doi: 10.1016/j.lungcan.2013.11.001. Epub 2013 Nov 13..  PubMed   PDF

Last update June 20, 2016