The van de Rijn & West Lab In The Department of Pathology

Publications

2018

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 V1, van de Rijn 9, Napel S1, 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

To the top of the list

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 lineages Genome 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

To the top of the list

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

To the top of the list

Footer Links: