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

Publications

2016

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

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2015

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

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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

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