Publications

2020

Cyrta J, Augspach A, de Filippo MR, Prandi D, Thienger P, Benelli M, Cooley V, Bareja R, Wilkes D, Chae S-S, Cavaliere P, Dephure N, Uldry A-C, Lagache SB, Roma L, Cohen S, Jaquet M, Brandt LP, Alshalalfa M, Sboner A, Feng F, Wang S, Beltran H, Lotan T, Spahn M, Kruithof-de Julio M, Chen Y, Ballman KV, Demichelis F, Piscuoglio S, Rubin MA*. Role of Specialized Composition of SWI/SNF Complexes in Prostate Cancer Lineage Plasticity. Nat Commun. 2020; 11: 5549. https://doi.org/10.1038/s41467-020-19328-1 *Corresponding Author

Arriaga  J, Panja S, Alshalalfa M, Zhao J, Zou M, Giacobbe A, Madubata CJ, Kim JY, Rodriguez A, Coleman I, Virk RK, Hibshoosh H, Ertunc  O, Ozbek B, Fountain J, Karnes RJ, Luo J, Antonarakis ES, Nelson PS, Feng  FY, Rubin MA, De Marzo AM, Rabadan R, Sims PA, Mitrofanova  A, Abate-Shen C. A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nat Cancer. 2020; https://doi.org/10.1038/s43018-020-00125-0

Bailey MH, Meyerson WU, Dursi LJ; Wang L, Dong G, Liang W, Weerasinghe A, Li S, Kelso S, MC3 Working Group, PCAWG novel somatic mutation calling methods working group,  Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding Li, PCAWG Consortium. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020; 11: 4748. https://doi.org/10.1038/s41467-020-18151-y

Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium. Sex differences in oncogenic mutational processes. Nat Commun. 2020;11: 4330. https://doi.org/10.1038/s41467-020-17359-2

Aurélie Auguste, Félix Blanc-Durand, Marc Deloger, Audrey Le Formal, Rohan Bareja, David C. Wilkes, Catherine Richon, Béatrice Brunn, Olivier Caron, Mojgan Devouassoux-Shisheboran, Sébastien Gouy, Philippe Morice, Enrica Bentivegna, Andrea Sboner, Olivier Elemento, Mark A. Rubin, Patricia Pautier, Catherine Genestie, Joanna Cyrta, Alexandra Leary. Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis. Cells. 2020 Jun 19; 9(6), 1496; https://doi.org/10.3390/cells9061496

Pisapia DJ, Ohara K, Bareja R, Wilkes DC, Hissong E, Croyle JA, Kim JH, Saab J, MacDonald TY, Beg S, O'Reilly C, Kudman S; Rubin MA, Elemento O, Sboner A, Greenfield J, Mosquera JM. Fusions involving BCOR and CREBBP are rare events in infiltrating glioma. Acta Neuropathol Commun 2020 Jun 3;8(1):80. https://doi.org/10.1186/s40478-020-00951-4

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium [1341 authors]. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93. https://doi.org/10.1038/s41586-020-1969-6

Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell P, López-Bigas N, PCAWG Drivers and Functional Interpretation Working Group [128 authors], PCAWG Structural Variation Working Group [73 authors], Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G , PCAWG Consortium. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 Feb;578(7793):102-111. https://doi.org/10.1038/s41586-020-1965-x

Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, PCAWG Drivers and Functional Interpretation Working Group [103 authors], Raphael BJ, PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications. 2020 February 05; 11(1):729. https://doi.org/10.1038/s41467-020-14367-0

Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, PCAWG Drivers and Functional Interpretation Working Group [130 authors], Johnson R, PCAWG Consortium. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology. 2020 February 05; 3(1):56. https://doi.org/10.1038/s42003-019-0741-7

Shuai S, PCAWG Drivers and Functional Interpretation Working Group [128 authors], Gallinger S, Stein L, PCAWG Consortium. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications. 2020 February 05; 11(1):734. https://doi.org/10.1038/s41467-019-13929-1

Jiao W, Atwal G, Polak P, Karlic R, Cuppen E, PCAWG Tumor Subtypes and Clinical Translation Working Group [48 authors], Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD, PCAWG Consortium. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications. 2020 February 05; 11(1):728. https://doi.org/10.1038/s41467-019-13825-8

Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group [126 authors], Reimand J, PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. Nature Communications. 2020 February 05; 11(1):735. https://doi.org/10.1038/s41467-019-13983-9

Lotan TL, Tomlins SA, Bismar TA, Van der Kwast TH, Grignon D, Egevad L, Kristiansen G, Pritchard CC, Rubin MA, Bubendorf L. Report from the International Society of Urological Pathology (ISUP) Consultation Conference on Molecular Pathology of Urogenital Cancers: I. Molecular Biomarkers in Prostate Cancer. American Journal of Surgical Pathology. 2020 Feb 10. doi: 10.1097. DOI: 10.1097/pas.0000000000001450

2019

Beltran H, Oromendia C, Danila DC, Montgomery B, Hoimes C, Szmulewitz RZ, Vaishampayan U, Armstrong AJ, Stein M, Pinski J, et al. A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers. Clinical Cancer Reseach. 2019; 25(1):43-51. doi: 10.1158/1078-0432.CCR-18-1912

Skvortsova K, Masle-Farquhar E, Luu P-L, Song JZ, Qu W, Zotenko E, Gould CM, Du Q, Peters TJ, Colino-Sanguino Y, Pidsley R, Nair SS, Khoury A, Smith GC, Miosge LA, Reed JH, Kench JG, Rubin MA, Horvath L, Bogdanovic O, Lim SM, Polo JM, Goodnow CC, Stirzaker C, Clark SJ. DNA Hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation Patterns. Cancer Cell. 2019 Feb 11; 35(2):297-314.e298. https://doi.org/10.1016/j.ccell.2019.01.004

Karkampouna S, Grosjean J, Klima I, Genitsch V, Sboner A, K. Y. Ng C, De Filippo MR, Piscuoglio S, Spahn M, Rubin MA, Thalmann GN, Kruithof-De Julio M. Establishment of an androgen-sensitive patient derived xenograft model of prostate cancer. European Urology Supplements. 2019 March 1; 18(1):e1154. https://doi.org/10.1016/S1569-9056(19)30831-0

Lee RS, Zhang L, Berger A, Lawrence MG, Song J, Niranjan B, Davies RG, Lister NL, Sandhu SK, Rubin MA, Risbridger GP, Taylor RA, Rickman DS, Horvath LG, Daly RJ. Characterization of the ERG-regulated kinome in prostate cancer identifies TNIK as a potential therapeutic target. Neoplasia. 2019 April 01; 21(4):389-400. https://doi.org/10.1016/j.neo.2019.02.005

Abida W, Cyrta J, Heller G, Prandi D, Armenia J, Coleman I, Cieslik M, Benelli M, Robinson D, Van Allen EM, et al. Genomic correlates of clinical outcome in advanced prostate cancer. PNAS. 2019. doi: 10.1073/pnas.1902651116

Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EW, Chen Y, et al. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell. 2019; 35(4):603-617. doi: 10.1016/j.ccell.2019.03.001

Persi E, Prandi D, Wolf YI, Pozniak Y, Barnabas GD, Levanon K, Barshack I, Barbieri C, Gasperini P, Beltran H, Faltas BM, Rubin MA, Geiger T, Koonin EV, Demichelis F, Horn D. Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. PNAS. 2019 August 20, 116 (34) 16987-16996. https://doi.org/10.1073/pnas.1908790116

Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. PLOS Genetics. 2019 Aug 30; 15(8):e1007860. https://doi.org/10.1371/journal.pgen.1007860

2018

Aytes A, Giacobbe A, Mitrofanova A, Ruggero K, Cyrta J, Arriaga J, Palomero L, Farran-Matas S, Rubin MA, Shen MM, Califano A, Abate-Shen C. NSD2 is a conserved driver of metastatic prostate cancer progression. Nature Communications. 2018;9(1):5201. doi: 10.1038/s41467-018-07511-4

Boysen G, Rodrigues DN, Rescigno P, Seed G, Dolling D, Riisnaes R, Crespo M, Zafeiriou Z, Sumanasuriya S, Bianchini D, et al. SPOP-Mutated/CHD1-Deleted Lethal Prostate Cancer and Abiraterone Sensitivity. Clinical Cancer Research. 2018; 24(22):5585-5593. doi: 10.1158/1078-0432.CCR-18-0937

Nava Rodrigues D, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, et al. Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. The Journal of Clinical Investigation. 2018; 128(10):4441-4453. doi: 10.1172/JCI121924

Cotter K, Rubin MA; Sequence of events in prostate cancer Nature 2018 Aug 24, doi: 10.1038/d41586-018-06029-5

Hopkins BD, Pauli C, Du X, Wang DG, Li X, Wu D, Amadiume SC, Goncalves MD, Hodakoski C, Lundquist MR, Bareja R, Ma Y, Harris EM, Sboner A, Beltran H, Rubin MA, Mukherjee S, Cantley LC. Suppression of insulin feedback enhances the efficacy of PI3K inhibitors. Nature. 2018; 560(7719):499-503. doi: 10.1038/s41586-018-0343-4

Puca L, Bareja R, Prandi D, Shaw R, Benelli M, Karthaus WR, Hess J, Sigouros M, Donoghue A, Kossai M, et al. Patient derived organoids to model rare prostate cancer phenotypes. Nature Communications. 2018; 9(1):2404. doi: 10.1038/s41467-018-04495-z.

Triscott J, Rubin MA; Prostate Power Play: Does Pik3ca Accelerate Pten-Deficient Cancer Progression? Cancer Discovery June 2018. 8.6: 682-685. doi: 10.1158/2159-8290.CD-18-0369

Lundquist MR, Goncalves MD, Loughran RM, Possik E, Vijayaraghavan T, Yang A, Pauli C, Ravi A, Verma A, Yang Z, et al. Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy. Molecular Cell. 2018; 70(3):531-544.e9. doi: 10.1016/j.molcel.2018.03.037.

Mateo J, Cheng HH, Beltran H, Dolling D, Xu W, Pritchard CC, Mossop H, Rescigno P, Perez-Lopez R, Sailer V, Kolinsky M, Balasopoulou A, Bertan C, Nanus DM, Tagawa ST, Thorne H, Montgomery B, Carreira S, Sandhu S, Rubin MA, Nelson PS, de Bono JS. Clinical Outcome of Prostate Cancer Patients with Germline DNA Repair Mutations: Retrospective Analysis from an International Study. European Urology. 2018; 73(5):687-693. doi: 10.1016/j.eururo.2018.01.010

Demichelis F, Rubin MA; The Genomics of Prostate Cancer: A Historic Perspective Cold Spring Harb Perspect Med. 2018 Apr 30. pii: a034942. doi: 10.1101/cshperspect.a034942.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, et al. The Immune Landscape of Cancer. Immunity. 2018; 48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023

Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, et al. The long tail of oncogenic drivers in prostate cancer, Nat Genet. 2018 Apr 2. doi: 10.1038/s41588-018-0078-z.

Sailer V, Schiffman MH, Kossai M, Cyrta J, Beg S, Sullivan B, Pua BB, Lee KS, Talenfeld AD, Nanus DM, Tagawa ST, Robinson BD, Rao RA, Pauli C, Bareja R, Beltran LS, Sigaras A, Eng KW, Elemento O, Sboner A, Rubin MA, Beltran H, Mosquera JM. Bone biopsy protocol for advanced prostate cancer in the era of precision medicine. Cancer. 2018; 124(5):1008-1015. doi: 10.1002/cncr.31173

McNair C, Xu K, Mandigo AC, Benelli M, Leiby B, Rodrigues D, Lindberg J, Gronberg H, Crespo M, De Laere B, Dirix L, Visakorpi T, Li F, Feng FY, de Bono J, Demichelis F, Rubin MA, Brown M, Knudsen KE. Differential impact of RB status on E2F1 reprogramming in human cancer. The Journal of Clinical Investigation. 2018; 128(1):341-358. doi: 10.1172/JCI93566

Gillessen S, Attard G, Beer TM, Beltran H, Bossi A, Bristow R, Carver B, Castellano D, Chung BH, Clarke N, et al. Management of Patients with Advanced Prostate Cancer: The Report of the Advanced Prostate Cancer Consensus Conference APCCC 2017. European Urology. 2018; 73(2):178-211. doi: 10.1016/j.eururo.2017.06.002.

Shoag J, Liu D, Blattner M, Sboner A, Park K, Deonarine L, Robinson BD, Mosquera JM, Chen Y, Rubin MA, Barbieri CE. SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG. The Journal of Clinical Investigation. 2018; 128(1):381-386. doi: 10.1172/JCI96551

D'Alfonso TM, Subramaniyam S, Ginter PS, Mosquera JM, Croyle J, Liu YF, Rubin MA, Shin SJ. Characterization of CD34-deficient myofibroblastomas of the breast. The Breast Journal. 2018; 24(1):55-61. doi: 10.1111/tbj.12835

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