Publications
All Chinnaiyan lab publications
Select Recent Publications:
Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gumus ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyo D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell. 2019 Oct 31;179(4):964-983.e31. doi: 10.1016/j.cell.2019.10.007. Erratum in: Cell. 2020 Jan 9;180(1):207. PubMed PMID: 31675502.
Kregel S, Malik R, Asangani IA, Wilder-Romans K, Rajendiran T, Xiao L, Vo JN, Soni T, Cieslik M, Fernadez-Salas E, Zhou B, Cao X, Speers C, Wang S, Chinnaiyan AM. Functional and Mechanistic Interrogation of BET Bromodomain Degraders for the Treatment of Metastatic Castration-resistant Prostate Cancer. Clin Cancer Res. 2019 Jul 1;25(13):4038-4048. doi: 10.1158/1078-0432.CCR-18-3776. Epub 2019 Mar 27. PubMed PMID: 30918020; PubMed Central PMCID: PMC6606381.
Parolia A, Cieslik M, Chu SC, Xiao L, Ouchi T, Zhang Y, Wang X, Vats P, Cao X, Pitchiaya S, Su F, Wang R, Feng FY, Wu YM, Lonigro RJ, Robinson DR, Chinnaiyan AM. Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer. Nature. 2019 Jul;571(7765):413-418. doi: 10.1038/s41586-019-1347-4. Epub 2019 Jun 26. PubMed PMID: 31243372; PubMed Central PMCID: PMC6661908.
Vo JN, Cieslik M, Zhang Y, Shukla S, Xiao L, Zhang Y, Wu YM, Dhanasekaran SM, Engelke CG, Cao X, Robinson DR, Nesvizhskii AI, Chinnaiyan AM. The Landscape of Circular RNA in Cancer. Cell. 2019 Feb 7;176(4):869-881.e13. doi: 10.1016/j.cell.2018.12.021. PubMed PMID: 30735636; PubMed Central PMCID: PMC6601354.
Wu YM, Cieslik M, Lonigro RJ, Vats P, Reimers MA, Cao X, Ning Y, Wang L, Kunju LP, de Sarkar N, Heath EI, Chou J, Feng FY, Nelson PS, de Bono JS, Zou W, Montgomery B, Alva A; PCF/SU2C International Prostate Cancer Dream Team, Robinson DR, Chinnaiyan AM. Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer. Cell. 2018 Jun 14;173(7):1770-1782.e14. doi: 10.1016/j.cell.2018.04.034. PubMed PMID: 29906450; PubMed Central PMCID: PMC6084431.
Zhang Y, Pitchiaya S, Cieslik M, Niknafs YS, Tien JC, Hosono Y, Iyer MK, Yazdani S, Subramaniam S, Shukla SK, Jiang X, Wang L, Liu TY, Uhl M, Gawronski AR, Qiao Y, Xiao L, Dhanasekaran SM, Juckette KM, Kunju LP, Cao X, Patel U, Batish M, Shukla GC, Paulsen MT, Ljungman M, Jiang H, Mehra R, Backofen R, Sahinalp CS, Freier SM, Watt AT, Guo S, Wei JT, Feng FY, Malik R, Chinnaiyan AM. Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. Nat Genet. 2018 Jun;50(6):814-824. doi: 10.1038/s41588-018-0120-1. Epub 2018 May 28. PubMed PMID: 29808028; PubMed Central PMCID: PMC5980762.
Hosono Y, Niknafs YS, Prensner JR, Iyer MK, Dhanasekaran SM, Mehra R, Pitchiaya S, Tien J, Escara-Wilke J, Poliakov A, Chu SC, Saleh S, Sankar K, Su F, Guo S, Qiao Y, Freier SM, Bui HH, Cao X, Malik R, Johnson TM, Beer DG, Feng FY, Zhou W, Chinnaiyan AM. Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. Cell. 2017 Dec 14;171(7):1559-1572.e20. doi: 10.1016/j.cell.2017.11.040. PubMed PMID: 29245011; PubMed Central PMCID: PMC5734106.
Robinson DR, Wu YM, Lonigro RJ, Vats P, Cobain E, Everett J, Cao X, Rabban E, Kumar-Sinha C, Raymond V, Schuetze S, Alva A, Siddiqui J, Chugh R, Worden F, Zalupski MM, Innis J, Mody RJ, Tomlins SA, Lucas D, Baker LH, Ramnath N, Schott AF, Hayes DF, Vijai J, Offit K, Stoffel EM, Roberts JS, Smith DC, Kunju LP, Talpaz M, Cieslik M, Chinnaiyan AM. Integrative clinical genomics of metastatic cancer. Nature. 2017 Aug 17;548(7667):297-303. doi: 10.1038/nature23306. Epub 2017 Aug 2. PubMed PMID: 28783718.
Wang X, Qiao Y, Asangani IA, Ateeq B, Poliakov A, Cieslik M, Pitchiaya S, Chakravarthi BVSK, Cao X, Jing X, Wang CX, Apel IJ, Wang R, Tien JC, Juckette KM, Yan W, Jiang H, Wang S, Varambally S, Chinnaiyan AM. Development of Peptidomimetic Inhibitors of the ERG Gene Fusion Product in Prostate Cancer. Cancer Cell. 2017 Jun 12;31(6):844-847. doi: 10.1016/j.ccell.2017.05.001. PubMed PMID: 28609659.
Shankar S, Pitchiaya S, Malik R, Kothari V, Hosono Y, Yocum AK, Gundlapalli H, White Y, Firestone A, Cao X, Dhanasekaran SM, Stuckey JA, Bollag G, Shannon K, Walter NG, Kumar-Sinha C, Chinnaiyan AM. KRAS Engages AGO2 to Enhance Cellular Transformation. Cell Rep. 2016 Feb 16;14(6):1448-61. doi:10.1016/j.celrep.2016.01.034. Epub 2016 Feb 4. PubMed PMID: 26854235; PubMed Central PMCID: PMC4758864
Asangani IA, Wilder-Romans K, Dommeti VL, Krishnamurthy PM, Apel IJ, Escara-Wilke J, Plymate SR, Navone NM, Wang S, Feng FY, Chinnaiyan AM. BET Bromodomain Inhibitors Enhance Efficacy and Disrupt Resistance to AR Antagonists in the Treatment of Prostate Cancer. Mol Cancer Res. 2016 Apr;14(4):324-31. doi: 10.1158/1541-7786.MCR-15-0472. Epub 2016 Jan 20. PubMed PMID: 26792867; PubMed Central PMCID: PMC4834259
Mehra R, Udager AM, Ahearn TU, Cao X, Feng FY, Loda M, Petimar JS, Kantoff P, Mucci LA, Chinnaiyan AM. Overexpression of the Long Non-coding RNA SChLAP1 Independently Predicts Lethal Prostate Cancer. Eur Urol. 2015 Dec 23. pii: S0302-2838(15)01211-7. doi: 10.1016/j.eururo.2015.12.003. [Epub ahead of print] PubMed PMID: 26724257; PubMed Central PMCID: PMC4919276
Veeneman BA, Shukla S, Dhanasekaran SM, Chinnaiyan AM, Nesvizhskii AI. Two-pass alignment improves novel splice junction quantification. Bioinformatics. 2016 Jan 1;32(1):43-9. doi: 10.1093/bioinformatics/btv642. Epub 2015 Oct 30. PubMed PMID: 26519505; PubMed Central PMCID: PMC5006238
Mateo J, Carreira S, Sandhu S, Miranda S, Mossop H, Perez-Lopez R, Nava Rodrigues D, Robinson D, Omlin A, Tunariu N, Boysen G, Porta N, Flohr P, Gillman A, Figueiredo I, Paulding C, Seed G, Jain S, Ralph C, Protheroe A, Hussain S, Jones R, Elliott T, McGovern U, Bianchini D, Goodall J, Zafeiriou Z, Williamson CT, Ferraldeschi R, Riisnaes R, Ebbs B, Fowler G, Roda D, Yuan W, Wu YM, Cao X, Brough R, Pemberton H, A'Hern R, Swain A, Kunju LP, Eeles R, Attard G, Lord CJ, Ashworth A, Rubin MA, Knudsen KE, Feng FY, Chinnaiyan AM, Hall E, de Bono JS. DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer. N Engl J Med. 2015 Oct 29;373(18):1697-708. doi: 10.1056/NEJMoa1506859. PubMed PMID: 26510020
Mody RJ, Wu YM, Lonigro RJ, Cao X, Roychowdhury S, Vats P, Frank KM, Prensner JR, Asangani I, Palanisamy N, Dillman JR, Rabah RM, Kunju LP, Everett J, Raymond VM, Ning Y, Su F, Wang R, Stoffel EM, Innis JW, Roberts JS, Robertson PL, Yanik G, Chamdin A, Connelly JA, Choi S, Harris AC, Kitko C, Rao RJ, Levine JE, Castle VP, Hutchinson RJ, Talpaz M, Robinson DR, Chinnaiyan AM. Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth. JAMA. 2015 Sep 1;314(9):913-25. doi: 10.1001/jama.2015.10080. PubMed PMID: 26325560; PubMed Central PMCID: PMC4758114
Cieslik M, Chugh R, Wu YM, Wu M, Brennan C, Lonigro R, Su F, Wang R, Siddiqui J, Mehra R, Cao X, Lucas D, Chinnaiyan AM, Robinson D. The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing. Genome Res. 2015 Sep;25(9):1372-81. doi: 10.1101/gr.189621.115. Epub 2015 Aug 7. PubMed PMID: 26253700; PubMed Central PMCID: PMC4561495
Harms PW, Vats P, Verhaegen ME, Robinson DR, Wu YM, Dhanasekaran SM, Palanisamy N, Siddiqui J, Cao X, Su F, Wang R, Xiao H, Kunju LP, Mehra R, Tomlins SA, Fullen DR, Bichakjian CK, Johnson TM, Dlugosz AA, Chinnaiyan AM. The Distinctive Mutational Spectra of Polyomavirus-Negative Merkel Cell Carcinoma. Cancer Res. 2015 Sep 15;75(18):3720-7. doi: 10.1158/0008-5472.CAN-15-0702. Epub 2015 Aug 3. PubMed PMID: 26238782; PubMed Central PMCID: PMC4573907
Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, Poliakov A, Cao X, Dhanasekaran SM, Wu YM, Robinson DR, Beer DG, Feng FY, Iyer HK, Chinnaiyan AM. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015 Jan 19. doi: 10.1038/ng.3192. [Epub ahead of print] PubMed PMID: 25599403.
Dhanasekaran SM, Alejandro Balbin O, Chen G, Nadal E, Kalyana-Sundaram S, Pan J, Veeneman B, Cao X, Malik R, Vats P, Wang R, Huang S, Zhong J, Jing X, Iyer M, Wu YM, Harms PW, Lin J, Reddy R, Brennan C, Palanisamy N, Chang AC, Truini A, Truini M, Robinson DR, Beer DG, Chinnaiyan AM. Transcriptome meta-analysis of lung cancer reveals recurrent aberrations in NRG1 and Hippo pathway genes. Nat Commun. 2014 Dec 22;5:5893. doi: 10.1038/ncomms6893. PubMed PMID: 25531467; PubMed Central PMCID: PMC4274748.
Mehra R, Shi Y, Udager AM, Prensner JR, Sahu A, Iyer MK, Siddiqui J, Cao X, Wei J, Jiang H, Feng FY, Chinnaiyan AM. A Novel RNA In Situ Hybridization Assay for the Long Noncoding RNA SChLAP1 Predicts Poor Clinical Outcome After Radical Prostatectomy in Clinically Localized Prostate Cancer. Neoplasia. 2014 Dec;16(12):1121-7. doi: 10.1016/j.neo.2014.11.006. PubMed PMID: 25499224.
Prensner JR, Zhao S, Erho N, Schipper M, Iyer MK, Dhanasekaran SM, Magi-Galluzzi C, Mehra R, Sahu A, Siddiqui J, Davicioni E, Den RB, Dicker AP, Karnes RJ, Wei JT, Klein EA, Jenkins RB, Chinnaiyan AM, Feng FY. RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1. Lancet Oncol. 2014 Dec;15(13):1469-80. doi: 10.1016/S1470-2045(14)71113-1. Epub 2014 Nov 17. PubMed PMID: 25456366.
Wei IH, Shi Y, Jiang H, Kumar-Sinha C, Chinnaiyan AM. RNA-Seq accurately identifies cancer biomarker signatures to distinguish tissue of origin. Neoplasia. 2014 Nov 20;16(11):918-27. doi: 10.1016/j.neo.2014.09.007. eCollection 2014 Nov. PubMed PMID: 25425966; PubMed Central PMCID: PMC4240918.
Prensner JR, Chen W, Han S, Iyer MK, Cao Q, Kothari V, Evans JR, Knudsen KE, Paulsen MT, Ljungman M, Lawrence TS, Chinnaiyan AM, Feng FY. The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc. Neoplasia. 2014 Nov 20;16(11):900-8. doi: 10.1016/j.neo.2014.09.001. eCollection 2014 Nov. PubMed PMID: 25425964; PubMed Central PMCID: PMC4240923.
Parsons DW, Roy A, Plon SE, Roychowdhury S, Chinnaiyan AM. Clinical tumor sequencing: an incidental casualty of the American College of Medical Genetics and Genomics recommendations for reporting of incidental findings. J Clin Oncol. 2014 Jul 20;32(21):2203-5. doi: 10.1200/JCO.2013.54.8917. Epub 2014 Jun 23. PubMed PMID: 24958819; PubMed Central PMCID: PMC4188159.
Feng FY, Brenner JC, Hussain M, Chinnaiyan AM. Molecular pathways: targeting ETS gene fusions in cancer. Clin Cancer Res. 2014 Sep 1;20(17):4442-8. doi: 10.1158/1078-0432.CCR-13-0275. Epub 2014 Jun 23. PubMed PMID: 24958807; PubMed Central PMCID: PMC4155001.
Asangani IA, Chinnaiyan AM. BETting on a new prostate cancer treatment. Cell Cycle. 2014 Jul 1;13(13):2015-6. doi: 10.4161/cc.29459. Epub 2014 Jun 6. PubMed PMID: 24905827; PubMed Central PMCID: PMC4111688.
Asangani IA, Dommeti VL, Wang X, Malik R, Cieslik M, Yang R, Escara-Wilke J, Wilder-Romans K, Dhanireddy S, Engelke C, Iyer MK, Jing X, Wu YM, Cao X, Qin ZS, Wang S, Feng FY, Chinnaiyan AM. Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature. 2014 Apr 23. doi: 10.1038/nature13229. [Epub ahead of print] PubMed PMID: 24759320.
Prensner JR, Sahu A, Iyer MK, Malik R, Chandler B, Asangani IA, Poliakov A, Vergara IA, Alshalalfa M, Jenkins RB, Davicioni E, Feng FY, Chinnaiyan AM. The lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer. Oncotarget. 2014 Mar 23. [Epub ahead of print] PubMed PMID: 24727738.
Prensner JR, Chen W, Iyer MK, Cao Q, Ma T, Han S, Sahu A, Malik R, Wilder-Romans K, Navone N, Logothetis CJ, Araujo JC, Pisters LL, Tewari AK, Canman CE, Knudsen KE, Kitabayashi N, Rubin MA, Demichelis F, Lawrence TS, Chinnaiyan AM, Feng FY. PCAT-1, a long noncoding RNA, regulates BRCA2 and controls homologous recombination in cancer. Cancer Res. 2014 Mar 15;74(6):1651-60. doi: 10.1158/0008-5472.CAN-13-3159. Epub 2014 Jan 28. PubMed PMID: 24473064.
Cao Q, Wang X, Zhao M, Yang R, Malik R, Qiao Y, Poliakov A, Yocum AK, Li Y, Chen W, Cao X, Jiang X, Dahiya A, Harris C, Feng FY, Kalantry S, Qin ZS, Dhanasekaran SM, Chinnaiyan AM. The central role of EED in the orchestration of polycomb group complexes. Nat Commun. 2014;5:3127. doi: 10.1038/ncomms4127. PubMed PMID: 24457600.
Robinson DR, Wu YM, Vats P, Su F, Lonigro RJ, Cao X, Kalyana-Sundaram S, Wang R, Ning Y, Hodges L, Gursky A, Siddiqui J, Tomlins SA, Roychowdhury S, Pienta KJ, Kim SY, Roberts JS, Rae JM, Van Poznak CH, Hayes DF, Chugh R, Kunju LP, Talpaz M, Schott AF, Chinnaiyan AM. Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat Genet. 2013 Dec;45(12):1446-51. doi: 10.1038/ng.2823. Epub 2013 Nov 3. PubMed PMID: 24185510.
Balbin OA, Prensner JR, Sahu A, Yocum A, Shankar S, Malik R, Fermin D, Dhanasekaran SM, Chandler B, Thomas D, Beer DG, Cao X, Nesvizhskii AI, Chinnaiyan AM. Reconstructing targetable pathways in lung cancer by integrating diverse omics data. Nat Commun. 2013 Oct 18;4:2617. doi: 10.1038/ncomms3617. PubMed PMID: 24135919.
Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan W, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet. 2013 Sep 29. doi: 10.1038/ng.2771. [Epub ahead of print] PubMed PMID: 24076601.
Khan AP, Rajendiran TM, Ateeq B, Asangani IA, Athanikar JN, Yocum AK, Mehra R, Siddiqui J, Palapattu G, Wei JT, Michailidis G, Sreekumar A, Chinnaiyan AM. The role of sarcosine metabolism in prostate cancer progression. Neoplasia. 2013 May;15(5):491-501. PubMed PMID: 23633921; PubMed Central PMCID: PMC3638352.
Wu YM, Su F, Kalyana-Sundaram S, Khazanov N, Ateeq B, Cao X, Lonigro RJ, Vats P, Wang R, Lin SF, Cheng AJ, Kunju LP, Siddiqui J, Tomlins SA, Wyngaard P, Sadis S, Roychowdhury S, Hussain M, Feng FY, Zalupski MM, Talpaz M, Pienta KJ, Rhodes DR, Robinson DR, Chinnaiyan AM. Identification of Targetable FGFR Gene Fusions in Diverse Cancers. Cancer Discov. 2013 Apr 4. [Epub ahead of print] PubMed PMID: 23558953.
Kothari V, Wei I, Shankar S, Kalyana-Sundaram S, Wang L, Ma LW, Vats P, Grasso CS, Robinson DR, Wu YM, Cao X, Simeone DM, Chinnaiyan AM, Kumar-Sinha C. Outlier kinase expression by RNA sequencing as targets for precision therapy. Cancer Discov. 2013 Mar;3(3):280-93. doi: 10.1158/2159-8290.CD-12-0336. Epub 2013 Feb 5. PubMed PMID: 23384775; PubMed Central PMCID: PMC3597439.
Robinson DR, Wu YM, Kalyana-Sundaram S, Cao X, Lonigro RJ, Sung YS, Chen CL, Zhang L, Wang R, Su F, Iyer MK, Roychowdhury S, Siddiqui J, Pienta KJ, Kunju LP, Talpaz M, Mosquera JM, Singer S, Schuetze SM, Antonescu CR, Chinnaiyan AM. Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing. Nat Genet. 2013 Feb;45(2):180-5. doi: 10.1038/ng.2509. Epub 2013 Jan 13. PubMed PMID: 23313952.