2023
The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer
Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, Gleave M, Lara PN, Reiter RE, Rettig MB, Witte ON, Wyatt AW, Feng FY, Small EJ, Quigley DA. Cancer Res. 2023 Aug 15;83(16):2763-2774. doi: 10.1158/0008-5472.CAN-23-0593. PMID: 37289025; PMCID: PMC10425725.
Chappidi MR, Sjöström M, Greenland NY, Cowan JE, Baskin AS, Shee K, Simko JP, Chan E, Stohr BA, Washington SL 3rd, Nguyen HG, Quigley DA, Davicioni E, Feng FY, Carroll PR, Cooperberg MR. Eur Urol Oncol. 2023 Jul 18:S2588-9311(23)00120-7. doi: 10.1016/j.euo.2023.06.007. Epub ahead of print. PMID: 37474400.
Immunotherapeutic Targeting and PET Imaging of DLL3 in Small-Cell Neuroendocrine Prostate Cancer
Chou J, Egusa EA, Wang S, Badura ML, Lee F, Bidkar AP, Zhu J, Shenoy T, Trepka K, Robinson TM, Steri V, Huang J, Wang Y, Small EJ, Chan E, Stohr BA, Ashworth A, Delafontaine B, Rottey S, Cooke KS, Hashemi Sadraei N, Yu B, Salvati M, Bailis JM, Feng FY, Flavell RR, Aggarwal R. Cancer Res. 2023 Jan 18;83(2):301-315. doi: 10.1158/0008-5472.CAN-22-1433. PMID: 36351060; PMCID: PMC10263373.
2022
The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. Cancer Res. 2022 Oct 17:OF1-OF15. doi: 10.1158/0008-5472. CAN-22-1123. Epub ahead of print. PMID: 36251389
Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials.
Esteva A, Feng J, van der Wal D, Huang SC, Simko JP, DeVries S, Chen E, Schaeffer EM, Morgan TM, Sun Y, Ghorbani A, Naik N, Nathawani D, Socher R, Michalski JM, Roach M 3rd, Pisansky TM, Monson JM, Naz F, Wallace J, Ferguson MJ, Bahary JP, Zou J, Lungren M, Yeung S, Ross AE; NRG Prostate Cancer AI Consortium, Sandler HM, Tran PT, Spratt DE, Pugh S, Feng FY, Mohamad O.
NPJ Digit Med. 2022 Jun 8;5(1):71. doi: 10.1038/s41746-022-00613-w. PMID: 35676445
Dynamic expression of SNAI2 in prostate cancer predicts tumor progression and drug sensitivity.
Mazzu YZ, Liao Y, Nandakumar S, Sjöström M, Jehane LE, Ghale R, Govindarajan B, Gerke TA, Lee GM, Luo JH, Chinni SR, Mucci LA, Feng FY, Kantoff PW.
Mol Oncol. 2022 Jul;16(13):2451-2469. doi: 10.1002/1878-0261.13140. PMID: 34792282
TROP2 Expression Across Molecular Subtypes of Urothelial Carcinoma and Enfortumab Vedotin-resistant Cells.
Chou J, Trepka K, Sjöström M, Egusa EA, Chu CE, Zhu J, Chan E, Gibb EA, Badura ML, Contreras-Sanz A, Stohr BA, Meng MV, Pruthi RS, Lotan Y, Black PC, Porten SP, Koshkin VS, Friedlander TW, Feng FY.
Eur Urol Oncol. 2022 Feb 22:S2588-9311(21)00215-7. doi: 10.1016/j.euo.2021.11.005. PMID: 35216942
2021
Prognosis Associated With Luminal and Basal Subtypes of Metastatic Prostate Cancer.
Aggarwal R, Rydzewski NR, Zhang L, Foye A, Kim W, Helzer KT, Bakhtiar H, Chang SL, Perry MD, Gleave M, Reiter RE, Huang J, Evans CP, Alumkal JJ, Lang JM, Yu M, Quigley DA, Sjöström M, Small EJ, Feng FY, Zhao SG.
JAMA Oncol. 2021 Nov 1;7(11):1644-1652. doi: 10.1001/jamaoncol.2021.3987. PMID: 34554200
Heterogeneity in NECTIN4 Expression Across Molecular Subtypes of Urothelial Cancer Mediates Sensitivity to Enfortumab Vedotin.
Chu CE, Sjöström M, Egusa EA, Gibb EA, Badura ML, Zhu J, Koshkin VS, Stohr BA, Meng MV, Pruthi RS, Friedlander TW, Lotan Y, Black PC, Porten SP, Feng FY, Chou J.
Clin Cancer Res. 2021 Sep 15;27(18):5123-5130. doi: 10.1158/1078-0432.CCR-20-4175. PMID: 34108177
An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer.
Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA.
Nat Commun. 2021 Jul 29;12(1):4601. doi: 10.1038/s41467-021-24919-7. PMID: 34326322
Prostate-specific Membrane Antigen and Fluciclovine Transporter Genes are Associated with Variable Clinical Features and Molecular Subtypes of Primary Prostate Cancer.
Chu CE, Alshalalfa M, Sjöström M, Zhao SG, Liu Y, Chou J, Herlemann A, Mahal B, Kishan AU, Spratt DE, Cooperberg M, Small E, Wong A, Porten S, Hope TA, Ross AE, Davicioni E, Nguyen P, Karnes RJ, Carroll PR, Schaeffer E, Feng FY.
Eur Urol. 2021 Jun;79(6):717-721. doi: 10.1016/j.eururo.2021.03.017. PMID: 33840559
Differential treatment outcomes in BRCA1/2-, CDK12-, and ATM-mutated metastatic castration-resistant prostate cancer.
Kwon DH, Chou J, Yip SM, Reimers MA, Zhang L, Wright F, Dhawan MS, Borno HT, Desai A, Aggarwal RR, Wyatt AW, Small EJ, Alva AS, Chi KN, Feng FY, Koshkin VS.
Cancer. 2021 Jun 15;127(12):1965-1973. doi: 10.1002/cncr.33487. PMID: 33690902
2020
Novel Transcriptomic Interactions Between Immune Content and Genomic Classifier Predict Lethal Outcomes in High-grade Prostate Cancer.
Yamoah K, Awasthi S, Mahal BA, Zhao SG, Grass GD, Berglund A, Abraham-Miranda J, Gerke T, Rounbehler RJ, Davicioni E, Liu Y, Park J, Cleveland JL, Pow-Sang JM, Fernandez D, Torres-Roca J, Karnes RJ, Schaeffer E, Freedland SJ, Spratt DE, Den RB, Rebbeck TR, Feng F.
Eur Urol. 2020 Dec 7:S0302-2838(20)30939-8. doi: 10.1016/j.eururo.2020.11.038. [Online ahead of print].PMID: 33303244
Autoantibody Landscape in Patients with Advanced Prostate Cancer.
Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY.
Clin Cancer Res. 2020 Dec 1;26(23):6204-6214. doi: 10.1158/1078-0432.CCR-20-1966. Epub 2020 Sep 23.PMID: 32967941
Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity.
Cyrta J, Augspach A, De Filippo MR, Prandi D, Thienger P, Benelli M, Cooley V, Bareja R, Wilkes D, Chae SS, Cavaliere P, Dephoure N, Uldry AC, Lagache SB, Roma L, Cohen S, Jaquet M, Brandt LP, Alshalalfa M, Puca L, 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.
Nat Commun. 2020 Nov 3;11(1):5549. doi: 10.1038/s41467-020-19328-1. PMID: 33144576
A Phase Ib/IIa Study of the Pan-BET Inhibitor ZEN-3694 in Combination with Enzalutamide in Patients with Metastatic Castration-resistant Prostate Cancer.
Aggarwal RR, Schweizer MT, Nanus DM, Pantuck AJ, Heath EI, Campeau E, Attwell S, Norek K, Snyder M, Bauman L, Lakhotia S, Feng FY, Small EJ, Abida W, Alumkal JJ.
Clin Cancer Res. 2020 Oct 15;26(20):5338-5347. doi: 10.1158/1078-0432.CCR-20-1707. Epub 2020 Jul 21. PMID: 32694156
The splicing modulator sulfonamide indisulam reduces AR-V7 in prostate cancer cells.
Melnyk JE, Steri V, Nguyen HG, Hann B, Feng FY, Shokat KM.
Bioorg Med Chem. 2020 Oct 15;28(20):115712. doi: 10.1016/j.bmc.2020.115712. Epub 2020 Aug 18.PMID: 33069070
SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression.
Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA.
Sci Rep. 2020 Sep 28;10(1):15890. doi: 10.1038/s41598-020-71168-7.PMID: 32985524
Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer.
Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P Jr, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, Quigley DA, Foye A, Chen WS, Youngren J, Weinstein AS, Stuart JM, Feng FY, Small EJ, Xia Z, Alumkal JJ.
Clin Cancer Res. 2020 Sep 1;26(17):4616-4624. doi: 10.1158/1078-0432.CCR-19-2303. Epub 2020 Jul 29.PMID: 32727885
The DNA Methylation Landscape of Advanced Prostate Cancer
Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY.Nat Genet. 2020 Aug;52(8):778-789. doi: 10.1038/s41588-020-0648-8. Epub 2020 Jul 13.PMID: 32661416
Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance.
Alumkal JJ, Sun D, Lu E, Beer TM, Thomas GV, Latour E, Aggarwal R, Cetnar J, Ryan CJ, Tabatabaei S, Bailey S, Turina CB, Quigley DA, Guan X, Foye A, Youngren JF, Urrutia J, Huang J, Weinstein AS, Friedl V, Rettig M, Reiter RE, Spratt DE, Gleave M, Evans CP, Stuart JM, Chen Y, Feng FY, Small EJ, Witte ON, Xia Z.
Proc Natl Acad Sci U S A. 2020 Jun 2;117(22):12315-12323. doi: 10.1073/pnas.1922207117. Epub 2020 May 18.PMID: 32424106
Clinical Outcomes in Cyclin-dependent Kinase 12 Mutant Advanced Prostate Cancer.Reimers MA, Yip SM, Zhang L, Cieslik M, Dhawan M, Montgomery B, Wyatt AW, Chi KN, Small EJ, Chinnaiyan AM, Alva AS, Feng FY, Chou J.
Eur Urol. 2020 Mar;77(3):333-341. doi: 10.1016/j.eururo.2019.09.036. Epub 2019 Oct 20.PMID: 31640893
Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy.
Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A.Cancer Discov. 2020 Mar;10(3):351-370. doi: 10.1158/2159-8290.CD-19-0528. Epub 2020 Feb 18.PMID: 32071145 Review.
Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer.
Li Y, Yang R, Henzler CM, Ho Y, Passow C, Auch B, Carreira S, Nava Rodrigues D, Bertan C, Hwang TH, Quigley DA, Dang HX, Morrissey C, Fraser M, Plymate SR, Maher CA, Feng FY, de Bono JS, Dehm SM.
Clin Cancer Res. 2020 Apr 15;26(8):1965-1976. doi: 10.1158/1078-0432.CCR-19-3023. Epub 2020 Jan 13.PMID: 31932493
2019
Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer.
Chen WS, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley DA, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, Xia Z, Chi KN, Reiter RE, Maher CA, Feng FY, Small EJ, Alumkal JJ; West Coast Prostate Cancer Dream Team.
Eur Urol. 2019 Nov;76(5):562-571. doi: 10.1016/j.eururo.2019.03.020. Epub 2019 Mar 28.PMID: 30928160
Genomic Risk Predicts Molecular Imaging-detected Metastatic Nodal Disease in Prostate Cancer.
Xu MJ, Kornberg Z, Gadzinski AJ, Diao D, Cowan JE, Wu SY, Boreta L, Spratt DE, Behr SC, Nguyen HG, Cooperberg MR, Davicioni E, Roach M 3rd, Hope TA, Carroll PR, Feng FY.
Eur Urol Oncol. 2019 Nov;2(6):685-690. doi: 10.1016/j.euo.2018.11.002. Epub 2019 Jan 15.PMID: 31411984
Pleiotropic Impact of DNA-PK in Cancer and Implications for Therapeutic Strategies.
Dylgjeri E, McNair C, Goodwin JF, Raymon HK, McCue PA, Shafi AA, Leiby BE, de Leeuw R, Kothari V, McCann JJ, Mandigo AC, Chand SN, Schiewer MJ, Brand LJ, Vasilevskaya I, Gordon N, Laufer TS, Gomella LG, Lallas CD, Trabulsi EJ, Feng FY, Filvaroff EH, Hege K, Rathkopf D, Knudsen KE.
Clin Cancer Res. 2019 Sep 15;25(18):5623-5637. doi: 10.1158/1078-0432.CCR-18-2207. Epub 2019 Jul 2.PMID: 31266833
Expanding Role of Germline DNA Repair Alterations in Prostate Cancer Risk and Early Onset.
Knudsen KE, Feng FY.
Eur Urol. 2019 Sep;76(3):338-339. doi: 10.1016/j.eururo.2019.03.005. Epub 2019 Mar 15.PMID: 30885533
Identification of TP53RK-Binding Protein (TPRKB) Dependency in TP53-Deficient Cancers.
Goswami MT, VanDenBerg KR, Han S, Wang LL, Singh B, Weiss T, Barlow M, Kamberov S, Wilder-Romans K, Rhodes DR, Feng FY, Tomlins SA.
Mol Cancer Res. 2019 Aug;17(8):1652-1664. doi: 10.1158/1541-7786.MCR-19-0144. Epub 2019 May 20.PMID: 31110156
Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms.
Emami NC, Kachuri L, Meyers TJ, Das R, Hoffman JD, Hoffmann TJ, Hu D, Shan J, Feng FY, Ziv E, Van Den Eeden SK, Witte JS.
Nat Commun. 2019 Jul 15;10(1):3107. doi: 10.1038/s41467-019-10808-7.PMID: 31308362
Impact of Immune and Stromal Infiltration on Outcomes Following Bladder-Sparing Trimodality Therapy for Muscle-Invasive Bladder Cancer.
Efstathiou JA, Mouw KW, Gibb EA, Liu Y, Wu CL, Drumm MR, da Costa JB, du Plessis M, Wang NQ, Davicioni E, Feng FY, Seiler R, Black PC, Shipley WU, Miyamoto DT.
Eur Urol. 2019 Jul;76(1):59-68. doi: 10.1016/j.eururo.2019.01.011. Epub 2019 Feb 1.PMID: 30712971
DNA-Dependent Protein Kinase Drives Prostate Cancer Progression Through Transcriptional Regulation of the Wnt Signaling Pathway Kothari V, Goodwin JF, Zhao SG, Drake JM, Yin Y, Chang SL, Evans JR, Wilder-Romans K, Gabbara K, Dylgjeri E, Chou J, Sun G, Tomlins SA, Mehra R, Hege K, Filvaroff EH, Schaeffer EM, Karnes RJ, Quigley DA, Rathkopf DE, He HH, Speers C, Spratt DE, Gilbert LA, Ashworth A, Chinnaiyan AM, Raj GV, Knudsen KE, Feng FY.
Clin Cancer Res. 2019 Jul 2. doi: 10.1158/1078-0432.CCR-18-2387. [Epub ahead of print] PubMed PMID: 31266829.
Novel RB1-Loss Transcriptomic Signature Is Associated with Poor Clinical Outcomes across Cancer Types Chen WS, Alshalalfa M, Zhao SG, Liu Y, Mahal BA, Quigley DA, Wei T, Davicioni E, Rebbeck TR, Kantoff PW, Maher CA, Knudsen KE, Small EJ, Nguyen PL, Feng FY.
Clin Cancer Res. 2019 Jul 15;25(14):4290-4299. doi: 10.1158/1078-0432.CCR-19-0404. Epub 2019 Apr 22. PubMed PMID: 31010837.
Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas
Zhao SG, Chen WS, Das R, Chang SL, Tomlins SA, Chou J, Quigley DA, Dang HX, Barnard TJ, Mahal BA, Gibb EA, Liu Y, Davicioni E, Duska LR, Posadas EM, Jolly S, Spratt DE, Nguyen PL, Maher CA, Small EJ, Feng FY.
Clin Cancer Res. 2019 Apr 15;25(8):2450-2457. doi: 10.1158/1078-0432.CCR-18-3121. Epub 2018 Dec 20. PubMed PMID: 30573691.
Lethal clues to cancer-cell vulnerability.
Feng FY, Gilbert LA.
Nature. 2019 Apr;568(7753):463-464. doi: 10.1038/d41586-019-01086-w.PMID: 31000834
Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer.
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.
Nature. 2019 Jul;571(7765):413-418. doi: 10.1038/s41586-019-1347-4. Epub 2019 Jun 26.PMID: 31243372
Whole-Genome and Transcriptional Analysis of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer Demonstrates Intraclass Heterogeneity.
Aggarwal RR, Quigley DA, Huang J, Zhang L, Beer TM, Rettig MB, Reiter RE, Gleave ME, Thomas GV, Foye A, Playdle D, Lloyd P, Chi KN, Evans CP, Lara PN, Feng FY, Alumkal JJ, Small EJ.
Mol Cancer Res. 2019 Jun;17(6):1235-1240. doi: 10.1158/1541-7786.MCR-18-1101. Epub 2019 Mar 27.PMID: 30918106
Activation of MAPK Signaling by CXCR7 Leads to Enzalutamide Resistance in Prostate Cancer.
Li S, Fong KW, Gritsina G, Zhang A, Zhao JC, Kim J, Sharp A, Yuan W, Aversa C, Yang XJ, Nelson PS, Feng FY, Chinnaiyan AM, de Bono JS, Morrissey C, Rettig MB, Yu J.
Cancer Res. 2019 May 15;79(10):2580-2592. doi: 10.1158/0008-5472.CAN-18-2812. Epub 2019 Apr 5.PMID: 30952632
A Circulating Tumor Cell-RNA Assay for Assessment of Androgen Receptor Signaling Inhibitor Sensitivity in Metastatic Castration-Resistant Prostate Cancer.
Jan YJ, Yoon J, Chen JF, Teng PC, Yao N, Cheng S, Lozano A, Chu GCY, Chung H, Lu YT, Chen PJ, Wang JJ, Lee YT, Kim M, Zhu Y, Knudsen BS, Feng FY, Garraway IP, Gao AC, Chung LWK, Freeman MR, You S, Tseng HR, Posadas EM.
Theranostics. 2019 Apr 13;9(10):2812-2826. doi: 10.7150/thno.34485. eCollection 2019.PMID: 31244925
A Tumor-Agnostic NTRK (TRK) Inhibitor.
Huang FW, Feng FY.
Cell. 2019 Mar 21;177(1):8. doi: 10.1016/j.cell.2019.02.049.PMID: 30901551
The Immune Landscape of Prostate Cancer and Nomination fo PD-L2 as a Potential Therapeutic Target Zhao SG, Lehrer J, Chang SL, Das R, Erho N, Liu Y, Sjöström M, Den RB, Freedland SJ, Klein EA, Karnes RJ, Schaeffer EM, Xu M, Speers C, Nguyen PL, Ross AE, Chan JM, Cooperberg MR, Carroll PR, Davicioni E, Fong L, Spratt DE, Feng FY.
J Natl Cancer Inst. 2019 Mar 1;111(3):301-310. doi: 10.1093/jnci/djy141. PubMed PMID: 30321406.
Widespread and Functional RNA Circularization in Localized Prostate Cancer.
Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, Hua JT, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua MLK, Heisler LE, Foucal A, Fox NS, Fraser M, Bhandari V, Shiah YJ, Guan J, Li J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Liu S, Feng F, Wu X, Shao YW, Komor MA, Sahinalp C, Collins C, Hoogstrate Y, de Jong M, Fijneman RJA, Fei T, Jenster G, van der Kwast T, Bristow RG, Boutros PC, He HH.
Cell. 2019 Feb 7;176(4):831-843.e22. doi: 10.1016/j.cell.2019.01.025.PMID: 30735634
ONECUT2 is a driver of neuroendocrine prostate cancer.
Guo H, Ci X, Ahmed M, Hua JT, Soares F, Lin D, Puca L, Vosoughi A, Xue H, Li E, Su P, Chen S, Nguyen T, Liang Y, Zhang Y, Xu X, Xu J, Sheahan AV, Ba-Alawi W, Zhang S, Mahamud O, Vellanki RN, Gleave M, Bristow RG, Haibe-Kains B, Poirier JT, Rudin CM, Tsao MS, Wouters BG, Fazli L, Feng FY, Ellis L, van der Kwast T, Berlin A, Koritzinsky M, Boutros PC, Zoubeidi A, Beltran H, Wang Y, He HH.
Nat Commun. 2019 Jan 17;10(1):278. doi: 10.1038/s41467-018-08133-6.PMID: 30655535
Genomic Risk Predicts Molecular Imaging-detected Metastatic Nodal Disease in Prostate Cancer.
Xu MJ, Kornberg Z, Gadzinski AJ, Diao D, Cowan JE, Wu SY, Boreta L, Spratt DE, Behr SC, Nguyen HG, Cooperberg MR, Davicioni E, Roach M 3rd, Hope TA, Carroll PR, Feng FY.
Eur Urol Oncol. 2019 Jan 14. pii: S2588-9311(18)30194-9. doi: 10.1016/j.euo.2018.11.002. [Epub ahead of print] PubMed PMID: 31411984.
2018
PARP-1 regulates DNA repair factor availability.
Schiewer MJ, Mandigo AC, Gordon N, Huang F, Gaur S, de Leeuw R, Zhao SG, Evans J, Han S, Parsons T, Birbe R, McCue P, McNair C, Chand SN, Cendon-Florez Y, Gallagher P, McCann JJ, Poudel Neupane N, Shafi AA, Dylgjeri E, Brand LJ, Visakorpi T, Raj GV, Lallas CD, Trabulsi EJ, Gomella LG, Dicker AP, Kelly WK, Leiby BE, Knudsen B, Feng FY, Knudsen KE.
EMBO Mol Med. 2018 Dec;10(12):e8816. doi: 10.15252/emmm.201708816.PMID: 30467127
Integrative epigenetic taxonomy of primary prostate cancer.
Stelloo S, Nevedomskaya E, Kim Y, Schuurman K, Valle-Encinas E, Lobo J, Krijgsman O, Peeper DS, Chang SL, Feng FY, Wessels LFA, Henrique R, Jerónimo C, Bergman AM, Zwart W.
Nat Commun. 2018 Nov 21;9(1):4900. doi: 10.1038/s41467-018-07270-2.PMID: 30464211
EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins.
Gollavilli PN, Pawar A, Wilder-Romans K, Natesan R, Engelke CG, Dommeti VL, Krishnamurthy PM, Nallasivam A, Apel IJ, Xu T, Qin ZS, Feng FY, Asangani IA.Cancer Res. 2018 Aug 15;78(16):4760-4773. doi: 10.1158/0008-5472.CAN-18-0484.
Epub 2018 Jun 13.PMID: 29898995
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.
Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN Jr, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY.
Cell. 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039. Epub 2018 Jul 19.PMID: 30033370
Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19.
Hua JT, Ahmed M, Guo H, Zhang Y, Chen S, Soares F, Lu J, Zhou S, Wang M, Li H, Larson NB, McDonnell SK, Patel PS, Liang Y, Yao CQ, van der Kwast T, Lupien M, Feng FY, Zoubeidi A, Tsao MS, Thibodeau SN, Boutros PC, He HH.
Cell. 2018 Jul 26;174(3):564-575.e18. doi: 10.1016/j.cell.2018.06.014. Epub 2018 Jul 19.PMID: 30033362
Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer.
Wu YM, Cieślik 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.
Cell. 2018 Jun 14;173(7):1770-1782.e14. doi: 10.1016/j.cell.2018.04.034.PMID: 29906450
Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. Zhang Y, Pitchiaya S, Cieślik 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.
Nat Genet. 2018 Jun;50(6):814-824. doi: 10.1038/s41588-018-0120-1. Epub 2018 May 28.
Genomic Biomarkers in Prostate Cancer
Kornberg Z, Cooperberg MR, Spratt DE, Feng FY.
Transl Androl Urol. 2018 Jun;7(3):459-471. doi: 10.21037/tau.2018.06.02. Review. PubMed PMID: 30050804; PubMed Central PMCID: PMC6043739.
Targeting Androgen Receptor and DNA Repair in Metastatic Castration-Resistant Prostate Cancer: Results From NCI 9012. Hussain M, Daignault-Newton S, Twardowski PW, Albany C, Stein MN, Kunju LP, Siddiqui J, Wu YM, Robinson D, Lonigro RJ, Cao X, Tomlins SA, Mehra R, Cooney KA, Montgomery B, Antonarakis ES, Shevrin DH, Corn PG, Whang YE, Smith DC, Caram MV, Knudsen KE, Stadler WM, Feng FY, Chinnaiyan AM.
J Clin Oncol. 2018 Apr 1;36(10):991-999. doi: 10.1200/JCO.2017.75.7310. Epub 2017 Dec 20.
2017
Associations of Luminal and Basal Subtyping of Prostate Cancer With Prognosis and Response to Androgen Deprivation Therapy.
Zhao SG, Chang SL, Erho N, Yu M, Lehrer J, Alshalalfa M, Speers C, Cooperberg MR, Kim W, Ryan CJ, Den RB, Freedland SJ, Posadas E, Sandler H, Klein EA, Black P, Seiler R, Tomlins SA, Chinnaiyan AM, Jenkins RB, Davicioni E, Ross AE, Schaeffer EM, Nguyen PL, Carroll PR, Karnes RJ, Spratt DE, Feng FY. JAMA Oncol. 2017 May 11. doi: 10.1001/jamaoncol.2017.0751.
Analysis of Circulating Cell-free DNA Identifies Multi-clonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors.
Quigley D, Alumkal JJ, Wyatt AW, Kothari V, Foye A, Lloyd P, Aggarwal R, Kim W, Lu E, Schwartzman J, Beja K, Annala M, Das R, Diolaiti M, Pritchard CC, Thomas GV, Tomlins SA, Knudsen KE, Lord CJ, Ryan CJ, Youngren J, Beer TM, Ashworth A, Small EJ, Feng FY. Cancer Discov. 2017 Apr 27. pii: CD-17-0146. doi: 10.1158/2159-8290.CD-17-0146.
Individual Patient-Level Meta-Analysis of the Performance of the Decipher Genomic Classifier in High-Risk Men After Prostatectomy to Predict Development of Metastatic Disease.
Spratt DE, Yousefi K, Deheshi S, Ross AE, Den RB, Schaeffer EM, Trock BJ, Zhang J, Glass AG, Dicker AP, Abdollah F, Zhao SG, Lam LLC, du Plessis M, Choeurng V, Haddad Z, Buerki C, Davicioni E, Weinmann S, Freedland SJ, Klein EA, Karnes RJ, Feng FY. J Clin Oncol. 2017 Jun 20;35(18):1991-1998. doi: 10.1200/JCO.2016.70.2811. Epub 2017 Mar 30.
Utilization of biopsy-based genomic classifier to predict distant metastasis after definitive radiation and short-course ADT for intermediate and high-risk prostate cancer.
Nguyen PL, Martin NE, Choeurng V, Palmer-Aronsten B, Kolisnik T, Beard CJ, Orio PF, Nezolosky MD, Chen YW, Shin H, Davicioni E, Feng FY.
Prostate Cancer Prostatic Dis. 2017 Jun;20(2):186-192. doi: 10.1038/pcan.2016.58. Epub 2017 Jan 24.
Radiation with or without Antiandrogen Therapy in Recurrent Prostate Cancer.
Shipley WU, Seiferheld W, Lukka HR, Major PP, Heney NM, Grignon DJ, Sartor O, Patel MP, Bahary JP, Zietman AL, Pisansky TM, Zeitzer KL, Lawton CA, Feng FY, Lovett RD, Balogh AG, Souhami L, Rosenthal SA, Kerlin KJ, Dignam JJ, Pugh SL, Sandler HM; NRG Oncology RTOG.
N Engl J Med. 2017 Feb 2;376(5):417-428. doi: 10.1056/NEJMoa1607529.
Biomarkers of Outcome in Patients With Localized Prostate Cancer Treated With Radiotherapy.
Hall WA, Lawton CA, Jani AB, Pollack A, Feng FY.
Semin Radiat Oncol. 2017 Jan;27(1):11-20. doi: 10.1016/j.semradonc.2016.09.001. Epub 2016 Sep 16. Review.
2016
Maternal Embryonic Leucine Zipper Kinase (MELK) as a Novel Mediator and Biomarker of Radioresistance in Human Breast Cancer.
Speers C, Zhao SG, Kothari V, Santola A, Liu M, Wilder-Romans K, Evans J, Batra N, Bartelink H, Hayes DF, Lawrence TS, Brown PH, Pierce LJ, Feng FY.
Clin Cancer Res. 2016 Dec 1;22(23):5864-5875.
Development and validation of a 24-gene predictor of response to postoperative radiotherapy in prostate cancer: a matched, retrospective analysis.
Zhao SG, Chang SL, Spratt DE, Erho N, Yu M, Ashab HA, Alshalalfa M, Speers C, Tomlins SA, Davicioni E, Dicker AP, Carroll PR, Cooperberg MR, Freedland SJ, Karnes RJ, Ross AE, Schaeffer EM, Den RB, Nguyen PL, Feng FY.
Lancet Oncol. 2016 Nov;17(11):1612-1620. doi: 10.1016/S1470-2045(16)30491-0.
The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression.
Niknafs YS, Han S, Ma T, Speers C, Zhang C, Wilder-Romans K, Iyer MK, Pitchiaya S, Malik R, Hosono Y, Prensner JR, Poliakov A, Singhal U, Xiao L, Kregel S, Siebenaler RF, Zhao SG, Uhl M, Gawronski A, Hayes DF, Pierce LJ, Cao X, Collins C, Backofen R, Sahinalp CS, Rae JM, Chinnaiyan AM, Feng FY.
Nat Commun. 2016 Sep 26;7:12791. doi: 10.1038/ncomms12791.
Long noncoding RNAs in prostate cancer: overview and clinical implications.
Malik B, Feng FY.
Asian J Androl. 2016 Jul-Aug;18(4):568-74. doi: 10.4103/1008-682X.177123.
MDM2 Inhibition Sensitizes Prostate Cancer Cells to Androgen Ablation and Radiotherapy in a p53-Dependent Manner.
Feng FY, Zhang Y, Kothari V, Evans JR, Jackson WC, Chen W, Johnson SB, Luczak C, Wang S, Hamstra DA.
Neoplasia. 2016 Apr;18(4):213-22. doi: 10.1016/j.neo.2016.01.006.
Patient-Level DNA Damage and Repair Pathway Profiles and Prognosis After Prostatectomy for High-Risk Prostate Cancer.
Evans JR, Zhao SG, Chang SL, Tomlins SA, Erho N, Sboner A, Schiewer MJ, Spratt DE, Kothari V, Klein EA, Den RB, Dicker AP, Karnes RJ, Yu X, Nguyen PL, Rubin MA, de Bono J, Knudsen KE, Davicioni E, Feng FY.
JAMA Oncol. 2016 Apr 1;2(4):471-80.
The Landscape of Prognostic Outlier Genes in High-Risk Prostate Cancer.
Zhao SG, Evans JR, Kothari V, Sun G, Larm A, Mondine V, Schaeffer EM, Ross AE, Klein EA, Den RB, Dicker AP, Karnes RJ, Erho N, Nguyen PL, Davicioni E, Feng FY.
Clin Cancer Res. 2016 Apr 1;22(7):1777-86.
Driven to Metastasize: Kinases as Potential Therapeutic Targets in Prostate Cancer.
Feng FY, Kothari V.
Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):473-5. doi: 10.1073/pnas.1522938113. No abstract available.
2015
DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer.
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.
N Engl J Med. 2015 Oct 29;373(18):1697-708.
DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis.
Goodwin JF, Kothari V, Drake JM, Zhao S, Dylgjeri E, Dean JL, Schiewer MJ, McNair C, Jones JK, Aytes A, Magee MS, Snook AE, Zhu Z, Den RB, Birbe RC, Gomella LG, Graham NA, Vashisht AA, Wohlschlegel JA, Graeber TG, Karnes RJ, Takhar M, Davicioni E, Tomlins SA, Abate-Shen C, Sharifi N, Witte ON, Feng FY*, Knudsen KE*. *Co-senior authors
Cancer Cell. 2015 Jul 13;28(1):97-113.
Chromatin to Clinic: The Molecular Rationale for PARP1 Inhibitor Function.
Feng FY, de Bono JS, Rubin MA, Knudsen KE.
Mol Cell. 2015 Jun 18;58(6):925-34.
Characterization of 1577 primary prostate cancers reveals novel biological and clinicopathologic insights into molecular subtypes.
Tomlins SA, Alshalalfa M, Davicioni E, Erho N, Yousefi K, Zhao S, Haddad Z, Den RB, Dicker AP, Trock BJ, DeMarzo AM, Ross AE, Schaeffer EM, Klein EA, Magi-Galluzzi C, Karnes RJ, Jenkins RB, Feng FY.
Eur Urol. 2015 Oct;68(4):555-67.
Development and Validation of a Novel Radiosensitivity Signature in Human Breast Cancer.
Speers C, Zhao S, Liu M, Bartelink H, Pierce LJ, Feng FY.
Clin Cancer Res. 2015 Aug 15;21(16):3667-77.
Targeting the MLL complex in castration-resistant prostate cancer.
Malik R, Khan AP, Asangani IA, Cieslik M, Prensner JR, Wang X, Iyer MK, Jiang X, Borkin D, Escara-Wilke J, Stender R, Wu YM, Niknafs YS, Jing X, Qiao Y, Palanisamy N, Kunju LP, Krishnamurthy PM, Yocum AK, Mellacheruvu D, Nesvizhskii AI, Cao X, Dhanasekaran SM, Feng FY, Grembecka J, Cierpicki T, Chinnaiyan AM.
Nat Med. 2015 Apr;21(4):344-52.
The landscape of long noncoding RNAs in the human transcriptome.
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.
Nat Genet. 2015 Mar;47(3):199-208.
2014
RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1.
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.
Lancet Oncol. 2014 Dec;15(13):1469-80.
The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc.
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.
Neoplasia. 2014 Nov 20;16(11):900-8.
A tissue biomarker-based model that identifies patients with a high risk of distant metastasis and differential survival by length of androgen deprivation therapy in RTOG protocol 92-02.
Pollack A, Dignam JJ, Diaz DA, Wu Q, Stoyanova R, Bae K, Dicker AP, Sandler H, Hanks GE, Feng FY.
Clin Cancer Res. 2014 Dec 15;20(24):6379-88.
Targeted radiosensitization with PARP1 inhibition: optimization of therapy and identification of biomarkers of response in breast cancer.
Feng FY, Speers C, Liu M, Jackson WC, Moon D, Rinkinen J, Wilder-Romans K, Jagsi R, Pierce LJ.
Breast Cancer Res Treat. 2014 Aug;147(1):81-94.
Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer.
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.
Nature. 2014 Jun 12;510(7504):278-82.
PCAT-1, a long noncoding RNA, regulates BRCA2 and controls homologous recombination in cancer.
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.
Cancer Res. 2014 Mar 15;74(6):1651-60.