Selected Publications

UCSF Mission Bay Campus

UCSF Mission Bay Campus

2017

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.

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.

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. 


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. 

2014