Research Summary

Our lab studies how prostate tumors develop resistance to targeted therapy. We study patient tumors directly to discover how genomic and epigenomic alterations acquired by the tumor affect patient outcomes. This knowledge can help us to develop novel therapies and identify predictive and prognostic biomarkers. Recent projects, in collaboration with physicians and experimental biologists, have used large-scale genome sequencing to identify non-coding DNA structural variants and epigenetic changes associated with therapy resistance in advanced prostate cancer (Lundberg et al. Cancer Research 2023; Zhang et al. Nature Cell Biology 2024; Zhao et al Nature Genetics 2024). Dr. Quigley's research receives support from the National Institutes of Health, the United States Department of Defense, the Prostate Cancer Foundation and the Benioff Initiative for Prostate Cancer Research.

Research Funding

  • May 1, 2024 - April 30, 2027 - Discovering transcriptional drivers of therapy-resistant metastatic prostate cancer , PI . Sponsor: DOD, Sponsor Award ID: PC230564
  • September 6, 2022 - September 5, 2024 - Advancing the Drug Development Process in Metastatic Prostate Cancer through Machine Learning , co-PI . Sponsor: Prostate Cancer Foundation, Sponsor Award ID: 22CHAS02

Education

Carleton College, BA, 1998, Computer Science
Columbia University, MA, 2006, Biomedical Informatics
University of Oslo, PhD, 2014, Genetics

Honors & Awards

  • 1998
    National Merit Scholar. B.A. degree awarded Magna Cum Laude
  • 2006
    M.A. degree awarded with honors
  • 2014
    AACR Scholar in Training award
  • 2017
    Prostate Cancer Foundation Young Investigator Award
  • 2018
    BRCA Foundation Young Investigator Award
  • 2024
    Robert Sutherland Award, PacRim Breast and Prostate Cancer Meeting
  • 2024
    Outstanding Faculty Mentorship Award, UCSF Students of the Graduate Division

Selected Publications

  1. Thienger P, Paassen I, Yao X, Rubin PD, Lehner M, Lillis N, Benjak A, Shah SR, Leung AK, de Brot S, Naveed A, Daniel B, Shi M, Tremblay J, Triscott J, Cassanmagnago GA, Bolis M, Mela L, Beltran H, Chen Y, Piscuoglio S, Yu H, Ng CKY, Quigley DA, Yauch RL, Rubin MA A double-negative prostate cancer subtype is vulnerable to SWI/SNF-targeting degrader molecules.  View on PubMed
  2. Mout L, Moreno-Rodriguez T, Grillo G, Nand A, Keshavarzian T, Bahl S, Kang K, Bootsma M, Minnee E, Zhou S, Burns KH, Corey E, Nelson P, Dehm SM, Zhao SG, Zwart W, Feng F, Quigley D, Lupien M Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer.  View on PubMed
  3. Kumaraswamy A, Hu YM, Yates JA, Zhang C, Rodansky E, Khokhani D, Flores D, Duan Z, Zhang Y, Tabatabaei S, Slottke R, Ye S, Lara P, Foye A, Ryan CJ, Quigley DA, Huang J, Aggarwal R, Reiter RE, Wicha MS, Beer TM, Rettig M, Gleave M, Evans CP, Witte ON, Stuart JM, Thomas GV, Feng FY, Small EJ, Xia Z, Alumkal JJ Transcriptional profiling clarifies a program of enzalutamide extreme non-response in lethal prostate cancer.  View on PubMed
  4. Liu T, Zhang M, Farsh T, Li H, Kishishita A, Barpanda A, Leung SG, Zhu J, Jung H, Hua JT, Zhu X, Kim AB, Goo YA, Son M, Kim J, Subramanian A, Sjöström M, Fuh KC, Chapman JS, Carnevale J, Gilbert LA, Lakkaraju A, Bruno PM, Quigley D, Wiita AP, Feng FY, DeSelm CJ. Exploitable mechanisms of antibody and CAR mediated macrophage cytotoxicity. Nat Commun. 2025 Jul 01; 16(1):5616.  View on PubMed
  5. Mizuno K, Ku SY, Venkadakrishnan VB, Bakht MK, Sigouros M, Chan J, Trigos A, Driskill JH, Manohar J, King A, Presser AG, Kim MJ, Tewari AK, Long HW, Quigley D, Choueiri TK, Balk S, Hill S, Mosquera JM, Einstein D, Sandhu S, Taplin ME, Beltran H Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer.  View on PubMed
  6. Duan Z, Shi M, Kumaraswamy A, Lin D, Khokhani D, Wang Y, Zhang C, Flores D, Rodansky E, Swaim OA, Storck WK, Beck HN, Patel RA, Sayar E, Hanratty BP, Xue H, Dong X, Maylin ZR, Wan R, Quigley DA, Sjöström M, Hu YM, Zhao F, Xia Z, Cheng S, Yu X, Feng FY, Zhang L, Aggarwal R, Small EJ, Ravikumar V, Rao A, Bedi K, Lee JK, Morrissey C, Coleman I, Nelson PS, Corey E, Udager AM, Rebernick RJ, Cieslik MP, Chinnaiyan AM, Yates JA, Haffner MC, Wang Y, Alumkal JJ. PROX1 is an early driver of lineage plasticity in prostate cancer. J Clin Invest. 2025 Jun 02; 135(11).  View on PubMed
  7. Sha Zhu, Mikhail Dias, Yuxin Yang, Emma Dolan, Thaidy Moreno Rodriguez, Tamilla Nechiporuk, Jun Zhu, Derek Xiang, Tianyi Liu, Tatyanah Farsh, Meng Zhang, Gabriel Eades, Stanley G. Leung, Lisa Chesner, Peter Bruno, Matthew R. Cooperberg, David Quigley, Felix Y Feng, Haolong Li, Carissa E Chu FACS-based whole-genome CRISPRi screen to uncover STEAP1 regulators in prostate cancer.  View on PubMed
  8. Anbarasu Kumaraswamy, Ya-Mei Hu, Joel Yates, Chao Zhang, Shangyuan Ye, Charles J. Ryan, David Quigley, Rahul Raj Aggarwal, Robert Evan Reiter, Tomasz M. Beer, Matthew Rettig, Martin Gleave, Primo N. Lara, Josh Stuart, George V. Thomas, Felix Y. Feng, Eric J. Small, Zheng Xia, Joshi J. Alumkal Transcriptional profiling to identify a program of enzalutamide extreme non-response in lethal prostate cancer.  View on PubMed
  9. Li H, Melnyk JE, Fu BXH, Shrestha R, Zhang M, Sjöström M, Feng S, Anderson JA, Han W, Chesner LN, Shin HJ, Farsh T, Suarez HJ, Nath S, Chou J, Das R, Egusa EA, Zhu J, Winters A, Maheshwari A, Hua JT, Alshalalfa M, Chen WS, Calvert M, Davicioni E, Kishishita A, Barpanda A, Liu T, Wiita AP, Stohr BA, Siddiqui J, Huang B, Small EJ, Shokat KM, Nelson P, Quigley DA, Wasmuth EV, Gilbert LA, Feng FY. Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator. bioRxiv. 2025 May 31.  View on PubMed
  10. Feng E, Feng E, Berg T, Nguyen IS, Nguyen LG, Chen W, Zhang M, Quigley D, Sharifi M, Li H, Coleman I, Nelson PS, Sjöström M, Zhao SG Identifying prognostic targets in metastatic prostate cancer beyond AR.  View on PubMed
  11. Sha Zhu, Mikhail Dias, Yuxin Yang, Meng Zhang, Emma Dolan, Thaidy Moreno-Rodriguez, Jun Zhu, Derek Xiang, Tianyi Liu, Tatyanah Farsh, Gabriel Eades, Stanley Leung, Lisa Chesner, Xiekui Cui, Xiaolin Zhu, Noah Younger, John Liu, Peter Bruno, David Quigley, Haolong Li, Felix Feng, Carissa Chu PD35-07 FACS-BASED WHOLE-GENOME CRISPRi SCREEN TO UNCOVER STEAP1 REGULATORS IN PROSTATE CANCER.  View on PubMed
  12. Rensheng Wan, Raunak Shrestha, Gulfem Guler, Yuhong Ning, Aishwarya Subramanian, Adam Foye, Meng Zhang, Xiaolin Zhu, Thaidy Moreno-Rodriguez, Haolong Li, Shuang G. Zhao, Joshi J. Alumkal, Rahul Aggarwal, Alexander W. Wyatt, David Quigley, Samuel Levy, Eric Small, Felix Feng, Martin Sjöström. Abstract 1985: 5hmC-sequencing of matched cfDNA and tissue from men with mCRPC is concordant and identifies loss of AR signaling in NEPC and DNPC. Cancer Research. 2025 Apr 21; 85(8_Supplement_1):1985-1985.  View on PubMed
  13. Ceyda Coruh, Onur Sakarya, Yuhong Ning, Yuan Xue, Michael Cipriano, Kyle Hazen, Alexander W. Wyatt, David Quigley, Felix Feng, Martin Sjostrom, Gulfem Guler, Wayne Volkmuth, Samuel Levy Abstract 3681: A tumor-naive method for estimating tumor fraction using 5-hydroxymethylation cytosine in cell-free DNA.  View on PubMed
  14. Carissa Chu, David Quigley. Felix Feng (1975–2024). Nature Cancer. 2025 Apr 18; 1-1.  View on PubMed
  15. Feng EM, Vo-Phamhi J, Subramanian AN, Dias M, Foye A, Vinson J, Hong JC, Freedland SJ, Alumkal JJ, Beltran H, Morrissey C, Nelson PS, Chinnaiyan AM, Aggarwal R, Small EJ, Quigley DA, Sjöström M, Zhao SG, Chen WS. Racial variation in the advanced prostate cancer genome. Prostate Cancer Prostatic Dis. 2025 Mar 31.  View on PubMed
  16. Ettori F, Mandal D, Quigley D Low-temperature nucleation rate calculations using the N-Fold way.  View on PubMed
  17. Aggarwal RR, Vuky J, VanderWeele D, Rettig M, Heath EI, Quigley D, Huang J, Chumber A, Cheung A, Foye A, Leung S, Abbey J, Dorr A, Nasoff M, Hunter J, Wang S, Flavell RR, Fong L, Liu B, Small EJ. Phase I, First-in-Human Study of FOR46 (FG-3246), an Immune-Modulating Antibody-Drug Conjugate Targeting CD46, in Patients With Metastatic Castration-Resistant Prostate Cancer. J Clin Oncol. 2025 May 20; 43(15):1824-1834.  View on PubMed
  18. Chesner LN, Polesso F, Graff JN, Hawley JE, Smith AK, Lundberg A, Das R, Shenoy T, Sjöström M, Zhao F, Hu YM, Linder S, Chen WS, Hawkins RM, Shrestha R, Zhu X, Foye A, Li H, Kim LM, Bhalla M, O'loughlin T, Kuzuoglu-Ozturk D, Hua JT, Badura ML, Wilkinson S, Trostel SY, Bergman AM, Ruggero D, Drake CG, Sowalsky AG, Fong L, Cooperberg MR, Zwart W, Guan X, Ashworth A, Xia Z, Quigley DA, Gilbert LA, Feng FY, Moran AE. Androgen Receptor Inhibition Increases MHC Class I Expression and Improves Immune Response in Prostate Cancer. Cancer Discov. 2025 Mar 03; 15(3):481-494.  View on PubMed
  19. Sharifi MN, Feng E, Rydzewski NR, Taylor AK, Sperger JM, Shi Y, Helzer KT, Bootsma ML, Carreno V, Chang AH, Nunamaker LA, Blitzer GC, Shang TA, Subramanian A, Bjartell A, Josefsson A, Wikström P, Feng E, Kohli M, Yang R, Dehm SM, Small EJ, Aggarwal R, Quigley DA, Lang JM, Zhao SG, Sjöström M. Adverse prognosis gene expression patterns in metastatic castration-resistant prostate cancer. Mol Oncol. 2025 Feb 22.  View on PubMed
  20. William S. Chen, Mikhail Dias, Chien-Kuang Cornelia Ding, Stefanie Engler, Sophie Déglise, Aishwarya Subramanian, Haolong Li, Andrea Jacobs, Martin Sjöström, Jonathan Chou, Julian C. Hong, Shuang Zhao, Jeffry Simko, Eric J. Small, Alan Ashworth, David Alan Quigley, Peter Carroll, Matthew R. Cooperberg, Bernd Bodenmiller, Felix Y Feng. Improving prostate cancer risk stratification using spatial single-cell tumor profiling. Journal of Clinical Oncology. 2025 Feb 10; 43(5_suppl):413-413.  View on PubMed

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