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. 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
  2. Chu C, Quigley D. Felix Feng (1975-2024). Nat Cancer. 2025 Apr 18.  View on PubMed
  3. Carissa Chu, David Quigley. Felix Feng (1975–2024). Nature Cancer. 2025 Apr 18; 1-1.  View on PubMed
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. Chou J, Robinson TM, Egusa EA, Lodha R, Zhang M, Badura M, Mikayelyan M, Delavan HM, Swinderman J, Wilson C, Zhu J, Das R, Nguyen M, Loehr A, Golsorkhi T, Simmons A, Abida W, Chinnaiyan AM, Arkin MR, Small EJ, Quigley DA, Yang L, Kim M, Ashworth A, Feng FY. Synthetic Lethal Targeting of CDK12-Deficient Prostate Cancer with PARP Inhibitors. Clin Cancer Res. 2024 Dec 02; 30(23):5445-5458.  View on PubMed
  10. Seed G, Beije N, Yuan W, Bertan C, Goodall J, Lundberg A, Tyler M, Figueiredo I, Pereira R, Baker C, Bogdan D, Gallagher L, Cieslik JP, Greening S, Lambros M, Neves R, Magraner-Pardo L, Fowler G, Ebbs B, Miranda S, Flohr P, Bianchini D, Rescigno P, Porta N, Hall E, Gurel B, Tunariu N, Sharp A, Pettit S, Stoecklein NH, Sandhu S, Quigley D, Lord CJ, Mateo J, Carreira S, de Bono J. Elucidating acquired PARP inhibitor resistance in advanced prostate cancer. Cancer Cell. 2024 Dec 09; 42(12):2113-2123.e4.  View on PubMed
  11. E. Feng, J.M.A. Vo-Phamhi, A. Foye, J. Vinson, J.C. Hong, S.J. Freedland, J. Alumkal, H. Beltran, C. Morrissey, P. Nelson, A. Chinnaiyan, C. Sawyers, R. Aggarwal, E. Small, D. Quigley, M. Sjostrom, S.G. Zhao, W.S. Chen. Racial Variation in the Advanced Prostate Cancer Genome. International Journal of Radiation Oncology • Biology • Physics. 2024 Oct 1; 120(2):e519.  View on PubMed
  12. Shrestha R, Chesner LN, Zhang M, Zhou S, Foye A, Lundberg A, Weinstein AS, Sjöström M, Zhu X, Moreno-Rodriguez T, Li H, SU2C/PCF West Coast Prostate Cancer Dream Team, Alumkal JJ, Aggarwal R, Small EJ, Lupien M, Quigley DA, Feng FY. An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression. Cancer Res. 2024 Sep 16; 84(18):3086-3100.  View on PubMed
  13. Zhu X, Farsh T, Vis D, Yu I, Li H, Liu T, Sjöström M, Shrestha R, Kneppers J, Severson T, Zhang M, Lundberg A, Moreno Rodriguez T, Weinstein AS, Foye A, Mehra N, Aggarwal RR, Bergman AM, Small EJ, Lack NA, Zwart W, Quigley DA, van der Heijden MS, Feng FY. Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer. J Clin Invest. 2024 Aug 13; 134(19).  View on PubMed
  14. Zhu X, Chan E, Turski ML, Mendez CE, Hsu SC, Kumar V, Shipp C, Jindal T, Chang K, Onodera C, Devine WP, Grenert JP, Stohr BA, Ding CC, Stachler MD, Quigley DA, Feng FY, Chu CE, Porten SP, Chou J, Friedlander TW, Koshkin VS. HER2 overexpression in urothelial carcinoma with GATA3 and PPARG copy number gains. Oncologist. 2024 Aug 05; 29(8):e1094-e1097.  View on PubMed
  15. Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y, West Coast Dream Team Consortium, Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA, Lupien M, Feng FY. Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer. Nat Genet. 2024 Aug; 56(8):1689-1700.  View on PubMed
  16. Zhang M, Sjöström M, Cui X, Foye A, Farh K, Shrestha R, Lundberg A, Dang HX, Li H, Febbo PG, Aggarwal R, Alumkal JJ, Small EJ, SU2C/PCF West Coast Prostate Cancer Dream Team, Maher CA, Feng FY, Quigley DA. Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression. Nat Cell Biol. 2024 Jul; 26(7):1176-1186.  View on PubMed
  17. Subramanian A, Zhang M, Sharifi M, Moreno-Rodriguez T, Feng E, Rydzewski NR, Shrestha R, Zhu X, Zhao SG, Aggarwal R, Small EJ, Ding CC, Quigley DA, Sjöström M. A prostate cancer gastrointestinal transcriptional phenotype may be associated with diminished response to AR-targeted therapy. bioRxiv. 2024 Jun 03.  View on PubMed
  18. Ali Sabbagh, David Alan Quigley, Nicholas Lillis, Li Zhang, Isabel D Friesner, Adina Bailey, Rahul Raj Aggarwal, Meera Reddy Chappidi, Hari Singhal, Ke Zhang, Joel Greshock, Jinhui Li, Margaret K. Yu, Eric J. Small, Julian C. Hong. Development of a machine learning model to predict overall survival results from randomized clinical trials of patients with metastatic prostate cancer. Journal of Clinical Oncology. 2024 Jun 1; 42(16_suppl):5065-5065.  View on PubMed
  19. Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A. Stem-cell states converge in multistage cutaneous squamous cell carcinoma development. Science. 2024 05 31; 384(6699):eadi7453.  View on PubMed
  20. Raunak Shrestha, Lisa N. Chesner, Meng Zhang, Stanley Zhou, Adam Foye, Arian Lundberg, Alana S. Weinstein, Martin Sjöström, Xiaolin Zhu, Thaidy Moreno-Rodriguez, Haolong Li, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Mathieu Lupien, David A. Quigley, Felix Y. Feng. Abstract LB196: An atlas of accessible chromatin in advanced prostate cancer. Cancer Research. 2024 Apr 5; 84(7_Supplement):lb196-lb196.  View on PubMed

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