Pamela L. Paris, PhD

Pamela L. Paris, PhD

Adjunct Professor, Department of Urology, UCSF

Phone: (415) 514-2559 (voice)
Box 3110, UCSF
San Francisco, CA 94143-3110

UCSF Profiles

Cancer Center Membership

Program Member » Prostate Cancer

Research Summary

My background is in biophysical chemistry, which I’ve applied to the field of cancer genomics. As a postdoctoral fellow at the Cleveland Clinic, I carried out whole-genome, linkage disequilibrium experiments to identify susceptibility loci for aggressive prostate cancer. At UCSF, I embarked on biomarker discovery as a Translational Research Fellow for the UCSF Prostate SPORE program and discovered a DNA-based biomarker set to assess risk of recurrence after primary treatment for prostate cancer. My landmark paper in the American Journal of Pathology set the stage for the use of formalin-fixed paraffin-embedded (FFPE) prostate cancer tissue with microarrays for copy-number assessment. Similarly, I was the first to demonstrate FFPE prostate biopsy tissue could be profiled on high-resolution microarrays. I continued to grow my biomarker research program as a Researcher in the Cancer Center and in the Department of Urology. As a Professor, I established myself as a translational researcher in prostate cancer, both in solid tumor and circulating biomarkers, as part of the Division of Hematology-Oncology. I helped move the circulating tumor cell (CTC) field beyond enumeration and was the first to genomically profile prostate cancer CTCs. The overarching goal of my research program is to identify prognostic biomarkers to aid in clinical decision-making.


John Carroll University, Cleveland, Ohio, B.S., 1992, Chemistry
University of Rochester, Rochester, New York, M.S., 1995, Biophysical Chemistry
University of Rochester, Rochester, New York, Ph.D., 1998, Biophysical Chemistry
Cleveland Clinic Foundation, Cleveland, Ohio, Postdoc, 1998-2001, Prostate cancer genetics
University of California at San Francisco, San Francisco, California, Postdoc, 2001-2003, Prostate cancer genomics

Professional Experience

  • 1993-1998
    Graduate Student, University of Rochester, Rochester, New York (Advisor: Eric T. Kool)
  • 1998-2001
    Postdoctoral Research Fellow, Cleveland Clinic Foundation, Lerner Research Institute, Cancer Biology Department, Cleveland, Ohio
  • 2001-2003
    Translational Research Fellow, Prostate SPORE, Dept of Urology, UCSF, San Francisco, CA
  • 2003-2006
    Assistant Researcher, UCSF Comprehensive Cancer Center, San Francisco, California
  • 2006-2009
    Associate Researcher, Department of Urology, UCSF, San Francisco, California
  • 2009-2012
    Associate Adjunct Professor, Department of Urology, UCSF, San Francisco, California
  • 2010-present
    Joint Appointment, Division of Hematology-Oncology, Department of Medicine, UCSF
  • 2010-present
    UCSF Helen Diller Family Comprehensive Cancer Center Member
  • 2012-present
    Professor, Department of Urology, UCSF

Honors & Awards

  • 1990
    Phi Lambda Upsilon, Honorary Chemical Society
  • 1992
    Magna cum laude
  • 1993-1998
    Sherman Clarke Fellow
  • 1995-1996
    Merck Fellow
  • 2000
    Society for Basic Urologic Research Travel Award
  • 2001-2003
    UCSF Prostate Cancer Research Fellow
  • 2003-present
    NCI Cancer Prevention and Epidemiology Review Committee
  • 2005
    Gordon Research Conference (New Frontiers: Cancer Detection and Diagnosis) Poster Award
  • 2005
    UCSF, Prostate Cancer Annual Retreat, Poster Award
  • 2008
    Longevity Consortium Member

Selected Publications

  1. Premasekharan G, Gilbert E, Okimoto RA, Hamirani A, Lindquist KJ, Ngo VT, Roy R, Hough J, Edwards M, Paz R, Foye A, Sood R, Copren KA, Gubens M, Small EJ, Bivona TG, Collisson EA, Friedlander TW, Paris PL. An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer. Cancer Lett. 2016 Sep 28; 380(1):144-52.
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  2. Lindquist KJ, Paris PL, Hoffmann TJ, Cardin NJ, Kazma R, Mefford JA, Simko JP, Ngo V, Chen Y, Levin AM, Chitale D, Helfand BT, Catalona WJ, Rybicki BA, Witte JS. Mutational Landscape of Aggressive Prostate Tumors in African American Men. Cancer Res. 2016 Apr 1; 76(7):1860-8.
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  3. Nordström T, Van Blarigan EL, Ngo V, Roy R, Weinberg V, Song X, Simko J, Carroll PR, Chan JM, Paris PL. Associations between circulating carotenoids, genomic instability and the risk of high-grade prostate cancer. Prostate. 2016 Mar; 76(4):339-48.
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  4. Alva A, Friedlander T, Clark M, Huebner T, Daignault S, Hussain M, Lee C, Hafez K, Hollenbeck B, Weizer A, Premasekharan G, Tran T, Fu C, Ionescu-Zanetti C, Schwartz M, Fan A, Paris P. Circulating Tumor Cells as Potential Biomarkers in Bladder Cancer. J Urol. 2015 Sep; 194(3):790-8.
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  5. Azad AA, Volik SV, Wyatt AW, Haegert A, Le Bihan S, Bell RH, Anderson SA, McConeghy B, Shukin R, Bazov J, Youngren J, Paris P, Thomas G, Small EJ, Wang Y, Gleave ME, Collins CC, Chi KN. Androgen Receptor Gene Aberrations in Circulating Cell-Free DNA: Biomarkers of Therapeutic Resistance in Castration-Resistant Prostate Cancer. Clin Cancer Res. 2015 May 15; 21(10):2315-24.
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  6. Hashizume R, Andor N, Ihara Y, Lerner R, Gan H, Chen X, Fang D, Huang X, Tom MW, Ngo V, Solomon D, Mueller S, Paris PL, Zhang Z, Petritsch C, Gupta N, Waldman TA, James CD. Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma. Nat Med. 2014 Dec; 20(12):1394-6.
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  7. Wang J, Paris PL, Chen J, Ngo V, Yao H, Frazier ML, Killary AM, Liu CG, Liang H, Mathy C, Bondada S, Kirkwood K, Sen S. Next generation sequencing of pancreatic cyst fluid microRNAs from low grade-benign and high grade-invasive lesions. Cancer Lett. 2015 Jan 28; 356(2 Pt B):404-9.
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  8. Heselmeyer-Haddad KM, Berroa Garcia LY, Bradley A, Hernandez L, Hu Y, Habermann JK, Dumke C, Thorns C, Perner S, Pestova E, Burke C, Chowdhury SA, Schwartz R, Schäffer AA, Paris PL, Ried T. Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis. Am J Pathol. 2014 Oct; 184(10):2671-86.
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  9. Levin AM, Lindquist KJ, Avila A, Witte JS, Paris PL, Rybicki BA. Performance of the Genomic Evaluators of Metastatic Prostate Cancer (GEMCaP) tumor biomarker for identifying recurrent disease in African American patients. Cancer Epidemiol Biomarkers Prev. 2014 Aug; 23(8):1677-82.
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  10. Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res. 2014 May; 24(5):761-74.
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  11. Friedlander TW, Ngo VT, Dong H, Premasekharan G, Weinberg V, Doty S, Zhao Q, Gilbert EG, Ryan CJ, Chen WT, Paris PL. Detection and characterization of invasive circulating tumor cells derived from men with metastatic castration-resistant prostate cancer. Int J Cancer. 2014 May 15; 134(10):2284-93.
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  12. Friedlander TW, Premasekharan G, Paris PL. Looking back, to the future of circulating tumor cells. Pharmacol Ther. 2014 Jun; 142(3):271-80.
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  13. Friedlander TW, Roy R, Tomlins SA, Ngo VT, Kobayashi Y, Azameera A, Rubin MA, Pienta KJ, Chinnaiyan A, Ittmann MM, Ryan CJ, Paris PL. Common structural and epigenetic changes in the genome of castration-resistant prostate cancer. Cancer Res. 2012 Feb 1; 72(3):616-25.
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  14. Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ. Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinformatics. 2011; 12:114.
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  15. Paris PL, Weinberg V, Albo G, Roy R, Burke C, Simko J, Carroll P, Collins C. A group of genome-based biomarkers that add to a Kattan nomogram for predicting progression in men with high-risk prostate cancer. Clin Cancer Res. 2010 Jan 1; 16(1):195-202.
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  16. Paris PL, Kobayashi Y, Zhao Q, Zeng W, Sridharan S, Fan T, Adler HL, Yera ER, Zarrabi MH, Zucker S, Simko J, Chen WT, Rosenberg J. Functional phenotyping and genotyping of circulating tumor cells from patients with castration resistant prostate cancer. Cancer Lett. 2009 May 18; 277(2):164-73.
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  17. Paris PL. A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue. Methods Mol Biol. 2009; 556:89-98.
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  18. Paris PL, Sridharan S, Hittelman AB, Kobayashi Y, Perner S, Huang G, Simko J, Carroll P, Rubin MA, Collins C. An oncogenic role for the multiple endocrine neoplasia type 1 gene in prostate cancer. Prostate Cancer Prostatic Dis. 2009; 12(2):184-91.
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  19. Mosquera JM, Perner S, Genega EM, Sanda M, Hofer MD, Mertz KD, Paris PL, Simko J, Bismar TA, Ayala G, Shah RB, Loda M, Rubin MA. Characterization of TMPRSS2-ERG fusion high-grade prostatic intraepithelial neoplasia and potential clinical implications. Clin Cancer Res. 2008 Jun 1; 14(11):3380-5.
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  20. Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol. 2008; 9(3):R59.
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