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.

Research Funding

  • April 5, 2011 - March 31, 2016 - External validation of GEMCaP, a prognostic DNA biomarker set for CaP recurrence, Principal Investigator. Sponsor: NIH/NCI, Sponsor Award ID: R01CA158200
  • September 1, 2005 - June 30, 2011 - CaP Metastasis Biomarkers: Validation/Genomics/Biology, Principal Investigator. Sponsor: NIH/NCI, Sponsor Award ID: R01CA115484
  • April 5, 2011 - March 31, 2016 - External validation of GEMCaP, a prognostic DNA biomarker set for CaP recurrence, Principal Investigator. Sponsor: NIH/NCI, Sponsor Award ID: R01CA158200
  • September 1, 2005 - June 30, 2011 - CaP Metastasis Biomarkers: Validation/Genomics/Biology, Principal Investigator. Sponsor: NIH/NCI, Sponsor Award ID: R01CA115484

Education

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

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. Chen E, Cario CL, Leong L, Lopez K, Márquez CP, Li PS, Oropeza E, Tenggara I, Cowan J, Simko JP, Kageyama R, Wells DK, Chan JM, Friedlander T, Aggarwal R, Paris PL, Feng F, Carroll PR, Witte JS. Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer Via Targeted, Multiregion Sequencing. JCO Precis Oncol. 2021; 5.  View on PubMed
  2. Dittmar RL, Liu S, Tai MC, Rajapakshe K, Huang Y, Longton G, DeCapite C, Hurd MW, Paris PL, Kirkwood KS, Coarfa C, Maitra A, Brand RE, Killary AM, Sen S. Plasma miRNA Biomarkers in Limited Volume Samples for Detection of Early-stage Pancreatic Cancer. Cancer Prev Res (Phila). 2021 Jul; 14(7):729-740.  View on PubMed
  3. Chen E, Cario CL, Leong L, Lopez K, Márquez CP, Chu C, Li PS, Oropeza E, Tenggara I, Cowan J, Simko JP, Chan JM, Friedlander T, Wyatt AW, Aggarwal R, Paris PL, Carroll PR, Feng F, Witte JS. Cell-free DNA concentration and fragment size as a biomarker for prostate cancer. Sci Rep. 2021 Mar 03; 11(1):5040.  View on PubMed
  4. Cooperberg MR, Cowan JE, Lindquist KJ, Kobayashi Y, Simko JP, Bengtsson H, Singh K, Ngo V, Avila A, Newcomb LF, Tretriakova M, Lin DW, Stone S, Carroll PR, Paris PL. Multiple Tissue Biomarkers Independently and Additively Predict Prostate Cancer Pathology Outcomes. Eur Urol. 2021 01; 79(1):141-149.  View on PubMed
  5. Cario CL, Chen E, Leong L, Emami NC, Lopez K, Tenggara I, Simko JP, Friedlander TW, Li PS, Paris PL, Carroll PR, Witte JS. A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer. BMC Cancer. 2020 Aug 28; 20(1):820.  View on PubMed
  6. Chen Y, Sadasivan SM, She R, Datta I, Taneja K, Chitale D, Gupta N, Davis MB, Newman LA, Rogers CG, Paris PL, Li J, Rybicki BA, Levin AM. Breast and prostate cancers harbor common somatic copy number alterations that consistently differ by race and are associated with survival. BMC Med Genomics. 2020 08 20; 13(1):116.  View on PubMed
  7. Friedlander TW, Welty C, Anantharaman A, Schonhoft JD, Jendrisak A, Lee J, Li P, Hough J, Stromlund A, Edwards M, Sangar S, Kobayashi Y, Simko J, Farrokhian N, Lindquist K, Greene S, Ontiveros P, Graf R, Rodriquez A, Suraneni M, Wang Y, Landers M, Carroll P, Cooperberg MR, Dittamore R, Paris PL. Identification and Characterization of Circulating Tumor Cells in Men Who have Undergone Prostatectomy for Clinically Localized, High Risk Prostate Cancer. J Urol. 2019 10; 202(4):732-741.  View on PubMed
  8. Su Y, Liu Y, Behrens CR, Bidlingmaier S, Lee NK, Aggarwal R, Sherbenou DW, Burlingame AL, Hann BC, Simko JP, Premasekharan G, Paris PL, Shuman MA, Seo Y, Small EJ, Liu B. Targeting CD46 for both adenocarcinoma and neuroendocrine prostate cancer. JCI Insight. 2018 09 06; 3(17).  View on PubMed
  9. Lindquist KJ, Sanford T, Friedlander TW, Paris PL, Porten SP. Copy number gains at chr3p25 and chr11p11 are associated with lymph node involvement and survival in muscle-invasive bladder tumors. PLoS One. 2017; 12(11):e0187975.  View on PubMed
  10. Nguyen HG, Welty C, Lindquist K, Ngo V, Gilbert E, Bengtsson H, Magi-Galluzzi C, Jean-Gilles J, Yao J, Cooperberg M, Messing E, Klein EA, Carroll PR, Paris PL. Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy. J Urol. 2018 03; 199(3):719-725.  View on PubMed
  11. Kim SC, Premasekharan G, Clark IC, Gemeda HB, Paris PL, Abate AR. Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA. Microsyst Nanoeng. 2017; 3.  View on PubMed
  12. Aggarwal R, Behr SC, Paris PL, Truillet C, Parker MFL, Huynh LT, Wei J, Hann B, Youngren J, Huang J, Premasekharan G, Ranatunga N, Chang E, Gao KT, Ryan CJ, Small EJ, Evans MJ. Real-Time Transferrin-Based PET Detects MYC-Positive Prostate Cancer. Mol Cancer Res. 2017 09; 15(9):1221-1229.  View on PubMed
  13. Friedlander TW, Graff JN, Zejnullahu K, Anantharaman A, Zhang L, Paz R, Premasekharan G, Russell C, Huang Y, Kim W, Aggarwal RR, Lin AM, Fong L, Alumkal JJ, Beer TM, Sharifi N, Alyamani M, Dittamore R, Small EJ, Paris PL, Ryan CJ. High-Dose Abiraterone Acetate in Men With Castration Resistant Prostate Cancer. Clin Genitourin Cancer. 2017 12; 15(6):733-741.e1.  View on PubMed
  14. Anantharaman A, Friedlander T, Lu D, Krupa R, Premasekharan G, Hough J, Edwards M, Paz R, Lindquist K, Graf R, Jendrisak A, Louw J, Dugan L, Baird S, Wang Y, Dittamore R, Paris PL. Programmed death-ligand 1 (PD-L1) characterization of circulating tumor cells (CTCs) in muscle invasive and metastatic bladder cancer patients. BMC Cancer. 2016 Sep 22; 16(1):744.  View on PubMed
  15. 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 09 28; 380(1):144-52.  View on PubMed
  16. 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 04 01; 76(7):1860-8.  View on PubMed
  17. 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.  View on PubMed
  18. 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.  View on PubMed
  19. 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.  View on PubMed
  20. 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.  View on PubMed

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