Pamela Paris, PhD
Professor Emeritus
Urology
School of Medicine

Research Interests Our laboratory conducts translational cancer genomics research. The overarching goal is to identify drug targets with associated prognostic biomarkers. To date, their primary focus has been primary and metastatic prostate cancer.

Websites

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• Profile at urology.ucsf.edu (urology.ucsf.edu)

Grants and Projects

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• External validation of GEMCaP, a prognostic DNA biomarker set for CaP recurrence, NIH, 2011-2016
• CaP Metastasis Biomarkers: Validation/Genomics/Biology, NIH, 2005-2011

Publications (62)

Top publication keywords:
Prostatic NeoplasmsNucleic Acid HybridizationCarotenoidsNucleic Acid Amplification TechniquesNeoplastic Cells, CirculatingDNA, NeoplasmBiomarkers, TumorProstatectomyProstateProstatic Neoplasms, Castration-ResistantGenome, HumanNeoplasm Recurrence, LocalDNA Copy Number VariationsComparative Genomic HybridizationNeoplasm Metastasis

• Evaluation of Culture Conducive to Academic Success by Gender at a Comprehensive Cancer Center.
  The oncologist 2024 Keenan BP, Sibley A, Zhang L, Westring AF, Velazquez AI, Bank EM, Bergsland EK, Boreta L, Conroy P, Daras M, Hermiston M, Hsu G, Paris PL, Piawah S, Sinha S, Sosa JA, Tsang M, Venook AP, Wong M, Yom …
• A Phase Ib/II Study of the CDK4/6 Inhibitor Ribociclib in Combination with Docetaxel plus Prednisone in Metastatic Castration-Resistant Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2022 de Kouchkovsky I, Rao A, Carneiro BA, Zhang L, Lewis C, Phone A, Small EJ, Friedlander T, Fong L, Paris PL, Ryan CJ, Szmulewitz RZ, Aggarwal R
• Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer Via Targeted, Multiregion Sequencing.
  JCO precision oncology 2021 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
• Plasma miRNA Biomarkers in Limited Volume Samples for Detection of Early-stage Pancreatic Cancer.
  Cancer prevention research (Philadelphia, Pa.) 2021 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
• Cell-free DNA concentration and fragment size as a biomarker for prostate cancer.
  Scientific reports 2021 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

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• Multiple Tissue Biomarkers Independently and Additively Predict Prostate Cancer Pathology Outcomes.
  European urology 2020 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
• A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer.
  BMC cancer 2020 Cario CL, Chen E, Leong L, Emami NC, Lopez K, Tenggara I, Simko JP, Friedlander TW, Li PS, Paris PL, Carroll PR, Witte JS
• Breast and prostate cancers harbor common somatic copy number alterations that consistently differ by race and are associated with survival.
  BMC medical genomics 2020 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
• Identification and Characterization of Circulating Tumor Cells in Men Who have Undergone Prostatectomy for Clinically Localized, High Risk Prostate Cancer.
  The Journal of urology 2019 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…
• Targeting CD46 for both adenocarcinoma and neuroendocrine prostate cancer.
  JCI insight 2018 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
• Copy number gains at chr3p25 and chr11p11 are associated with lymph node involvement and survival in muscle-invasive bladder tumors.
  PloS one 2017 Lindquist KJ, Sanford T, Friedlander TW, Paris PL, Porten SP
• Validation of GEMCaP as a DNA Based Biomarker to Predict Prostate Cancer Recurrence after Radical Prostatectomy.
  The Journal of urology 2017 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
• Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA.
  Microsystems & nanoengineering 2017 Kim SC, Premasekharan G, Clark IC, Gemeda HB, Paris PL, Abate AR
• Real-Time Transferrin-Based PET Detects MYC-Positive Prostate Cancer.
  Molecular cancer research : MCR 2017 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
• High-Dose Abiraterone Acetate in Men With Castration Resistant Prostate Cancer.
  Clinical genitourinary cancer 2017 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…
• Programmed death-ligand 1 (PD-L1) characterization of circulating tumor cells (CTCs) in muscle invasive and metastatic bladder cancer patients.
  BMC cancer 2016 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
• An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer.
  Cancer letters 2016 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, …
• Mutational Landscape of Aggressive Prostate Tumors in African American Men.
  Cancer research 2016 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
• Associations between circulating carotenoids, genomic instability and the risk of high-grade prostate cancer.
  The Prostate 2015 Nordström T, Van Blarigan EL, Ngo V, Roy R, Weinberg V, Song X, Simko J, Carroll PR, Chan JM, Paris PL
• Circulating Tumor Cells as Potential Biomarkers in Bladder Cancer.
  The Journal of urology 2015 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
• Androgen Receptor Gene Aberrations in Circulating Cell-Free DNA: Biomarkers of Therapeutic Resistance in Castration-Resistant Prostate Cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2015 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
• Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma.
  Nature medicine 2014 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
• Next generation sequencing of pancreatic cyst fluid microRNAs from low grade-benign and high grade-invasive lesions.
  Cancer letters 2014 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
• Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis.
  The American journal of pathology 2014 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
• Performance of the Genomic Evaluators of Metastatic Prostate Cancer (GEMCaP) tumor biomarker for identifying recurrent disease in African American patients.
  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2014 Levin AM, Lindquist KJ, Avila A, Witte JS, Paris PL, Rybicki BA
• Recurrent epimutations activate gene body promoters in primary glioblastoma.
  Genome research 2014 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
• Detection and characterization of invasive circulating tumor cells derived from men with metastatic castration-resistant prostate cancer.
  International journal of cancer 2014 Friedlander TW, Ngo VT, Dong H, Premasekharan G, Weinberg V, Doty S, Zhao Q, Gilbert EG, Ryan CJ, Chen WT, Paris PL
• Looking back, to the future of circulating tumor cells.
  Pharmacology & therapeutics 2013 Friedlander TW, Premasekharan G, Paris PL
• Common structural and epigenetic changes in the genome of castration-resistant prostate cancer.
  Cancer research 2011 Friedlander TW, Roy R, Tomlins SA, Ngo VT, Kobayashi Y, Azameera A, Rubin MA, Pienta KJ, Chinnaiyan A, Ittmann MM, Ryan CJ, Paris PL
• Detection of recurrent rearrangement breakpoints from copy number data.
  BMC bioinformatics 2011 Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ
• A group of genome-based biomarkers that add to a Kattan nomogram for predicting progression in men with high-risk prostate cancer.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2009 Paris PL, Weinberg V, Albo G, Roy R, Burke C, Simko J, Carroll P, Collins C
• Functional phenotyping and genotyping of circulating tumor cells from patients with castration resistant prostate cancer.
  Cancer letters 2009 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
• A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue.
  Methods in molecular biology (Clifton, N.J.) 2009 Paris PL
• An oncogenic role for the multiple endocrine neoplasia type 1 gene in prostate cancer.
  Prostate cancer and prostatic diseases 2008 Paris PL, Sridharan S, Hittelman AB, Kobayashi Y, Perner S, Huang G, Simko J, Carroll P, Rubin MA, Collins C
• Characterization of TMPRSS2-ERG fusion high-grade prostatic intraepithelial neoplasia and potential clinical implications.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2008 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
• A sequence-based survey of the complex structural organization of tumor genomes.
  Genome biology 2008 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…
• Evaluation of whole genome amplification protocols for array and oligonucleotide CGH.
  Diagnostic molecular pathology : the American journal of surgical pathology, part B 2007 Hittelman A, Sridharan S, Roy R, Fridlyand J, Loda M, Collins C, Paris PL
• High resolution oligonucleotide CGH using DNA from archived prostate tissue.
  The Prostate 2007 Paris PL, Sridharan S, Scheffer A, Tsalenko A, Bruhn L, Collins C
• TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion.
  The American journal of surgical pathology 2007 Perner S, Mosquera JM, Demichelis F, Hofer MD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, De Marzo AM, Rubin MA
• Morphological features of TMPRSS2-ERG gene fusion prostate cancer.
  The Journal of pathology 2007 Mosquera JM, Perner S, Demichelis F, Kim R, Hofer MD, Mertz KD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, Rubin MA
• Genomic profiling of hormone-naïve lymph node metastases in patients with prostate cancer.
  Neoplasia (New York, N.Y.) 2006 Paris PL, Hofer MD, Albo G, Kuefer R, Gschwend JE, Hautmann RE, Fridyland J, Simko J, Carroll PR, Rubin MA, Collins C
• Decoding the fine-scale structure of a breast cancer genome and transcriptome.
  Genome research 2006 Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins …
• Preliminary evaluation of prostate cancer metastatic risk biomarkers.
  The International journal of biological markers 2005 Paris PL, Weinberg V, Simko J, Andaya A, Albo G, Rubin MA, Carroll PR, Collins C
• Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization.
  Cytometry. Part A : the journal of the International Society for Analytical Cytology 2005 van Duin M, van Marion R, Watson JE, Paris PL, Lapuk A, Brown N, Oseroff VV, Albertson DG, Pinkel D, de Jong P, Nacheva EP, Dinjens W, van Dekken H, Collins C
• Evolution of 8p loss in transformed human prostate epithelial cells.
  Cancer genetics and cytogenetics 2004 Macoska JA, Paris P, Collins C, Andaya A, Beheshti B, Chaib H, Kant R, Begley L, MacDonald JW, Squire JA
• Molecular analysis of WFDC1/ps20 gene in prostate cancer.
  The Prostate 2004 Watson JE, Kamkar S, James K, Kowbel D, Andaya A, Paris PL, Simko J, Carroll P, McAlhany S, Rowley D, Collins C
• An analysis of CTLA-4 and proinflammatory cytokine genes in Wegener's granulomatosis.
  Arthritis and rheumatism 2004 Zhou Y, Huang D, Paris PL, Sauter CS, Prock KA, Hoffman GS
• Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer.
  Cancer research 2004 Rubin MA, Varambally S, Beroukhim R, Tomlins SA, Rhodes DR, Paris PL, Hofer MD, Storz-Schweizer M, Kuefer R, Fletcher JA, Hsi BL, Byrne JA, Pienta KJ, Collins C, Sellers WR, Chinnaiyan AM
• Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors.
  Human molecular genetics 2004 Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, …
• Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer.
  Oncogene 2004 Watson JE, Doggett NA, Albertson DG, Andaya A, Chinnaiyan A, van Dekken H, Ginzinger D, Haqq C, James K, Kamkar S, Kowbel D, Pinkel D, Schmitt L, Simko JP, Volik S, Weinberg VK, Paris PL, Collins C
• Association of prostate cancer risk and aggressiveness to androgen pathway genes: SRD5A2, CYP17, and the AR.
  The Prostate 2004 Cicek MS, Conti DV, Curran A, Neville PJ, Paris PL, Casey G, Witte JS
• Comprehensive evaluation of the association between prostate cancer and genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2.
  European journal of human genetics : EJHG 2004 Loukola A, Chadha M, Penn SG, Rank D, Conti DV, Thompson D, Cicek M, Love B, Bivolarevic V, Yang Q, Jiang Y, Hanzel DK, Dains K, Paris PL, Casey G, Witte JS
• Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis.
  Genes, chromosomes & cancer 2004 van Dekken H, Paris PL, Albertson DG, Alers JC, Andaya A, Kowbel D, van der Kwast TH, Pinkel D, Schröder FH, Vissers KJ, Wildhagen MF, Collins C
• CYP3A4 and CYP3A5 genotypes, haplotypes, and risk of prostate cancer.
  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2003 Plummer SJ, Conti DV, Paris PL, Curran AP, Casey G, Witte JS
• High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.
  The American journal of pathology 2003 Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schröder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H
• Prostate cancer aggressiveness locus on chromosome 7q32-q33 identified by linkage and allelic imbalance studies.
  Neoplasia (New York, N.Y.) 2002 Neville PJ, Conti DV, Paris PL, Levin H, Catalona WJ, Suarez BK, Witte JS, Casey G
• Diffuse large B-cell lymphoma of the stomach: assessment of microsatellite instability, allelic imbalance, and trisomy of chromosomes 3, 12, and 18.
  Diagnostic molecular pathology : the American journal of surgical pathology, part B 2002 Skacel M, Paris PL, Pettay JD, Tsiftsakis EK, Tubbs RR, Casey G, Hsi ED
• Identification and fine mapping of a region showing a high frequency of allelic imbalance on chromosome 16q23.2 that corresponds to a prostate cancer susceptibility locus.
  Cancer research 2000 Paris PL, Witte JS, Kupelian PA, Levin H, Klein EA, Catalona WJ, Casey G
• Association between a CYP3A4 genetic variant and clinical presentation in African-American prostate cancer patients.
  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 1999 Paris PL, Kupelian PA, Hall JM, Williams TL, Levin H, Klein EA, Casey G, Witte JS
• Probing DNA sequences in solution with a monomer-excimer fluorescence color change.
  Nucleic acids research 1998 Paris PL, Langenhan JM, Kool ET
• Experimental Measurement of Aromatic Stacking Affinities in the Context of Duplex DNA.
  Journal of the American Chemical Society 1996 Guckian KM, Schweitzer BA, Ren RX, Sheils CJ, Paris PL, Tahmassebi DC, Kool ET
• Naphthalene, Phenanthrene, and Pyrene as DNA Base Analogues: Synthesis, Structure, and Fluorescence in DNA.
  Journal of the American Chemical Society 1996 Ren RX, Chaudhuri NC, Paris PL, Rumney S, Kool ET