Prostate Cancer Research Group

You are here

Laboratory of Prostate Cancer Research Group

Mark A. Rubin, MD, Principal Investigator

Dr. Rubin is a Professor of Pathology and Laboratory Medicine and Director of the Englander Institute for Precision Medicine at Weill Cornell Medical College and NewYork-Presbyterian Hospital. As a laboratory based prostate cancer researcher, he has over 15 years experience in cancer genomics, biomarker discovery and cancer pathology. He was part of the team that co-discovered the common ETS rearrangements in prostate cancer and recently reported the first prostate cancer whole genomes including discovery of novel and clinically relevant biomarkers

Active Projects

  • The molecular characterization of prostate cancer
  • Characterizing the frequency and functional consequences of SPOP mutations
  • Functional characterization of NEPC
  • Biomarker discovery
  • RNA-sequencing
  • Identifying novel rearrangements and fusions
  • DNA damage response
  • “Organoid” cultures for drug sensitivity and molecular validation
  • Tumor modeling and functional characterization of somatic alterations and the development of novel FISH assays to validate them
  • Molecular profiling of urothelial bladder carcinoma

Active Grants

  • Integrative Genomics of Prostate Cancer Progression
    PI: Mark A. Rubin, MD
    Prostate Cancer Foundation Challenge Award
  • Prostate Cancer Research
    PI: Mark A. Rubin, MD
    New York State Department of Health Prostate Cancer Program Grant
  • Reconstructing Complex Loci in Lung Adenocarcinoma with Large-insert Whole Genome Sequencing
    PI: Marcin Imielinski, MD, PhD
    Career Award for Medical Scientists
  • Targeting EZH2 in Neuroendocrine Prostate Cancer
    PI: Loredana Puca, PhD
    American Italian Cancer Foundation Post-Doctoral Research Fellowship
  • SPORE in Prostate Cancer
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH) Research Subgrant
  • EDRN Biomarkers and Clinical Parameters Associated with Gleason Score Upgrading
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH) Research Subgrant
  • Molecular Signatures of Lethal and Indolent Prostate Cancer
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Comprehensive Prostate Cancer Characterization by Genomic and Transcriptomic Profiling
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Towards Understanding Prostate Cancer Heterogeneity
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Michigan/Cornell EDRN BDL: A Systems Biology Approach to the Development of Cancer Biomarkers
    Dual PIs: Mark A. Rubin, MD and Arul M. Chinnaiyan, MD, PhD
    National Cancer Institute (NIH)
  • Systematic Genetic Characterization of African American Prostate Cancer
    Co-PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Microtubule dependent AR signaling predicts taxane sensitivity
    Co-PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Functional Validation of Prostate Cancer Driving Mutations
    PI: Mark A. Rubin, MD
    Department of Defense Synergy Award (DOD)
  • Precision Therapy of Advanced Prostate Cancer
    PI: Mark A. Rubin, MD
    American Association of Cancer Research (AACR) - Stand Up To Cancer (SU2C)
  • Precision Medicine Sequencing
    PI: Mark A. Rubin, MD
    Prostate Cancer Foundation
  • Functional characterization of a molecularly homogenous subclass of prostate cancer using an in vivo model
    PI: Mark A. Rubin, MD
    Cancer Center of Weill Cornell Medical College and NewYork-Presbyterian Hospital
  • Interrogation of aberrant DNA repair in sporadic prostate cancer
    Co-PI: Mark A. Rubin, MD
    Prostate Cancer Foundation
  • Prioritizing rare variants associated with cancer using non-coding annotation
    PI: Mark Rubin, MD
    National Institutes of Health (NIH)
  • Epigenetic Therapy to Target Castration Resisitant Neuroendocrine Prostate Cancer
    PI: Loredana Puca, PhD
    Prostate Cancer Foundation - Young Investigator Award

Body

Laboratory of Prostate Cancer Research Group

Mark A. Rubin, MD, Principal Investigator

Dr. Rubin is a Professor of Pathology and Laboratory Medicine and Director of the Englander Institute for Precision Medicine at Weill Cornell Medical College and NewYork-Presbyterian Hospital. As a laboratory based prostate cancer researcher, he has over 15 years experience in cancer genomics, biomarker discovery and cancer pathology. He was part of the team that co-discovered the common ETS rearrangements in prostate cancer and recently reported the first prostate cancer whole genomes including discovery of novel and clinically relevant biomarkers

Active Projects

  • The molecular characterization of prostate cancer
  • Characterizing the frequency and functional consequences of SPOP mutations
  • Functional characterization of NEPC
  • Biomarker discovery
  • RNA-sequencing
  • Identifying novel rearrangements and fusions
  • DNA damage response
  • “Organoid” cultures for drug sensitivity and molecular validation
  • Tumor modeling and functional characterization of somatic alterations and the development of novel FISH assays to validate them
  • Molecular profiling of urothelial bladder carcinoma

Active Grants

  • Integrative Genomics of Prostate Cancer Progression
    PI: Mark A. Rubin, MD
    Prostate Cancer Foundation Challenge Award
  • Prostate Cancer Research
    PI: Mark A. Rubin, MD
    New York State Department of Health Prostate Cancer Program Grant
  • Reconstructing Complex Loci in Lung Adenocarcinoma with Large-insert Whole Genome Sequencing
    PI: Marcin Imielinski, MD, PhD
    Career Award for Medical Scientists
  • Targeting EZH2 in Neuroendocrine Prostate Cancer
    PI: Loredana Puca, PhD
    American Italian Cancer Foundation Post-Doctoral Research Fellowship
  • SPORE in Prostate Cancer
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH) Research Subgrant
  • EDRN Biomarkers and Clinical Parameters Associated with Gleason Score Upgrading
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH) Research Subgrant
  • Molecular Signatures of Lethal and Indolent Prostate Cancer
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Comprehensive Prostate Cancer Characterization by Genomic and Transcriptomic Profiling
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Towards Understanding Prostate Cancer Heterogeneity
    PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Michigan/Cornell EDRN BDL: A Systems Biology Approach to the Development of Cancer Biomarkers
    Dual PIs: Mark A. Rubin, MD and Arul M. Chinnaiyan, MD, PhD
    National Cancer Institute (NIH)
  • Systematic Genetic Characterization of African American Prostate Cancer
    Co-PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Microtubule dependent AR signaling predicts taxane sensitivity
    Co-PI: Mark A. Rubin, MD
    National Cancer Institute (NIH)
  • Functional Validation of Prostate Cancer Driving Mutations
    PI: Mark A. Rubin, MD
    Department of Defense Synergy Award (DOD)
  • Precision Therapy of Advanced Prostate Cancer
    PI: Mark A. Rubin, MD
    American Association of Cancer Research (AACR) - Stand Up To Cancer (SU2C)
  • Precision Medicine Sequencing
    PI: Mark A. Rubin, MD
    Prostate Cancer Foundation
  • Functional characterization of a molecularly homogenous subclass of prostate cancer using an in vivo model
    PI: Mark A. Rubin, MD
    Cancer Center of Weill Cornell Medical College and NewYork-Presbyterian Hospital
  • Interrogation of aberrant DNA repair in sporadic prostate cancer
    Co-PI: Mark A. Rubin, MD
    Prostate Cancer Foundation
  • Prioritizing rare variants associated with cancer using non-coding annotation
    PI: Mark Rubin, MD
    National Institutes of Health (NIH)
  • Epigenetic Therapy to Target Castration Resisitant Neuroendocrine Prostate Cancer
    PI: Loredana Puca, PhD
    Prostate Cancer Foundation - Young Investigator Award

Selected Publications EXPAND ALL ON THIS PAGE

Punctuated evolution of prostate cancer genomes.

April 25, 2013
Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barb

Punctuated evolution of prostate cancer genomes.

Cell. 2013 Apr 25;153(3):666-77.

Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA.

PMID: 23622249

Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer.

January 1, 2013
Mosquera JM, Beltran H, Park K, MacDonald TY, Robinson BD, Tagawa ST, Perner S, Bismar TA, Erbersdobler A, Dhir R, Nelson JB, Nanus DM, Rubin MA.

Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer.

Neoplasia. 2013 Jan;15(1):1-10.

Mosquera JM, Beltran H, Park K, MacDonald TY, Robinson BD, Tagawa ST, Perner S, Bismar TA, Erbersdobler A, Dhir R, Nelson JB, Nanus DM, Rubin MA.

PMID: 23358695

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer.

May 20, 2012
Juan Miguel Mosquera, Mark Rubin

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer.

Nat Genet. 2012 May 20;44(6):685-9. doi: 10.1038/ng.2279.

Barbieri CE, Baca SC, Lawrence MS, Demichelis F, Blattner M, Theurillat JP, White TA, Stojanov P, Van Allen E, Stransky N, Nickerson E, Chae SS, Boysen G, Auclair D, Onofrio RC, Park K, Kitabayashi N, MacDonald TY, Sheikh K, Vuong T, Guiducci C, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Hussain WM, Ramos AH, Winckler W, Redman MC, Ardlie K, Tewari AK, Mosquera JM, Rupp N, Wild PJ, Moch H, Morrissey C, Nelson PS, Kantoff PW, Gabriel SB, Golub TR, Meyerson M, Lander ES, Getz G, Rubin MA, Garraway LA.

PMID: 22610119; PMCID: PMC3673022

The genomic complexity of primary human prostate cancer.

February 10, 2011
Mark Rubin

The genomic complexity of primary human prostate cancer.

Nature. 2011 Feb 10;470(7333):214-20.

Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA.

PMID: 21307934

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.

January 1, 2010
Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA*, Gerstein MB*.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.

Genome Biol. 2010;11(10):R104.

Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB.

PMID: 20964841; PMCID: PMC3218660

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer.

August 1, 2009
Pflueger D, Rickman DS, Sboner A, Perner S, LaFargue CJ, Svensson MA, Moss BJ, Kitabayashi N, Pan Y, de la Taille A, Kuefer R, Tewari AK, Demichelis F, Chee MS, Gerstein MB, Rubin MA

N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer.

Neoplasia. 2009 Aug;11(8):804-11.

Pflueger D, Rickman DS, Sboner A, Perner S, LaFargue CJ, Svensson MA, Moss BJ, Kitabayashi N, Pan Y, de la Taille A, Kuefer R, Tewari AK, Demichelis F, Chee MS, Gerstein MB, Rubin MA.

PMID: 19649210; PMCID: PMC2713587

SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer

April 1, 2009
Rickman DS, Pflueger D, Moss B, VanDorn VE, Chen CX, de la Taille A, Kuefer R, Tewar AK, Setlur SR, Demichelis F, Rubin MA

SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer

Cancer Res. 2009 Apr 1;69(7):2734-8.

Rickman DS, Pflueger D, Moss B, VanDoren VE, Chen CX, de la Taille A, Kuefer R, Tewari AK, Setlur SR, Demichelis F, Rubin MA.

PMID: 19293179

Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer

April 1, 2009
Demichelis F, Setlur Sr, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina D, Hofer MD, Sboner A Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, Lee C, Gerstein MB, Kuefer R, Rubin MA

Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer

Genes Chromosomes Cancer. 2009 Apr;48(4):366-80.

Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, Lee C, Gerstein MB, Kuefer R, Rubin MA.

PMID: 19156837; PMCID: PMC2674964

Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer.

June 4, 2008
Setlur SR, Mertz KD, Hoshida Y, Demichelis F, Lupien M, Perner S, Sboner A, Pawitan, Y, Andrén O, Johnson LA,Tang J, Adami HO, Calza S, Chinnaiyan AM, Rhodes D, Tomlins S, Fall K, Mucci LA, Kantoff PW, Stampfer MJ, Andersson SO, Varenhorst E, Johansson

Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer.

J Natl Cancer Inst. 2008 Jun 4;100(11):815-25.

Setlur SR, Mertz KD, Hoshida Y, Demichelis F, Lupien M, Perner S, Sboner A, Pawitan Y, Andrén O, Johnson LA, Tang J, Adami HO, Calza S, Chinnaiyan AM, Rhodes D, Tomlins S, Fall K, Mucci LA, Kantoff PW, Stampfer MJ, Andersson SO, Varenhorst E, Johansson JE, Brown M, Golub TR, Rubin MA.

PMID: 18505969; PMCID: PMC3073404

Characterization of TMPRSS2-ERG fusion high-grade prostatic intraepithelial neoplasia and potential clinical implications

June 1, 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

Characterization of TMPRSS2-ERG fusion high-grade prostatic intraepithelial neoplasia and potential clinical implications

Clin Cancer Res. 2008 Jun 1;14(11):3380-5.

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.

PMID: 18519767; PMCID: PMC3717517

TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort

January 22, 2007
Demichelis F, Fall K, Perner S, Andren O, Schmidt F, Setlur SR, Hoshida Y, Mosquera JM, Pawitan Y, Lee C, Adami HO, Mucci LA, Kantoff PW, Andersson SO, Chinnaiyan AM, Johansson JE, Rubin MA

TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort

Oncogene. 2007 Jul 5;26(31):4596-9.

Demichelis F, Fall K, Perner S, Andrén O, Schmidt F, Setlur SR, Hoshida Y, Mosquera JM, Pawitan Y, Lee C, Adami HO, Mucci LA, Kantoff PW, Andersson SO, Chinnaiyan AM, Johansson JE, Rubin MA.

PMID: 17237811

TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer.

September 1, 2006
Perner S, Demichelis F, Beroukhim R, Schmidt FH, Mosquera JM, Setlur S, Tchinda J, Tomlins SA, Hofer MD, Pienta KG, Kuefer R, Vessella R, Sun XW, Meyerson M, Lee C, Sellers WR, Chinnaiyan AM, Rubin MA

TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer.

Cancer Res. 2006 Sep 1;66(17):8337-41.

Perner S, Demichelis F, Beroukhim R, Schmidt FH, Mosquera JM, Setlur S, Tchinda J, Tomlins SA, Hofer MD, Pienta KG, Kuefer R, Vessella R, Sun XW, Meyerson M, Lee C, Sellers WR, Chinnaiyan AM, Rubin MA.

PMID: 16951139

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer

October 28, 2005
Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer

Science. 2005 Oct 28;310(5748):644-8. 

Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM.

PMID: 16254181

alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer.

April 3, 2002
Rubin MA, Zhou M, Dhanasekaran S, Varambally S, Barrette TR, Sanda MG, Pienta KJ, Ghosh D, Chinnaiyan AM

alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer.

JAMA. 2002 Apr 3;287(13):1662-70.

Rubin MA, Zhou M, Dhanasekaran SM, Varambally S, Barrette TR, Sanda MG, Pienta KJ, Ghosh D, Chinnaiyan AM.

PMID: 11926890

Delineation of prognostic biomarkers in prostate cancer

August 23, 2001
Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM

Delineation of prognostic biomarkers in prostate cancer

Nature. 2001 Aug 23;412(6849):822-6. 

Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, Kurachi K, Pienta KJ, Rubin MA, Chinnaiyan AM.

PMID: 11518967

Research faculty

General Contact

Theresa MacDonald, Lab Manager
Pathology & Laboratory Medicine
Weill Cornell Medical College
Belfer Research Building
413 East 69th Street, Room 1450
New York, NY 10021
Tel: 646-962-6184
Fax: 646-962-0576
thm2008@med.cornell.edu

Visit Prostate Cancer Research Group

BACK TO TOP