Pathology & Laboratory Medicine

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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

  • Weill Cornell Medicine (WCM) SPORE in Prostate Cancer
    PI: Mark A. Rubin, MD
    National Institutes of Health (NIH) Specialized Program of Research Excellence
  • 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

Selected Publications

Modeling complex cancer rearrangement landscapes

Marcin Imielinski, MD, PhD

Modeling complex cancer rearrangement landscapes

Current Opinion in Systems Biology. 2016 Dec 26 [Epub ahead of print]

Maciejowski  J, Imielinski M. 

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Insertions and Deletions Target Lineage-Defining Genes in Human Cancers

Marcin Imielinski, MD, PhD

Insertions and Deletions Target Lineage-Defining Genes in Human Cancers

Cell. 2017 Jan 26;168(3):460-472.

Imielinski M, Guo G, Meyerson M.

PMID: 28089356

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The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

Marcin Imielinski, MD, PhD

The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

J Am Med Inform Assoc. 2016 Oct 27. [Epub ahead of print]

Huang L, Fernandes H, Zia H, Tavassoli P, Rennert H, Pisapia D, Imielinski M, Sboner A, Rubin MA, Kluk M, Elemento O.

PMID: 27789569

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High-throughput Phenotyping of Lung Cancer Somatic Mutations

Marcin Imielinski, MD, PhD

High-throughput Phenotyping of Lung Cancer Somatic Mutations

Cancer Cell2016 Aug 8;30(2):214-28.

Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS.

PMID: 27478040; PMCID: PMC5003022

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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Marcin Imielinski, MD, PhD

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Nat Genet. 2016 Jun;48(6):607-16. 

Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G; Cancer Genome Atlas Research Network., Artyomov MN, Schreiber R, Govindan R, Meyerson M.

PMID: 27158780; PMCID: PMC4884143

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Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

Marcin Imielinski, MD, PhD

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

Nat Genet. 2016 Feb;48(2):176-82. 

Zhang X, Choi PS, Francis JM, Imielinski M, Watanabe H, Cherniack AD, Meyerson M.

PMID: 26656844; PMCID: PMC4857881

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Genetic modifiers of EGFR dependence in non-small cell lung cancer

Marcin Imielinski, MD, PhD

Genetic modifiers of EGFR dependence in non-small cell lung cancer

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18661-6.

Sharifnia T, Rusu V, Piccioni F, Bagul M, Imielinski M, Cherniack AD, Pedamallu CS, Wong B, Wilson FH, Garraway LA, Altshuler D, Golub TR, Root DE, Subramanian A, Meyerson M.

PMID: 25512530; PMCID: PMC4284598

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Oncogenic RIT1 mutations in lung adenocarcinoma

Marcin Imielinski, MD, PhD

Oncogenic RIT1 mutations in lung adenocarcinoma

Oncogene. 2014 Aug 28;33(35):4418-23. 

Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi GX, Andres DA, Meyerson M. 

PMID: 24469055; PMCID: PMC4150988

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Comprehensive molecular profiling of lung adenocarcinoma

Marcin Imielinski, MD, PhD

Comprehensive molecular profiling of lung adenocarcinoma

Nature. 2014 Jul 31;511(7511):543-50. Erratum in: Nature. 2014 Oct 9;514(7521):262. Rogers, K [corrected to Rodgers, K].

Cancer Genome Atlas Research Network.. 

PubMed PMID: 25079552; PubMed Central PMCID: PMC4231481.

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Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma

Marcin Imielinski, MD, PhD

Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma

J Clin Invest. 2014 Apr;124(4):1582-6.

Imielinski M, Greulich H, Kaplan B, Araujo L, Amann J, Horn L, Schiller J, Villalona-Calero MA, Meyerson M, Carbone DP.

PMID: 24569458; PMCID: PMC3973082

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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

Marcin Imielinski, MD, PhD

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

PLoS One. 2014 Jan 31;9(1):e87361. 

Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M.

PMID:24498085; PMCID: PMC3909098

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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

Marcin Imielinski, MD, PhD

A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events

PLoS One. 2014 Jan 31;9(1):e87361.

Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M.

PMID: 24498085; PMCID: PMC3909098

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Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

Marcin Imielinski, MD, PhD

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

Cell. 2012 Sep 14;150(6):1107-20. 

Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M.

PMID: 22980975; PMCID: PMC3557932

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A landscape of driver mutations in melanoma

Marcin Imielinski, MD, PhD

A landscape of driver mutations in melanoma

Cell. 2012 Jul 20;150(2):251-63. 

Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, Davies MA, Gershenwald JE, Wagner SN, Hoon DS, Schadendorf D, Lander  ES, Gabriel SB, Getz G, Garraway LA, Chin L.

PMID: 22817889; PMCID: PMC3600117

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Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse

Marcin Imielinski, MD, PhD

Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse

Mol Cell Proteomics. 2012 Jun;11(6):M111.014910. 

Imielinski M, Cha S, Rejtar T, Richardson EA, Karger BL, Sgroi DC.

PMID: 22240506; PMCID: PMC3433899

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

Mark A. Rubin, MD, Juan Miguel Mosquera, MD

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

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The genomic complexity of primary human prostate cancer.

Mark A. Rubin, MD

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

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

Mark A. Rubin, MD

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

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

Mark A. Rubin, MD

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

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

Mark A. Rubin, MD

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

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

Mark A. Rubin, MD

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

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

Mark A. Rubin, MD

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

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

Mark A. Rubin, MD, Juan Miguel Mosquera, MD

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

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

Mark A. Rubin, MD, Juan Miguel Mosquera, MD

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

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

Mark A. Rubin, MD, Juan Miguel Mosquera, MD

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

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

Mark A. Rubin, MD

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

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

Mark A. Rubin, MD

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

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Delineation of prognostic biomarkers in prostate cancer

Mark A. Rubin, MD

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

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Weill Cornell Medicine Pathology & Laboratory Medicine 1300 York Avenue New York, NY 10065 Phone: (212) 746-6464 Fax: (212) 746-8192