Skip Navigation

Find a Researcher

Kornelia Polyak, MD, PhD

Researcher


Researcher

  • Professor of Medicine, Harvard Medical School

Contact Information

  • Office Phone Number617-632-2106
  • Fax617-580-8490

Bio

Dr. Polyak received her MD in 1991 from Albert Szent-Gyorgyi Medical University, Szeged, Hungary, and her PhD in 1995 from Cornell University/Memorial Sloan-Kettering Cancer Center. She completed a research fellowship in oncology at the Johns Hopkins Oncology Center, Baltimore, where she analyzed the mechanism of p53-mediated cell death. Joining DFCI in 1998, she is principally involved in basic laboratory research focusing on cancer genetics and the molecular basis of breast cancer.

Recent Awards:

  • V Foundation Scholar Award 2001
  • Sidney Kimmel Scholar Award 1999
  • 27th Annual Award for Outstanding Achievement in Cancer Research, American Association for Cancer Research 2007
  • Elected to the Johns Hopkins Society of Scholars 2008
  • Claire W. and Richard P. Morse Research Award, Dana-Farber Cancer Institute 2006
  • Tisch Family Outstanding Achievement Award, Dana-Farber Cancer Institute 2005
  • Paul Marks Award for Cancer Research, Sloan-Kettering Cancer Center, New York, NY 2011
  • AACR Outstanding Investigator Award for Breast Cancer Research, San Antonio, TX 2012

Research

Molecular Basis of Breast Tumor Evolution

Research in my laboratory is dedicated to the molecular analysis of human breast cancer. Our goal is to identify differences between normal and cancerous breast tissue, determine their consequences, and use this information to improve the clinical management of breast cancer patients. We have devoted much effort to develop new technologies that allow for the comprehensive molecular profiling of cells isolated from primary human tissue samples. Using these methods we have been at the forefront of studies analyzing purified cell populations from normal and neoplastic human breast tissue at genomic scale and utilizing interdisciplinary approaches for the better understanding of clinical breast cancer. We characterized molecular alterations that occur during breast tumor progression using SAGE (Serial Analysis of Gene Expression) for gene expression profiling, SNP (Single Nucleotide Polymorphism) arrays and array CGH (Comparative Genomic Hybridization) for genetic changes, MSDK (Methylation-Specific Digital Karyotyping) for the characterization of global DNA methylation profiles, and ChIP-Seq (Chromatin Immunoprecipitation and next generation sequencing) for the analysis of histone modification patterns. In addition to analyzing the tumor cells we also investigated all cell types that compose normal breast tissue and in situ and invasive breast carcinomas. Using these approaches we determined that gene expression and epigenetic changes occur in all cell types during breast tumor progression, whereas clonally selected genetic alterations are restricted to tumor epithelial cells. Several of the genes we identified as aberrantly methylated in breast cancer, including the SCGB3A (HIN-1) gene, are candidate diagnostic or prognostic markers. Based on our results we also proposed that the in situ to invasive breast carcinoma progression is determined by interactions among epithelial, myoepithelial, and stromal cells and that progression occurs due to the loss of normal myoepithelial cell function. These findings change the way we approach breast tumor progression, the identification of patients with high risk for progression, and can be used for designing better cancer preventative interventions. We have also characterized cells with stem cell characteristics from normal mammary epithelium and breast carcinomas. In the normal breast, we have been investigating molecular alterations induced by factors that influence breast cancer risk including pregnancy, breast density, and hereditary mutations in breast cancer genes with the aim of better understanding these changes and exploiting them for breast cancer preventative approaches. In breast cancer, we have been analyzing mechanisms that underlie intra-tumor heterogeneity including genetic, epigenetic, and non-hereditary changes, and the clinical consequences of intra-tumor diversity with special emphasis on tumor progression and therapeutic responses. We study breast tumors as ecosystems and apply ecological and evolutionary methods to better understand the clinical implications of tumor heterogeneity.

Hinohara K, Polyak K. Intratumoral Heterogeneity: More Than Just Mutations. Trends Cell Biol. 2019 Apr 12.
View in: PubMed

Ding L, Shunkwiler LB, Harper NW, Zhao Y, Hinohara K, Huh SJ, Ekram MB, Guz J, Kern MJ, Awgulewitsch A, Shull JD, Smits BMG, Polyak K. Deletion of Cdkn1b in ACI rats leads to increased proliferation and pregnancy-associated changes in the mammary gland due to perturbed systemic endocrine environment. PLoS Genet. 2019 03; 15(3):e1008002.
View in: PubMed

Hinohara K, Wu HJ, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2019 Feb 11; 35(2):330-332.
View in: PubMed

Garrido-Castro AC, Lin NU, Polyak K. Insights into Molecular Classifications of Triple-Negative Breast Cancer: Improving Patient Selection for Treatment. Cancer Discov. 2019 02; 9(2):176-198.
View in: PubMed

Punglia RS, Bifolck K, Golshan M, Lehman C, Collins L, Polyak K, Mittendorf E, Garber J, Hwang SE, Schnitt SJ, Partridge AH, King TA. Epidemiology, Biology, Treatment, and Prevention of Ductal Carcinoma In Situ (DCIS). JNCI Cancer Spectr. 2018 Nov; 2(4):pky063.
View in: PubMed

Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2018 Dec 10; 34(6):939-953.e9.
View in: PubMed

Witwicki RM, Ekram MB, Qiu X, Janiszewska M, Shu S, Kwon M, Trinh A, Frias E, Ramadan N, Hoffman G, Yu K, Xie Y, McAllister G, McDonald R, Golji J, Schlabach M, deWeck A, Keen N, Chan HM, Ruddy D, Rejtar T, Sovath S, Silver S, Sellers WR, Jagani Z, Hogarty MD, Roberts C, Brown M, Stegmaier K, Long H, Shivdasani RA, Pellman D, Polyak K. TRPS1 Is a Lineage-Specific Transcriptional Dependency in Breast Cancer. Cell Rep. 2018 Oct 30; 25(5):1255-1267.e5.
View in: PubMed

Rye IH, Trinh A, Saetersdal AB, Nebdal D, Lingjaerde OC, Almendro V, Polyak K, Børresen-Dale AL, Helland Å, Markowetz F, Russnes HG. Intratumor heterogeneity defines treatment-resistant HER2+ breast tumors. Mol Oncol. 2018 11; 12(11):1838-1855.
View in: PubMed

Cristea S, Polyak K. Dissecting the mammary gland one cell at a time. Nat Commun. 2018 06 26; 9(1):2473.
View in: PubMed

Janiszewska M, Polyak K. A confetti trail of tumour evolution. Nat Cell Biol. 2018 06; 20(6):639-641.
View in: PubMed

Stover DG, Gil Del Alcazar CR, Brock J, Guo H, Overmoyer B, Balko J, Xu Q, Bardia A, Tolaney SM, Gelman R, Lloyd M, Wang Y, Xu Y, Michor F, Wang V, Winer EP, Polyak K, Lin NU. Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer. NPJ Breast Cancer. 2018; 4:10.
View in: PubMed

Duivenvoorden HM, Rautela J, Edgington-Mitchell LE, Spurling A, Greening DW, Nowell CJ, Molloy TJ, Robbins E, Brockwell NK, Lee CS, Chen M, Holliday A, Selinger CI, Hu M, Britt KL, Stroud DA, Bogyo M, Möller A, Polyak K, Sloane BF, O'Toole SA, Parker BS. Myoepithelial cell-specific expression of stefin A as a suppressor of early breast cancer invasion. J Pathol. 2017 12; 243(4):496-509.
View in: PubMed

Woodward WA, Cristofanilli M, Merajver SD, Van Laere S, Pusztai L, Bertucci F, Berditchevski F, Polyak K, Overmoyer B, Devi GR, Sterneck E, Schneider R, Debeb BG, Wang X, van Golen KL, El-Zein R, Rahal OM, Alexander A, Reuben JM, Krishnamurthy S, Lucci A, Ueno NT. Scientific Summary from the Morgan Welch MD Anderson Cancer Center Inflammatory Breast Cancer (IBC) Program 10th Anniversary Conference. J Cancer. 2017; 8(17):3607-3614.
View in: PubMed

Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, Silva AS, Gerlinger M, Yuan Y, Pienta KJ, Anderson KS, Gatenby R, Swanton C, Posada D, Wu CI, Schiffman JD, Hwang ES, Polyak K, Anderson ARA, Brown JS, Greaves M, Shibata D. Classifying the evolutionary and ecological features of neoplasms. Nat Rev Cancer. 2017 10; 17(10):605-619.
View in: PubMed

Gil Del Alcazar CR, Huh SJ, Ekram MB, Trinh A, Liu LL, Beca F, Zi X, Kwak M, Bergholtz H, Su Y, Ding L, Russnes HG, Richardson AL, Babski K, Min Hui Kim E, McDonnell CH, Wagner J, Rowberry R, Freeman GJ, Dillon D, Sorlie T, Coussens LM, Garber JE, Fan R, Bobolis K, Allred DC, Jeong J, Park SY, Michor F, Polyak K. Immune Escape in Breast Cancer During In Situ to Invasive Carcinoma Transition. Cancer Discov. 2017 10; 7(10):1098-1115.
View in: PubMed

Wang H, Nicolay BN, Chick JM, Gao X, Geng Y, Ren H, Gao H, Yang G, Williams JA, Suski JM, Keibler MA, Sicinska E, Gerdemann U, Haining WN, Roberts TM, Polyak K, Gygi SP, Dyson NJ, Sicinski P. The metabolic function of cyclin D3-CDK6 kinase in cancer cell survival. Nature. 2017 06 15; 546(7658):426-430.
View in: PubMed

Hydbring P, Wang Y, Fassl A, Li X, Matia V, Otto T, Choi YJ, Sweeney KE, Suski JM, Yin H, Bogorad RL, Goel S, Yuzugullu H, Kauffman KJ, Yang J, Jin C, Li Y, Floris D, Swanson R, Ng K, Sicinska E, Anders L, Zhao JJ, Polyak K, Anderson DG, Li C, Sicinski P. Cell-Cycle-Targeting MicroRNAs as Therapeutic Tools against Refractory Cancers. Cancer Cell. 2017 04 10; 31(4):576-590.e8.
View in: PubMed

Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res. 2017 04 01; 77(7):1510-1541.
View in: PubMed

Temko D, Cheng YK, Polyak K, Michor F. Mathematical Modeling Links Pregnancy-Associated Changes and Breast Cancer Risk. Cancer Res. 2017 06 01; 77(11):2800-2809.
View in: PubMed

Liu L, Michowski W, Inuzuka H, Shimizu K, Nihira NT, Chick JM, Li N, Geng Y, Meng AY, Ordureau A, Kolodziejczyk A, Ligon KL, Bronson RT, Polyak K, Harper JW, Gygi SP, Wei W, Sicinski P. G1 cyclins link proliferation, pluripotency and differentiation of embryonic stem cells. Nat Cell Biol. 2017 03; 19(3):177-188.
View in: PubMed

Shu S, Polyak K. BET Bromodomain Proteins as Cancer Therapeutic Targets. Cold Spring Harb Symp Quant Biol. 2016; 81:123-129.
View in: PubMed

Oh H, Eliassen AH, Wang M, Smith-Warner SA, Beck AH, Schnitt SJ, Collins LC, Connolly JL, Montaser-Kouhsari L, Polyak K, Tamimi RM. Expression of estrogen receptor, progesterone receptor, and Ki67 in normal breast tissue in relation to subsequent risk of breast cancer. NPJ Breast Cancer. 2016; 2.
View in: PubMed

Marusyk A, Tabassum DP, Janiszewska M, Place AE, Trinh A, Rozhok AI, Pyne S, Guerriero JL, Shu S, Ekram M, Ishkin A, Cahill DP, Nikolsky Y, Chan TA, Rimawi MF, Hilsenbeck S, Schiff R, Osborne KC, Letai A, Polyak K. Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes. Cancer Res. 2016 11 15; 76(22):6495-6506.
View in: PubMed

Shlien A, Raine K, Fuligni F, Arnold R, Nik-Zainal S, Dronov S, Mamanova L, Rosic A, Ju YS, Cooke SL, Ramakrishna M, Papaemmanuil E, Davies HR, Tarpey PS, Van Loo P, Wedge DC, Jones DR, Martin S, Marshall J, Anderson E, Hardy C, Barbashina V, Aparicio SA, Sauer T, Garred Ø, Vincent-Salomon A, Mariani O, Boyault S, Fatima A, Langerød A, Borg Å, Thomas G, Richardson AL, Børresen-Dale AL, Polyak K, Stratton MR, Campbell PJ. Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer. Cell Rep. 2016 08 16; 16(7):2032-46.
View in: PubMed

Wang H, Bierie B, Li AG, Pathania S, Toomire K, Dimitrov SD, Liu B, Gelman R, Giobbie-Hurder A, Feunteun J, Polyak K, Livingston DM. BRCA1/FANCD2/BRG1-Driven DNA Repair Stabilizes the Differentiation State of Human Mammary Epithelial Cells. Mol Cell. 2016 07 21; 63(2):277-292.
View in: PubMed

Huh SJ, Oh H, Peterson MA, Almendro V, Hu R, Bowden M, Lis RL, Cotter MB, Loda M, Barry WT, Polyak K, Tamimi RM. The Proliferative Activity of Mammary Epithelial Cells in Normal Tissue Predicts Breast Cancer Risk in Premenopausal Women. Cancer Res. 2016 04 01; 76(7):1926-34.
View in: PubMed

Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T. Voices of biotech. Nat Biotechnol. 2016 Mar; 34(3):270-5.
View in: PubMed

Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, Roberts JM, Janiszewska M, Huh SJ, Liang Y, Ryan J, Doherty E, Mohammed H, Guo H, Stover DG, Ekram MB, Brown J, D'Santos C, Krop IE, Dillon D, McKeown M, Ott C, Qi J, Ni M, Rao PK, Duarte M, Wu SY, Chiang CM, Anders L, Young RA, Winer E, Letai A, Barry WT, Carroll JS, Long H, Brown M, Liu XS, Meyer CA, Bradner JE, Polyak K. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature. 2016 Jan 21; 529(7586):413-417.
View in: PubMed

Beca F, Polyak K. Intratumor Heterogeneity in Breast Cancer. Adv Exp Med Biol. 2016; 882:169-89.
View in: PubMed

Fumagalli D, Gacquer D, Rothé F, Lefort A, Libert F, Brown D, Kheddoumi N, Shlien A, Konopka T, Salgado R, Larsimont D, Polyak K, Willard-Gallo K, Desmedt C, Piccart M, Abramowicz M, Campbell PJ, Sotiriou C, Detours V. Principles Governing A-to-I RNA Editing in the Breast Cancer Transcriptome. Cell Rep. 2015 Oct 13; 13(2):277-89.
View in: PubMed

Yoo B, Kavishwar A, Ross A, Wang P, Tabassum DP, Polyak K, Barteneva N, Petkova V, Pantazopoulos P, Tena A, Moore A, Medarova Z. Combining miR-10b-Targeted Nanotherapy with Low-Dose Doxorubicin Elicits Durable Regressions of Metastatic Breast Cancer. Cancer Res. 2015 Oct 15; 75(20):4407-15.
View in: PubMed

Janiszewska M, Liu L, Almendro V, Kuang Y, Paweletz C, Sakr RA, Weigelt B, Hanker AB, Chandarlapaty S, King TA, Reis-Filho JS, Arteaga CL, Park SY, Michor F, Polyak K. In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nat Genet. 2015 Oct; 47(10):1212-9.
View in: PubMed

Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J. Toward understanding and exploiting tumor heterogeneity. Nat Med. 2015 Aug; 21(8):846-53.
View in: PubMed

Jin K, Park S, Teo WW, Korangath P, Cho SS, Yoshida T, Gyorffy B, Goswami CP, Nakshatri H, Cruz LA, Zhou W, Ji H, Su Y, Ekram M, Wu Z, Zhu T, Polyak K, Sukumar S. HOXB7 Is an ERa Cofactor in the Activation of HER2 and Multiple ER Target Genes Leading to Endocrine Resistance. Cancer Discov. 2015 Sep; 5(9):944-59.
View in: PubMed

Tabassum DP, Polyak K. Tumorigenesis: it takes a village. Nat Rev Cancer. 2015 Aug; 15(8):473-83.
View in: PubMed

Su Y, Subedee A, Bloushtain-Qimron N, Savova V, Krzystanek M, Li L, Marusyk A, Tabassum DP, Zak A, Flacker MJ, Li M, Lin JJ, Sukumar S, Suzuki H, Long H, Szallasi Z, Gimelbrant A, Maruyama R, Polyak K. Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer. Cell Rep. 2015 Jun 16; 11(10):1549-63.
View in: PubMed

Bancovik J, Moreira DF, Carrasco D, Yao J, Porter D, Moura R, Camargo A, Fontes-Oliveira CC, Malpartida MG, Carambula S, Vannier E, Strauss BE, Wakamatsu A, Alves VA, Logullo AF, Soares FA, Polyak K, Belizário JE. Dermcidin exerts its oncogenic effects in breast cancer via modulation of ERBB signaling. BMC Cancer. 2015 Feb 19; 15:70.
View in: PubMed

Yoshida T, Kim JH, Carver K, Su Y, Weremowicz S, Mulvey L, Yamamoto S, Brennan C, Mei S, Long H, Yao J, Polyak K. CLK2 Is an Oncogenic Kinase and Splicing Regulator in Breast Cancer. Cancer Res. 2015 Apr 01; 75(7):1516-26.
View in: PubMed

Huh SJ, Clement K, Jee D, Merlini A, Choudhury S, Maruyama R, Yoo R, Chytil A, Boyle P, Ran FA, Moses HL, Barcellos-Hoff MH, Jackson-Grusby L, Meissner A, Polyak K. Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells. Stem Cell Reports. 2015 Feb 10; 4(2):297-311.
View in: PubMed

Janiszewska M, Polyak K. Clonal evolution in cancer: a tale of twisted twines. Cell Stem Cell. 2015 Jan 08; 16(1):11-2.
View in: PubMed

Pathania S, Bade S, Le Guillou M, Burke K, Reed R, Bowman-Colin C, Su Y, Ting DT, Polyak K, Richardson AL, Feunteun J, Garber JE, Livingston DM. BRCA1 haploinsufficiency for replication stress suppression in primary cells. Nat Commun. 2014 Nov 17; 5:5496.
View in: PubMed

Cuiffo BG, Campagne A, Bell GW, Lembo A, Orso F, Lien EC, Bhasin MK, Raimo M, Hanson SE, Marusyk A, El-Ashry D, Hematti P, Polyak K, Mechta-Grigoriou F, Mariani O, Volinia S, Vincent-Salomon A, Taverna D, Karnoub AE. MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis. Cell Stem Cell. 2014 Dec 04; 15(6):762-74.
View in: PubMed

Janiszewska M, Beca F, Polyak K. Tumor heterogeneity: the Lernaean hydra of oncology? Oncology (Williston Park). 2014 Sep; 28(9):781-2, 784.
View in: PubMed

Marusyk A, Tabassum DP, Altrock PM, Almendro V, Michor F, Polyak K. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity. Nature. 2014 Oct 02; 514(7520):54-8.
View in: PubMed

Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C, Zhao X, Moen Vollan HK, Maruyama R, Ekram MB, Sun H, Kim JH, Carver K, Zucca M, Feng J, Almendro V, Bessarabova M, Rueda OM, Nikolsky Y, Caldas C, Liu XS, Polyak K. JARID1B is a luminal lineage-driving oncogene in breast cancer. Cancer Cell. 2014 Jun 16; 25(6):762-77.
View in: PubMed

Zou MR, Cao J, Liu Z, Huh SJ, Polyak K, Yan Q. Histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) controls mammary gland development by regulating key developmental and lineage specification genes. J Biol Chem. 2014 Jun 20; 289(25):17620-33.
View in: PubMed

Godinho SA, Picone R, Burute M, Dagher R, Su Y, Leung CT, Polyak K, Brugge JS, Théry M, Pellman D. Oncogene-like induction of cellular invasion from centrosome amplification. Nature. 2014 Jun 05; 510(7503):167-71.
View in: PubMed

Polyak K, Marusyk A. Cancer: Clonal cooperation. Nature. 2014 Apr 03; 508(7494):52-3.
View in: PubMed

Polyak K. Tumor heterogeneity confounds and illuminates: a case for Darwinian tumor evolution. Nat Med. 2014 Apr; 20(4):344-6.
View in: PubMed

Hines WC, Su Y, Kuhn I, Polyak K, Bissell MJ. Sorting out the FACS: a devil in the details. Cell Rep. 2014 Mar 13; 6(5):779-81.
View in: PubMed

Almendro V, Cheng YK, Randles A, Itzkovitz S, Marusyk A, Ametller E, Gonzalez-Farre X, Muñoz M, Russnes HG, Helland A, Rye IH, Borresen-Dale AL, Maruyama R, van Oudenaarden A, Dowsett M, Jones RL, Reis-Filho J, Gascon P, Gönen M, Michor F, Polyak K. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Rep. 2014 Feb 13; 6(3):514-27.
View in: PubMed

Almendro V, Kim HJ, Cheng YK, Gönen M, Itzkovitz S, Argani P, van Oudenaarden A, Sukumar S, Michor F, Polyak K. Genetic and phenotypic diversity in breast tumor metastases. Cancer Res. 2014 Mar 01; 74(5):1338-48.
View in: PubMed

Chin YR, Yoshida T, Marusyk A, Beck AH, Polyak K, Toker A. Targeting Akt3 signaling in triple-negative breast cancer. Cancer Res. 2014 Feb 01; 74(3):964-73.
View in: PubMed

Timmerman LA, Holton T, Yuneva M, Louie RJ, Padró M, Daemen A, Hu M, Chan DA, Ethier SP, van 't Veer LJ, Polyak K, McCormick F, Gray JW. Glutamine sensitivity analysis identifies the xCT antiporter as a common triple-negative breast tumor therapeutic target. Cancer Cell. 2013 Oct 14; 24(4):450-65.
View in: PubMed

McLaughlin SK, Olsen SN, Dake B, De Raedt T, Lim E, Bronson RT, Beroukhim R, Polyak K, Brown M, Kuperwasser C, Cichowski K. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor. Cancer Cell. 2013 Sep 09; 24(3):365-78.
View in: PubMed

Steenbergen RD, Ongenaert M, Snellenberg S, Trooskens G, van der Meide WF, Pandey D, Bloushtain-Qimron N, Polyak K, Meijer CJ, Snijders PJ, Van Criekinge W. Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis. J Pathol. 2013 Sep; 231(1):53-62.
View in: PubMed

Choudhury S, Almendro V, Merino VF, Wu Z, Maruyama R, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macintyre G, Cheng YK, Lopez-Bujanda Z, Kaspi A, Hu R, Robens J, Nikolskaya T, Haakensen VD, Schnitt SJ, Argani P, Ethington G, Panos L, Grant M, Clark J, Herlihy W, Lin SJ, Chew G, Thompson EW, Greene-Colozzi A, Richardson AL, Rosson GD, Pike M, Garber JE, Nikolsky Y, Blum JL, Au A, Hwang ES, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell Stem Cell. 2013 Jul 03; 13(1):117-30.
View in: PubMed

Pantel K, Diaz LA, Polyak K. Tracking tumor resistance using 'liquid biopsies'. Nat Med. 2013 Jun; 19(6):676-7.
View in: PubMed

Seo JH, Li Q, Fatima A, Eklund A, Szallasi Z, Polyak K, Richardson AL, Freedman ML. Deconvoluting complex tissues for expression quantitative trait locus-based analyses. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1620):20120363.
View in: PubMed

Marusyk A, Polyak K. Cancer. Cancer cell phenotypes, in fifty shades of grey. Science. 2013 Feb 01; 339(6119):528-9.
View in: PubMed

Eswaran J, Horvath A, Godbole S, Reddy SD, Mudvari P, Ohshiro K, Cyanam D, Nair S, Fuqua SA, Polyak K, Florea LD, Kumar R. RNA sequencing of cancer reveals novel splicing alterations. Sci Rep. 2013; 3:1689.
View in: PubMed

Vegfors J, Petersson S, Kovács A, Polyak K, Enerbäck C. The expression of Psoriasin (S100A7) and CD24 is linked and related to the differentiation of mammary epithelial cells. PLoS One. 2012; 7(12):e53119.
View in: PubMed

Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Res. 2012 Dec 15; 72(24):6319-24.
View in: PubMed

Almendro V, Marusyk A, Polyak K. Cellular heterogeneity and molecular evolution in cancer. Annu Rev Pathol. 2013 Jan 24; 8:277-302.
View in: PubMed

Polyak K, Metzger Filho O. SnapShot: breast cancer. Cancer Cell. 2012 Oct 16; 22(4):562-562.e1.
View in: PubMed

Bhatia S, Frangioni JV, Hoffman RM, Iafrate AJ, Polyak K. The challenges posed by cancer heterogeneity. Nat Biotechnol. 2012 Jul 10; 30(7):604-10.
View in: PubMed

Polyak K. On using functional genetics to understand breast cancer biology. Cold Spring Harb Perspect Biol. 2012 Jul 01; 4(7):a013516.
View in: PubMed

Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, Bautista-Piña V, Duke F, Francis J, Jung J, Maffuz-Aziz A, Onofrio RC, Parkin M, Pho NH, Quintanar-Jurado V, Ramos AH, Rebollar-Vega R, Rodriguez-Cuevas S, Romero-Cordoba SL, Schumacher SE, Stransky N, Thompson KM, Uribe-Figueroa L, Baselga J, Beroukhim R, Polyak K, Sgroi DC, Richardson AL, Jimenez-Sanchez G, Lander ES, Gabriel SB, Garraway LA, Golub TR, Melendez-Zajgla J, Toker A, Getz G, Hidalgo-Miranda A, Meyerson M. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012 Jun 20; 486(7403):405-9.
View in: PubMed

Marusyk A, Almendro V, Polyak K. Intra-tumour heterogeneity: a looking glass for cancer? Nat Rev Cancer. 2012 Apr 19; 12(5):323-34.
View in: PubMed

Martins FC, De S, Almendro V, Gönen M, Park SY, Blum JL, Herlihy W, Ethington G, Schnitt SJ, Tung N, Garber JE, Fetten K, Michor F, Polyak K. Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discov. 2012 Jun; 2(6):503-11.
View in: PubMed

Polyak K. On chromatin remodeling in mammary gland differentiation and breast tumorigenesis. Cold Spring Harb Perspect Biol. 2012 Mar 01; 4(3).
View in: PubMed

Polyak K, Vogt PK. Progress in breast cancer research. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2715-7.
View in: PubMed

Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, Sjöblom T. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers. Genes Chromosomes Cancer. 2012 May; 51(5):480-9.
View in: PubMed

Balko JM, Miller TW, Morrison MM, Hutchinson K, Young C, Rinehart C, Sánchez V, Jee D, Polyak K, Prat A, Perou CM, Arteaga CL, Cook RS. The receptor tyrosine kinase ErbB3 maintains the balance between luminal and basal breast epithelium. Proc Natl Acad Sci U S A. 2012 Jan 03; 109(1):221-6.
View in: PubMed

Shrestha Y, Schafer EJ, Boehm JS, Thomas SR, He F, Du J, Wang S, Barretina J, Weir BA, Zhao JJ, Polyak K, Golub TR, Beroukhim R, Hahn WC. PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling. Oncogene. 2012 Jul 19; 31(29):3397-408.
View in: PubMed

Place AE, Jin Huh S, Polyak K. The microenvironment in breast cancer progression: biology and implications for treatment. Breast Cancer Res. 2011; 13(6):227.
View in: PubMed

Polyak K. Heterogeneity in breast cancer. J Clin Invest. 2011 Oct; 121(10):3786-8.
View in: PubMed

Marotta LL, Polyak K. Unraveling the complexity of basal-like breast cancer. Oncotarget. 2011 Aug; 2(8):588-9.
View in: PubMed

Marotta LL, Almendro V, Marusyk A, Shipitsin M, Schemme J, Walker SR, Bloushtain-Qimron N, Kim JJ, Choudhury SA, Maruyama R, Wu Z, Gönen M, Mulvey LA, Bessarabova MO, Huh SJ, Silver SJ, Kim SY, Park SY, Lee HE, Anderson KS, Richardson AL, Nikolskaya T, Nikolsky Y, Liu XS, Root DE, Hahn WC, Frank DA, Polyak K. The JAK2/STAT3 signaling pathway is required for growth of CD44?CD24? stem cell-like breast cancer cells in human tumors. J Clin Invest. 2011 Jul; 121(7):2723-35.
View in: PubMed

Maruyama R, Choudhury S, Kowalczyk A, Bessarabova M, Beresford-Smith B, Conway T, Kaspi A, Wu Z, Nikolskaya T, Merino VF, Lo PK, Liu XS, Nikolsky Y, Sukumar S, Haviv I, Polyak K. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium. PLoS Genet. 2011 Apr; 7(4):e1001369.
View in: PubMed

Chaffer CL, Brueckmann I, Scheel C, Kaestli AJ, Wiggins PA, Rodrigues LO, Brooks M, Reinhardt F, Su Y, Polyak K, Arendt LM, Kuperwasser C, Bierie B, Weinberg RA. Normal and neoplastic nonstem cells can spontaneously convert to a stem-like state. Proc Natl Acad Sci U S A. 2011 May 10; 108(19):7950-5.
View in: PubMed

Bessarabova M, Pustovalova O, Shi W, Serebriyskaya T, Ishkin A, Polyak K, Velculescu VE, Nikolskaya T, Nikolsky Y. Functional synergies yet distinct modulators affected by genetic alterations in common human cancers. Cancer Res. 2011 May 15; 71(10):3471-81.
View in: PubMed

Polyak K, Garber J. Targeting the missing links for cancer therapy. Nat Med. 2011 Mar; 17(3):283-4.
View in: PubMed

Maruyama R, Shipitsin M, Choudhury S, Wu Z, Protopopov A, Yao J, Lo PK, Bessarabova M, Ishkin A, Nikolsky Y, Liu XS, Sukumar S, Polyak K. Altered antisense-to-sense transcript ratios in breast cancer. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2820-4.
View in: PubMed

Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 2010 Dec; 20(12):1730-9.
View in: PubMed

Michor F, Polyak K. The origins and implications of intratumor heterogeneity. Cancer Prev Res (Phila). 2010 Nov; 3(11):1361-4.
View in: PubMed

Polyak K. Going small is the new big. Nat Methods. 2010 Aug; 7(8):597, 599-600.
View in: PubMed

Irie HY, Shrestha Y, Selfors LM, Frye F, Iida N, Wang Z, Zou L, Yao J, Lu Y, Epstein CB, Natesan S, Richardson AL, Polyak K, Mills GB, Hahn WC, Brugge JS. PTK6 regulates IGF-1-induced anchorage-independent survival. PLoS One. 2010 Jul 23; 5(7):e11729.
View in: PubMed

Polyak K, Kalluri R. The role of the microenvironment in mammary gland development and cancer. Cold Spring Harb Perspect Biol. 2010 Nov; 2(11):a003244.
View in: PubMed

Miron A, Varadi M, Carrasco D, Li H, Luongo L, Kim HJ, Park SY, Cho EY, Lewis G, Kehoe S, Iglehart JD, Dillon D, Allred DC, Macconaill L, Gelman R, Polyak K. PIK3CA mutations in in situ and invasive breast carcinomas. Cancer Res. 2010 Jul 15; 70(14):5674-8.
View in: PubMed

Petersen OW, Polyak K. Stem cells in the human breast. Cold Spring Harb Perspect Biol. 2010 May; 2(5):a003160.
View in: PubMed

Park SY, Lee HE, Li H, Shipitsin M, Gelman R, Polyak K. Heterogeneity for stem cell-related markers according to tumor subtype and histologic stage in breast cancer. Clin Cancer Res. 2010 Feb 01; 16(3):876-87.
View in: PubMed

Lauring J, Cosgrove DP, Fontana S, Gustin JP, Konishi H, Abukhdeir AM, Garay JP, Mohseni M, Wang GM, Higgins MJ, Gorkin D, Reis M, Vogelstein B, Polyak K, Cowherd M, Buckhaults PJ, Park BH. Knock in of the AKT1 E17K mutation in human breast epithelial cells does not recapitulate oncogenic PIK3CA mutations. Oncogene. 2010 Apr 22; 29(16):2337-45.
View in: PubMed

Park SY, Gönen M, Kim HJ, Michor F, Polyak K. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J Clin Invest. 2010 Feb; 120(2):636-44.
View in: PubMed

Polyak K. Molecular markers for the diagnosis and management of ductal carcinoma in situ. J Natl Cancer Inst Monogr. 2010; 2010(41):210-3.
View in: PubMed

MacConaill LE, Campbell CD, Kehoe SM, Bass AJ, Hatton C, Niu L, Davis M, Yao K, Hanna M, Mondal C, Luongo L, Emery CM, Baker AC, Philips J, Goff DJ, Fiorentino M, Rubin MA, Polyak K, Chan J, Wang Y, Fletcher JA, Santagata S, Corso G, Roviello F, Shivdasani R, Kieran MW, Ligon KL, Stiles CD, Hahn WC, Meyerson ML, Garraway LA. Profiling critical cancer gene mutations in clinical tumor samples. PLoS One. 2009 Nov 18; 4(11):e7887.
View in: PubMed

Marusyk A, Polyak K. Tumor heterogeneity: causes and consequences. Biochim Biophys Acta. 2010 Jan; 1805(1):105-17.
View in: PubMed

Zhang Q, Gu J, Li L, Liu J, Luo B, Cheung HW, Boehm JS, Ni M, Geisen C, Root DE, Polyak K, Brown M, Richardson AL, Hahn WC, Kaelin WG, Bommi-Reddy A. Control of cyclin D1 and breast tumorigenesis by the EglN2 prolyl hydroxylase. Cancer Cell. 2009 Nov 06; 16(5):413-24.
View in: PubMed

Campbell I, Polyak K, Haviv I. Clonal mutations in the cancer-associated fibroblasts: the case against genetic coevolution. Cancer Res. 2009 Sep 01; 69(17):6765-8; discussion 6769.
View in: PubMed

Snyder EL, Bailey D, Shipitsin M, Polyak K, Loda M. Identification of CD44v6(+)/CD24- breast carcinoma cells in primary human tumors by quantum dot-conjugated antibodies. Lab Invest. 2009 Aug; 89(8):857-66.
View in: PubMed

Bloushtain-Qimron N, Yao J, Shipitsin M, Maruyama R, Polyak K. Epigenetic patterns of embryonic and adult stem cells. Cell Cycle. 2009 Mar 15; 8(6):809-17.
View in: PubMed

Polyak K, Weinberg RA. Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits. Nat Rev Cancer. 2009 Apr; 9(4):265-73.
View in: PubMed

Haviv I, Polyak K, Qiu W, Hu M, Campbell I. Origin of carcinoma associated fibroblasts. Cell Cycle. 2009 Feb 15; 8(4):589-95.
View in: PubMed

Hu M, Peluffo G, Chen H, Gelman R, Schnitt S, Polyak K. Role of COX-2 in epithelial-stromal cell interactions and progression of ductal carcinoma in situ of the breast. Proc Natl Acad Sci U S A. 2009 Mar 03; 106(9):3372-7.
View in: PubMed

Marotta LL, Polyak K. Cancer stem cells: a model in the making. Curr Opin Genet Dev. 2009 Feb; 19(1):44-50.
View in: PubMed

Behbod F, Kittrell FS, LaMarca H, Edwards D, Kerbawy S, Heestand JC, Young E, Mukhopadhyay P, Yeh HW, Allred DC, Hu M, Polyak K, Rosen JM, Medina D. An intraductal human-in-mouse transplantation model mimics the subtypes of ductal carcinoma in situ. Breast Cancer Res. 2009; 11(5):R66.
View in: PubMed

Polyak K, Haviv I, Campbell IG. Co-evolution of tumor cells and their microenvironment. Trends Genet. 2009 Jan; 25(1):30-8.
View in: PubMed

Hu M, Polyak K. Molecular characterisation of the tumour microenvironment in breast cancer. Eur J Cancer. 2008 Dec; 44(18):2760-5.
View in: PubMed

Nikolsky Y, Sviridov E, Yao J, Dosymbekov D, Ustyansky V, Kaznacheev V, Dezso Z, Mulvey L, Macconaill LE, Winckler W, Serebryiskaya T, Nikolskaya T, Polyak K. Genome-wide functional synergy between amplified and mutated genes in human breast cancer. Cancer Res. 2008 Nov 15; 68(22):9532-40.
View in: PubMed

Cao D, Polyak K, Halushka MK, Nassar H, Kouprina N, Iacobuzio-Donahue C, Wu X, Sukumar S, Hicks J, De Marzo A, Argani P. Serial analysis of gene expression of lobular carcinoma in situ identifies down regulation of claudin 4 and overexpression of matrix metalloproteinase 9. Breast Cancer Res. 2008; 10(5):R91.
View in: PubMed

Anderson KS, Wong J, Polyak K, Aronzon D, Enerbäck C. Detection of psoriasin/S100A7 in the sera of patients with psoriasis. Br J Dermatol. 2009 Feb; 160(2):325-32.
View in: PubMed

Bloushtain-Qimron N, Yao J, Snyder EL, Shipitsin M, Campbell LL, Mani SA, Hu M, Chen H, Ustyansky V, Antosiewicz JE, Argani P, Halushka MK, Thomson JA, Pharoah P, Porgador A, Sukumar S, Parsons R, Richardson AL, Stampfer MR, Gelman RS, Nikolskaya T, Nikolsky Y, Polyak K. Cell type-specific DNA methylation patterns in the human breast. Proc Natl Acad Sci U S A. 2008 Sep 16; 105(37):14076-81.
View in: PubMed

Kleer CG, Bloushtain-Qimron N, Chen YH, Carrasco D, Hu M, Yao J, Kraeft SK, Collins LC, Sabel MS, Argani P, Gelman R, Schnitt SJ, Krop IE, Polyak K. Epithelial and stromal cathepsin K and CXCL14 expression in breast tumor progression. Clin Cancer Res. 2008 Sep 01; 14(17):5357-67.
View in: PubMed

Mani SA, Guo W, Liao MJ, Eaton EN, Ayyanan A, Zhou AY, Brooks M, Reinhard F, Zhang CC, Shipitsin M, Campbell LL, Polyak K, Brisken C, Yang J, Weinberg RA. The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell. 2008 May 16; 133(4):704-15.
View in: PubMed

Hu M, Yao J, Carroll DK, Weremowicz S, Chen H, Carrasco D, Richardson A, Violette S, Nikolskaya T, Nikolsky Y, Bauerlein EL, Hahn WC, Gelman RS, Allred C, Bissell MJ, Schnitt S, Polyak K. Regulation of in situ to invasive breast carcinoma transition. Cancer Cell. 2008 May; 13(5):394-406.
View in: PubMed

Qiu W, Hu M, Sridhar A, Opeskin K, Fox S, Shipitsin M, Trivett M, Thompson ER, Ramakrishna M, Gorringe KL, Polyak K, Haviv I, Campbell IG. No evidence of clonal somatic genetic alterations in cancer-associated fibroblasts from human breast and ovarian carcinomas. Nat Genet. 2008 May; 40(5):650-5.
View in: PubMed

Campbell IG, Qiu W, Polyak K, Haviv I. Breast-cancer stromal cells with TP53 mutations. N Engl J Med. 2008 Apr 10; 358(15):1634-5; author reply 1636.
View in: PubMed

Shipitsin M, Polyak K. The cancer stem cell hypothesis: in search of definitions, markers, and relevance. Lab Invest. 2008 May; 88(5):459-63.
View in: PubMed

Paruchuri V, Prasad A, McHugh K, Bhat HK, Polyak K, Ganju RK. S100A7-downregulation inhibits epidermal growth factor-induced signaling in breast cancer cells and blocks osteoclast formation. PLoS One. 2008 Mar 05; 3(3):e1741.
View in: PubMed

Hu M, Polyak K. Microenvironmental regulation of cancer development. Curr Opin Genet Dev. 2008 Feb; 18(1):27-34.
View in: PubMed

Zhao X, Goswami M, Pokhriyal N, Ma H, Du H, Yao J, Victor TA, Polyak K, Sturgis CD, Band H, Band V. Cyclooxygenase-2 expression during immortalization and breast cancer progression. Cancer Res. 2008 Jan 15; 68(2):467-75.
View in: PubMed

Polyak K. Is breast tumor progression really linear? Clin Cancer Res. 2008 Jan 15; 14(2):339-41.
View in: PubMed

Polyak K. Breast cancer: origins and evolution. J Clin Invest. 2007 Nov; 117(11):3155-63.
View in: PubMed

Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science. 2007 Nov 16; 318(5853):1108-13.
View in: PubMed

Karnoub AE, Dash AB, Vo AP, Sullivan A, Brooks MW, Bell GW, Richardson AL, Polyak K, Tubo R, Weinberg RA. Mesenchymal stem cells within tumour stroma promote breast cancer metastasis. Nature. 2007 Oct 04; 449(7162):557-63.
View in: PubMed

Blackshaw S, Croix BS, Polyak K, Kim JB, Cai L. Serial analysis of gene expression (SAGE): experimental method and data analysis. Curr Protoc Mol Biol. 2007 Oct; Chapter 25:Unit 25B.6.
View in: PubMed

Campbell LL, Polyak K. Breast tumor heterogeneity: cancer stem cells or clonal evolution? Cell Cycle. 2007 Oct 01; 6(19):2332-8.
View in: PubMed

Boehm JS, Zhao JJ, Yao J, Kim SY, Firestein R, Dunn IF, Sjostrom SK, Garraway LA, Weremowicz S, Richardson AL, Greulich H, Stewart CJ, Mulvey LA, Shen RR, Ambrogio L, Hirozane-Kishikawa T, Hill DE, Vidal M, Meyerson M, Grenier JK, Hinkle G, Root DE, Roberts TM, Lander ES, Polyak K, Hahn WC. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell. 2007 Jun 15; 129(6):1065-79.
View in: PubMed

Polyak K. Breast cancer stem cells: a case of mistaken identity? Stem Cell Rev. 2007 Jun; 3(2):107-9.
View in: PubMed

Blackshaw S, St Croix B, Polyak K, Kim JB, Cai L. Serial analysis of gene expression (SAGE): experimental method and data analysis. Curr Protoc Hum Genet. 2007 Apr; Chapter 11:Unit 11.7.
View in: PubMed

Shipitsin M, Campbell LL, Argani P, Weremowicz S, Bloushtain-Qimron N, Yao J, Nikolskaya T, Serebryiskaya T, Beroukhim R, Hu M, Halushka MK, Sukumar S, Parker LM, Anderson KS, Harris LN, Garber JE, Richardson AL, Schnitt SJ, Nikolsky Y, Gelman RS, Polyak K. Molecular definition of breast tumor heterogeneity. Cancer Cell. 2007 Mar; 11(3):259-73.
View in: PubMed

Polyak K. The p27Kip1 tumor suppressor gene: Still a suspect or proven guilty? Cancer Cell. 2006 Nov; 10(5):352-4.
View in: PubMed

Yao J, Weremowicz S, Feng B, Gentleman RC, Marks JR, Gelman R, Brennan C, Polyak K. Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression. Cancer Res. 2006 Apr 15; 66(8):4065-78.
View in: PubMed

Polyak K. Pregnancy and breast cancer: the other side of the coin. Cancer Cell. 2006 Mar; 9(3):151-3.
View in: PubMed

Polyak K, Hahn WC. Roots and stems: stem cells in cancer. Nat Med. 2006 Mar; 12(3):296-300.
View in: PubMed

Porter D, Yao J, Polyak K. SAGE and related approaches for cancer target identification. Drug Discov Today. 2006 Feb; 11(3-4):110-8.
View in: PubMed

Hu M, Yao J, Polyak K. Methylation-specific digital karyotyping. Nat Protoc. 2006; 1(3):1621-36.
View in: PubMed

Hu M, Polyak K. Serial analysis of gene expression. Nat Protoc. 2006; 1(4):1743-60.
View in: PubMed

Krop I, März A, Carlsson H, Li X, Bloushtain-Qimron N, Hu M, Gelman R, Sabel MS, Schnitt S, Ramaswamy S, Kleer CG, Enerbäck C, Polyak K. A putative role for psoriasin in breast tumor progression. Cancer Res. 2005 Dec 15; 65(24):11326-34.
View in: PubMed

Krop I, Parker MT, Bloushtain-Qimron N, Porter D, Gelman R, Sasaki H, Maurer M, Terry MB, Parsons R, Polyak K. HIN-1, an inhibitor of cell growth, invasion, and AKT activation. Cancer Res. 2005 Nov 01; 65(21):9659-69.
View in: PubMed

Carlsson H, Yhr M, Petersson S, Collins N, Polyak K, Enerbäck C. Psoriasin (S100A7) and calgranulin-B (S100A9) induction is dependent on reactive oxygen species and is downregulated by Bcl-2 and antioxidants. Cancer Biol Ther. 2005 Sep; 4(9):998-1005.
View in: PubMed

Hu M, Yao J, Cai L, Bachman KE, van den Brûle F, Velculescu V, Polyak K. Distinct epigenetic changes in the stromal cells of breast cancers. Nat Genet. 2005 Aug; 37(8):899-905.
View in: PubMed

Polyak K, Hu M. Do myoepithelial cells hold the key for breast tumor progression? J Mammary Gland Biol Neoplasia. 2005 Jul; 10(3):231-47.
View in: PubMed

Peters BA, Diaz LA, Polyak K, Meszler L, Romans K, Guinan EC, Antin JH, Myerson D, Hamilton SR, Vogelstein B, Kinzler KW, Lengauer C. Contribution of bone marrow-derived endothelial cells to human tumor vasculature. Nat Med. 2005 Mar; 11(3):261-2.
View in: PubMed

Krop I, Player A, Tablante A, Taylor-Parker M, Lahti-Domenici J, Fukuoka J, Batra SK, Papadopoulos N, Richards WG, Sugarbaker DJ, Wright RL, Shim J, Stamey TA, Sellers WR, Loda M, Meyerson M, Hruban R, Jen J, Polyak K. Frequent HIN-1 promoter methylation and lack of expression in multiple human tumor types. Mol Cancer Res. 2004 Sep; 2(9):489-94.
View in: PubMed

DePinho RA, Polyak K. Cancer chromosomes in crisis. Nat Genet. 2004 Sep; 36(9):932-4.
View in: PubMed

Yao J, Polyak K. EMSY links breast cancer gene 2 to the 'Royal Family'. Breast Cancer Res. 2004; 6(5):201-3.
View in: PubMed

Allinen M, Beroukhim R, Cai L, Brennan C, Lahti-Domenici J, Huang H, Porter D, Hu M, Chin L, Richardson A, Schnitt S, Sellers WR, Polyak K. Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell. 2004 Jul; 6(1):17-32.
View in: PubMed

Mehrotra J, Vali M, McVeigh M, Kominsky SL, Fackler MJ, Lahti-Domenici J, Polyak K, Sacchi N, Garrett-Mayer E, Argani P, Sukumar S. Very high frequency of hypermethylated genes in breast cancer metastasis to the bone, brain, and lung. Clin Cancer Res. 2004 May 01; 10(9):3104-9.
View in: PubMed

Burstein HJ, Polyak K, Wong JS, Lester SC, Kaelin CM. Ductal carcinoma in situ of the breast. N Engl J Med. 2004 Apr 01; 350(14):1430-41.
View in: PubMed

Mehrotra J, Ganpat MM, Kanaan Y, Fackler MJ, McVeigh M, Lahti-Domenici J, Polyak K, Argani P, Naab T, Garrett E, Parmigiani G, Broome C, Sukumar S. Estrogen receptor/progesterone receptor-negative breast cancers of young African-American women have a higher frequency of methylation of multiple genes than those of Caucasian women. Clin Cancer Res. 2004 Mar 15; 10(6):2052-7.
View in: PubMed

Fackler MJ, McVeigh M, Evron E, Garrett E, Mehrotra J, Polyak K, Sukumar S, Argani P. DNA methylation of RASSF1A, HIN-1, RAR-beta, Cyclin D2 and Twist in in situ and invasive lobular breast carcinoma. Int J Cancer. 2003 Dec 20; 107(6):970-5.
View in: PubMed

Porter D, Polyak K. Cancer target discovery using SAGE. Expert Opin Ther Targets. 2003 Dec; 7(6):759-69.
View in: PubMed

Porter D, Weremowicz S, Chin K, Seth P, Keshaviah A, Lahti-Domenici J, Bae YK, Monitto CL, Merlos-Suarez A, Chan J, Hulette CM, Richardson A, Morton CC, Marks J, Duyao M, Hruban R, Gabrielson E, Gelman R, Polyak K. A neural survival factor is a candidate oncogene in breast cancer. Proc Natl Acad Sci U S A. 2003 Sep 16; 100(19):10931-6.
View in: PubMed

Polyak K. The hairy powers of oncogenes: from biological function to cancer therapy. Cancer Biol Ther. 2003 Sep-Oct; 2(5):592-4.
View in: PubMed

Buckhaults P, Zhang Z, Chen YC, Wang TL, St Croix B, Saha S, Bardelli A, Morin PJ, Polyak K, Hruban RH, Velculescu VE, Shih IeM. Identifying tumor origin using a gene expression-based classification map. Cancer Res. 2003 Jul 15; 63(14):4144-9.
View in: PubMed

Krop I, Maguire P, Lahti-Domenici J, Lodeiro G, Richardson A, Johannsdottir HK, Nevanlinna H, Borg A, Gelman R, Barkardottir RB, Lindblom A, Polyak K. Lack of HIN-1 methylation in BRCA1-linked and "BRCA1-like" breast tumors. Cancer Res. 2003 May 01; 63(9):2024-7.
View in: PubMed

Porter D, Lahti-Domenici J, Keshaviah A, Bae YK, Argani P, Marks J, Richardson A, Cooper A, Strausberg R, Riggins GJ, Schnitt S, Gabrielson E, Gelman R, Polyak K. Molecular markers in ductal carcinoma in situ of the breast. Mol Cancer Res. 2003 Mar; 1(5):362-75.
View in: PubMed

Polyak K. Breast cancer gene discovery. Expert Rev Mol Med. 2002 Aug 15; 4(18):1-18.
View in: PubMed

Seth P, Porter D, Lahti-Domenici J, Geng Y, Richardson A, Polyak K. Cellular and molecular targets of estrogen in normal human breast tissue. Cancer Res. 2002 Aug 15; 62(16):4540-4.
View in: PubMed

Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, De Souza SJ, Riggins GJ. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A. 2002 Aug 20; 99(17):11287-92.
View in: PubMed

Porter D, Lahti-Domenici J, Torres-Arzayus M, Chin L, Polyak K. Expression of high in normal-1 (HIN-1) and uteroglobin related protein-1 (UGRP-1) in adult and developing tissues. Mech Dev. 2002 Jun; 114(1-2):201-4.
View in: PubMed

Seth P, Krop I, Porter D, Polyak K. Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression). Oncogene. 2002 Jan 24; 21(5):836-43.
View in: PubMed

Polyak K. Molecular alterations in ductal carcinoma in situ of the breast. Curr Opin Oncol. 2002 Jan; 14(1):92-6.
View in: PubMed

Polyak K. Is p53 a breast cancer gene? Cancer Biol Ther. 2002 Jan-Feb; 1(1):37-8.
View in: PubMed

Enerbäck C, Porter DA, Seth P, Sgroi D, Gaudet J, Weremowicz S, Morton CC, Schnitt S, Pitts RL, Stampl J, Barnhart K, Polyak K. Psoriasin expression in mammary epithelial cells in vitro and in vivo. Cancer Res. 2002 Jan 01; 62(1):43-7.
View in: PubMed

Polyak K. On the birth of breast cancer. Biochim Biophys Acta. 2001 Nov 30; 1552(1):1-13.
View in: PubMed

Porter DA, Krop IE, Nasser S, Sgroi D, Kaelin CM, Marks JR, Riggins G, Polyak K. A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res. 2001 Aug 01; 61(15):5697-702.
View in: PubMed

Krop IE, Sgroi D, Porter DA, Lunetta KL, LeVangie R, Seth P, Kaelin CM, Rhei E, Bosenberg M, Schnitt S, Marks JR, Pagon Z, Belina D, Razumovic J, Polyak K. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells. Proc Natl Acad Sci U S A. 2001 Aug 14; 98(17):9796-801.
View in: PubMed

Polyak K, Riggins GJ. Gene discovery using the serial analysis of gene expression technique: implications for cancer research. J Clin Oncol. 2001 Jun 01; 19(11):2948-58.
View in: PubMed

Seth P, Lunetta KL, Bell DW, Gray H, Nasser SM, Rhei E, Kaelin CM, Iglehart DJ, Marks JR, Garber JE, Haber DA, Polyak K. Phenol sulfotransferases: hormonal regulation, polymorphism, and age of onset of breast cancer. Cancer Res. 2000 Dec 15; 60(24):6859-63.
View in: PubMed

Flatt PM, Polyak K, Tang LJ, Scatena CD, Westfall MD, Rubinstein LA, Yu J, Kinzler KW, Vogelstein B, Hill DE, Pietenpol JA. p53-dependent expression of PIG3 during proliferation, genotoxic stress, and reversible growth arrest. Cancer Lett. 2000 Aug 01; 156(1):63-72.
View in: PubMed

Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak K, Zawel L, Kinzler KW, et al. Analysis of human transcriptomes. Nat Genet. 1999 Dec; 23(4):387-8.
View in: PubMed

Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. A public database for gene expression in human cancers. Cancer Res. 1999 Nov 01; 59(21):5403-7.
View in: PubMed

da Costa LT, He TC, Yu J, Sparks AB, Morin PJ, Polyak K, Laken S, Vogelstein B, Kinzler KW. CDX2 is mutated in a colorectal cancer with normal APC/beta-catenin signaling. Oncogene. 1999 Sep 02; 18(35):5010-4.
View in: PubMed

Polyak K, Li Y, Zhu H, Lengauer C, Willson JK, Markowitz SD, Trush MA, Kinzler KW, Vogelstein B. Somatic mutations of the mitochondrial genome in human colorectal tumours. Nat Genet. 1998 Nov; 20(3):291-3.
View in: PubMed

Herman JG, Umar A, Polyak K, Graff JR, Ahuja N, Issa JP, Markowitz S, Willson JK, Hamilton SR, Kinzler KW, Kane MF, Kolodner RD, Vogelstein B, Kunkel TA, Baylin SB. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc Natl Acad Sci U S A. 1998 Jun 09; 95(12):6870-5.
View in: PubMed

Hermeking H, Lengauer C, Polyak K, He TC, Zhang L, Thiagalingam S, Kinzler KW, Vogelstein B. 14-3-3sigma is a p53-regulated inhibitor of G2/M progression. Mol Cell. 1997 Dec; 1(1):3-11.
View in: PubMed

Polyak K, Xia Y, Zweier JL, Kinzler KW, Vogelstein B. A model for p53-induced apoptosis. Nature. 1997 Sep 18; 389(6648):300-5.
View in: PubMed

Polyak K, Wu TT, Hamilton SR, Kinzler KW, Vogelstein B. Less death in the dying. Cell Death Differ. 1997 Apr; 4(3):242-6.
View in: PubMed

Polyak K, Hamilton SR, Vogelstein B, Kinzler KW. Early alteration of cell-cycle-regulated gene expression in colorectal neoplasia. Am J Pathol. 1996 Aug; 149(2):381-7.
View in: PubMed

Polyak K, Waldman T, He TC, Kinzler KW, Vogelstein B. Genetic determinants of p53-induced apoptosis and growth arrest. Genes Dev. 1996 Aug 01; 10(15):1945-52.
View in: PubMed

Fero ML, Rivkin M, Tasch M, Porter P, Carow CE, Firpo E, Polyak K, Tsai LH, Broudy V, Perlmutter RM, Kaushansky K, Roberts JM. A syndrome of multiorgan hyperplasia with features of gigantism, tumorigenesis, and female sterility in p27(Kip1)-deficient mice. Cell. 1996 May 31; 85(5):733-44.
View in: PubMed

Polyak K. Negative regulation of cell growth by TGF beta. Biochim Biophys Acta. 1996 Mar 18; 1242(3):185-99.
View in: PubMed

Leach FS, Polyak K, Burrell M, Johnson KA, Hill D, Dunlop MG, Wyllie AH, Peltomaki P, de la Chapelle A, Hamilton SR, Kinzler KW, Vogelstein B. Expression of the human mismatch repair gene hMSH2 in normal and neoplastic tissues. Cancer Res. 1996 Jan 15; 56(2):235-40.
View in: PubMed

Reynisdóttir I, Polyak K, Iavarone A, Massagué J. Kip/Cip and Ink4 Cdk inhibitors cooperate to induce cell cycle arrest in response to TGF-beta. Genes Dev. 1995 Aug 01; 9(15):1831-45.
View in: PubMed

Jeffrey PD, Russo AA, Polyak K, Gibbs E, Hurwitz J, Massagué J, Pavletich NP. Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex. Nature. 1995 Jul 27; 376(6538):313-20.
View in: PubMed

Ponce-Castañeda MV, Lee MH, Latres E, Polyak K, Lacombe L, Montgomery K, Mathew S, Krauter K, Sheinfeld J, Massague J, et al. p27Kip1: chromosomal mapping to 12p12-12p13.1 and absence of mutations in human tumors. Cancer Res. 1995 Mar 15; 55(6):1211-4.
View in: PubMed

Massagué J, Polyak K. Mammalian antiproliferative signals and their targets. Curr Opin Genet Dev. 1995 Feb; 5(1):91-6.
View in: PubMed

Koff A, Polyak K. p27KIP1, an inhibitor of cyclin-dependent kinases. Prog Cell Cycle Res. 1995; 1:141-7.
View in: PubMed

Nourse J, Firpo E, Flanagan WM, Coats S, Polyak K, Lee MH, Massague J, Crabtree GR, Roberts JM. Interleukin-2-mediated elimination of the p27Kip1 cyclin-dependent kinase inhibitor prevented by rapamycin. Nature. 1994 Dec 08; 372(6506):570-3.
View in: PubMed

Kato JY, Matsuoka M, Polyak K, Massagué J, Sherr CJ. Cyclic AMP-induced G1 phase arrest mediated by an inhibitor (p27Kip1) of cyclin-dependent kinase 4 activation. Cell. 1994 Nov 04; 79(3):487-96.
View in: PubMed

Polyak K, Lee MH, Erdjument-Bromage H, Koff A, Roberts JM, Tempst P, Massagué J. Cloning of p27Kip1, a cyclin-dependent kinase inhibitor and a potential mediator of extracellular antimitogenic signals. Cell. 1994 Jul 15; 78(1):59-66.
View in: PubMed

Roberts JM, Koff A, Polyak K, Firpo E, Collins S, Ohtsubo M, Massagué J. Cyclins, Cdks, and cyclin kinase inhibitors. Cold Spring Harb Symp Quant Biol. 1994; 59:31-8.
View in: PubMed

Polyak K, Kato JY, Solomon MJ, Sherr CJ, Massague J, Roberts JM, Koff A. p27Kip1, a cyclin-Cdk inhibitor, links transforming growth factor-beta and contact inhibition to cell cycle arrest. Genes Dev. 1994 Jan; 8(1):9-22.
View in: PubMed

Koff A, Ohtsuki M, Polyak K, Roberts JM, Massagué J. Negative regulation of G1 in mammalian cells: inhibition of cyclin E-dependent kinase by TGF-beta. Science. 1993 Apr 23; 260(5107):536-9.
View in: PubMed

Research Departments:

Research Website:

Location

Dana-Farber Cancer Institute
450 Brookline Avenue
Dana 740C
Boston, MA 02215
Get Directions

Top