DF/HCC Program Affiliation

Cancer Genetics
Leukemia
Cutaneous Oncology and Melanoma
Lymphoma and Myeloma
Prostate Cancer

Research Abstract

Our laboratory focuses on the use of genomic laboratory and computational methods to study biological and clinical questions in cancer. Particular emphasis is placed on the use of genomics methods for the discovery of clinically significant diagnostic and prognostic biomarkers and potential new therapeutic targets. Methods to incorporate genomic approaches into the drug discovery process are also being developed.

Publications

• Wagner BK, Kitami T, Gilbert TJ, Peck D, Ramanathan A, Schreiber SL, Golub TR, Mootha VK.Large-scale chemical dissection of mitochondrial function.Nat Biotechnol 2008 Mar;26(3):343-51.
  18297058
• Takeyama K, Monti S, Manis JP, Cin PD, Getz G, Beroukhim R, Dutt S, Aster JC, Alt FW, Golub TR, Shipp MA.Integrative analysis reveals 53BP1 copy loss and decreased expression in a subset of human diffuse large B-cell lymphomas.Oncogene 2007 Jul 16.
  17637749
• Golub TR.Genomics: global views of leukaemia.Nature 2007 Apr 12;446(7137):739-40.
  17429386
• Stegmaier K, Wong JS, Ross KN, Chow KT, Peck D, Wright RD, Lessnick SL, Kung AL, Golub TR.Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma.PLoS Med 2007 Apr;4(4):e122.
  17425403
• Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T.Impaired microRNA processing enhances cellular transformation and tumorigenesis.Nat Genet 2007 May;39(5):673-7.
  17401365
• Sherwood RI, Jitianu C, Cleaver O, Shaywitz DA, Lamenzo JO, Chen AE, Golub TR, Melton DA.Prospective isolation and global gene expression analysis of definitive and visceral endoderm.Dev Biol 2007 Apr 15;304(2):541-55.
  17328885
• Byers RJ, Di Vizio D, O'connell F, Tholouli E, Levenson RM, Gossard K, Twomey D, Yang Y, Benedettini E, Rose J, Ligon KL, Finn SP, Golub TR, Loda M.Semiautomated multiplexed quantum dot-based in situ hybridization and spectral deconvolution.J Mol Diagn 20
  17251332
• Pegtel DM, Subramanian A, Meritt D, Tsai CH, Sheen TS, Golub TR, Thorley-Lawson DA.IFN-alpha-stimulated genes and Epstein-Barr virus gene expression distinguish WHO type II and III nasopharyngeal carcinomas.Cancer Res 2007 Jan 15;67(2):474-81.
  17234754
• Kobayashi S, Shimamura T, Monti S, Steidl U, Hetherington CJ, Lowell AM, Golub T, Meyerson M, Tenen DG, Shapiro GI, Halmos B.Transcriptional profiling identifies cyclin D1 as a critical downstream effector of mutant epidermal growth factor receptor signal
  17145885
• Hieronymus H, Lamb J, Ross KN, Peng XP, Clement C, Rodina A, Nieto M, Du J, Stegmaier K, Raj SM, Maloney KN, Clardy J, Hahn WC, Chiosis G, Golub TR.Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modul
  17010675
• Wei G, Twomey D, Lamb J, Schlis K, Agarwal J, Stam RW, Opferman JT, Sallan SE, den Boer ML, Pieters R, Golub TR, Armstrong SA.Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance.Cancer Cell 200
  17010674
• Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ, Clemons PA, Wei R, Carr SA, Lander ES, Golub TR.The Connectivity Map: using gene-expression s
  17008526
• Tholouli E, Hoyland JA, Di Vizio D, O'Connell F, Macdermott SA, Twomey D, Levenson R, Yin JA, Golub TR, Loda M, Byers R.Imaging of multiple mRNA targets using quantum dot based in situ hybridization and spectral deconvolution in clinical biopsies.Biochem
  16893519
• Krivtsov AV, Twomey D, Feng Z, Stubbs MC, Wang Y, Faber J, Levine JE, Wang J, Hahn WC, Gilliland DG, Golub TR, Armstrong SA.Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9.Nature 2006 Jul 16.
  16862118
• Peck D, Crawford ED, Ross KN, Stegmaier K, Golub TR, Lamb J.A Method for High-Throughput Gene Expression Signature Analysis.Genome Biol 2006 Jul 19;7(7):R61.
  16859521
• Pikman Y, Lee BH, Mercher T, McDowell E, Ebert BL, Gozo M, Cuker A, Wernig G, Moore S, Galinsky I, Deangelo DJ, Clark JJ, Lee SJ, Golub TR, Wadleigh M, Gilliland DG, Levine RL.MPLW515L Is a Novel Somatic Activating Mutation in Myelofibrosis with Myeloid M
  16834459
• Smith R, Owen LA, Trem DJ, Wong JS, Whangbo JS, Golub TR, Lessnick SL.Expression profiling of EWS/FLI identifies NKX2.2 as a critical target gene in Ewing's sarcoma.Cancer Cell 2006 May;9(5):405-16.
  16697960
• Stanbrough M, Bubley GJ, Ross K, Golub TR, Rubin MA, Penning TM, Febbo PG, Balk SP.Increased expression of genes converting adrenal androgens to testosterone in androgen-independent prostate cancer.Cancer Res 2006 Mar 1;66(5):2815-25.
  16510604
• Bourquin JP, Subramanian A, Langebrake C, Reinhardt D, Bernard O, Ballerini P, Baruchel A, Cavé H, Dastugue N, Hasle H, Kaspers GL, Lessard M, Michaux L, Vyas P, van Wering E, Zwaan CM, Golub TR, Orkin SH.Identification of distinct molecular phenotypes in
  16492768
• Bassères DS, Levantini E, Ji H, Monti S, Elf S, Dayaram T, Fenyus M, Kocher O, Golub T, Wong KK, Halmos B, Tenen DG.Respiratory failure due to differentiation arrest and expansion of alveolar cells following lung-specific loss of the transcription factor
  16428462
• Febbo PG, Thorner A, Rubin MA, Loda M, Kantoff PW, Oh WK, Golub T, George D.Application of oligonucleotide microarrays to assess the biological effects of neoadjuvant imatinib mesylate treatment for localized prostate cancer.Clin Cancer Res 2006 Jan 1;12(
  16397037
• Pegtel DM, Subramanian A, Sheen TS, Tsai CH, Golub TR, Thorley-Lawson DA.Epstein-Barr-virus-encoded LMP2A induces primary epithelial cell migration and invasion: possible role in nasopharyngeal carcinoma metastasis.J Virol 2005 Dec;79(24):15430-42.
  16306614
• Solit DB, Garraway LA, Pratilas CA, Sawai A, Getz G, Basso A, Ye Q, Lobo JM, She Y, Osman I, Golub TR, Sebolt-Leopold J, Sellers WR, Rosen N.BRAF mutation predicts sensitivity to MEK inhibition.Nature 2006 Jan 19;439(7074):358-62.
  16273091
• Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.Proc Natl Acad Sci U
  16199517
• Shepard JL, Amatruda JF, Stern HM, Subramanian A, Finkelstein D, Ziai J, Finley KR, Pfaff KL, Hersey C, Zhou Y, Barut B, Freedman M, Lee C, Spitsbergen J, Neuberg D, Weber G, Golub TR, Glickman JN, Kutok JL, Aster JC, Zon LI.A zebrafish bmyb mutation caus
  16150706
• Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR.Integrative genomic analyses identify MITF as a lineage survival onc
  16001072
• Stegmaier K, Corsello SM, Ross KN, Wong JS, Deangelo DJ, Golub TR.Gefitinib induces myeloid differentiation of acute myeloid leukemia.Blood 2005 Oct 15;106(8):2841-8.
  15998836
• Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR.MicroRNA expression profiles classify human cancers.Nature 2005 Jun 9;435(7043):834-8.
  15944708
• Feuerhake F, Kutok JL, Monti S, Chen W, Lacasce AS, Cattoretti G, Kurtin P, Pinkus GS, de Leval L, Harris NL, Savage KJ, Neuberg D, Habermann TM, Dalla-Favera R, Golub TR, Aster JC, Shipp MA.NF{kappa}B activity, function and target gene signatures in prim
  15870177
• Levine RL, Wadleigh M, Cools J, Ebert BL, Wernig G, Huntly BJ, Boggon TJ, Wlodarska I, Clark JJ, Moore S, Adelsperger J, Koo S, Lee JC, Gabriel S, Mercher T, D'Andrea A, Frohling S, Dohner K, Marynen P, Vandenberghe P, Mesa RA, Tefferi A, Griffin JD, Eck
  15837627
• Febbo PG, Lowenberg M, Thorner AR, Brown M, Loda M, Golub TR.Androgen mediated regulation and functional implications of fkbp51 expression in prostate cancer.J Urol 2005 May;173(5):1772-7.
  15821585
• Ebert BL, Lee MM, Pretz JL, Subramanian A, Mak R, Golub TR, Sieff CA.An RNA interference model of RPS19 deficiency in Diamond Blackfan Anemia recapitulates defective hematopoiesis and rescue by dexamethasone: identification of dexamethasone responsive gen
  15755903
• Wang J, Iwasaki H, Krivtsov A, Febbo PG, Thorner AR, Ernst P, Anastasiadou E, Kutok JL, Kogan SC, Zinkel SS, Fisher JK, Hess JL, Golub TR, Armstrong SA, Akashi K, Korsmeyer SJ.Conditional MLL-CBP targets GMP and models therapy-related myeloproliferative d
  15635450
• Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T.An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis.Nat Genet.
• Berger R, Febbo PG, Majumder PK, Zhao JJ, Mukherjee S, Signoretti S, Campbell KT, Sellers WR, Roberts TM, Loda M, Golub TR, Hahn WC.Androgen-induced differentiation and tumorigenicity of human prostate epithelial cells.Cancer Res 2004 Dec 15;64(24):8867-7
  15604246
• Monti S, Savage KJ, Kutok JL, Feuerhake F, Kurtin P, Mihm M, Wu B, Pasqualucci L, Neuberg D, Aguiar RC, Dal Cin P, Ladd C, Pinkus GS, Salles G, Harris NL, Dalla-Favera R, Habermann TM, Aster JC, Golub TR, Shipp MA.Molecular profiling of diffuse large B-ce
  15550490
• Halmos B, Bassères DS, Monti S, D'Aló F, Dayaram T, Ferenczi K, Wouters BJ, Huettner CS, Golub TR, Tenen DG.A transcriptional profiling study of CCAAT/enhancer binding protein targets identifies hepatocyte nuclear factor 3 beta as a novel tumor suppressor
  15205324
• Majumder PK, Febbo PG, Bikoff R, Berger R, Xue Q, McMahon LM, Manola J, Brugarolas J, McDonnell TJ, Golub TR, Loda M, Lane HA, Sellers WR.mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-d
  15156201
• Fernandez-Teijeiro A, Betensky RA, Sturla LM, Kim JY, Tamayo P, Pomeroy SL.Combining gene expression profiles and clinical parameters for risk stratification in medulloblastomas.J Clin Oncol 2004 Mar 15;22(6):994-8.
  14970184
• Stegmaier K, Ross KN, Colavito SA, O'Malley S, Stockwell BR, Golub TR.Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation.Nat Genet 2004 Mar;36(3):257-63.
  14770183
• Armstrong SA, Golub TR, Korsmeyer SJ.MLL-rearranged leukemias: insights from gene expression profiling.Semin Hematol 2003 Oct;40(4):268-73.
  14582077
• Savage KJ, Monti S, Kutok JL, Cattoretti G, Neuberg D, De Leval L, Kurtin P, Dal Cin P, Ladd C, Feuerhake F, Aguiar RC, Li S, Salles G, Berger F, Jing W, Pinkus GS, Habermann T, Dalla-Favera R, Harris NL, Aster JC, Golub TR, Shipp MA.The molecular signatu
  12933571
• Lamb J, Ramaswamy S, Ford HL, Contreras B, Martinez RV, Kittrell FS, Zahnow CA, Patterson N, Golub TR, Ewen ME.A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer.Cell 2003 Aug 8;114(3):323-34.
  12914697
• Majumder PK, Yeh JJ, George DJ, Febbo PG, Kum J, Xue Q, Bikoff R, Ma H, Kantoff PW, Golub TR, Loda M, Sellers WR.Prostate intraepithelial neoplasia induced by prostate restricted Akt activation: the MPAKT model.Proc Natl Acad Sci U S A 2003 Jun 24;100(13)
  12799464
• Golub TR.Mining the genome for combination therapies.Nat Med 2003 May;9(5):510-1.
  12724758
• Nutt CL, Mani DR, Betensky RA, Tamayo P, Cairncross JG, Ladd C, Pohl U, Hartmann C, McLaughlin ME, Batchelor TT, Black PM, von Deimling A, Pomeroy SL, Golub TR, Louis DN.Gene expression-based classification of malignant gliomas correlates better with surv
  12670911
• Armstrong SA, Kung AL, Mabon ME, Silverman LB, Stam RW, Den Boer ML, Pieters R, Kersey JH, Sallan SE, Fletcher JA, Golub TR, Griffin JD, Korsmeyer SJ.Inhibition of FLT3 in MLL. Validation of a therapeutic target identified by gene expression based classif
  12620411
• Antipova AA, Tamayo P, Golub TR.A strategy for oligonucleotide microarray probe reduction.Genome Biol 2002;3(12):RESEARCH0073.
  12537562
• Ramaswamy S, Ross KN, Lander ES, Golub TR.A molecular signature of metastasis in primary solid tumors.Nat Genet 2003 Jan;33(1):49-54.
  12469122
• Kuwata T, Gongora C, Kanno Y, Sakaguchi K, Tamura T, Kanno T, Basrur V, Martinez R, Appella E, Golub T, Ozato K.Gamma interferon triggers interaction between ICSBP (IRF-8) and TEL, recruiting the histone deacetylase HDAC3 to the interferon-responsive elem
  12370291
• Humpherys D, Eggan K, Akutsu H, Friedman A, Hochedlinger K, Yanagimachi R, Lander ES, Golub TR, Jaenisch R.Abnormal gene expression in cloned mice derived from embryonic stem cell and cumulus cell nuclei.Proc Natl Acad Sci U S A 2002 Oct 1;99(20):12889-94
  12235366
• Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D'Amico AV, Richie JP, Lander ES, Loda M, Kantoff PW, Golub TR, Sellers WR.Gene expression correlates of clinical prostate cancer behavior.Cancer Cell 2002 Mar;1(2):203-9.
  12086878
• McGill GG, Horstmann M, Widlund HR, Du J, Motyckova G, Nishimura EK, Lin YL, Ramaswamy S, Avery W, Ding HF, Jordan SA, Jackson IJ, Korsmeyer SJ, Golub TR, Fisher DE.Bcl2 regulation by the melanocyte master regulator Mitf modulates lineage survival and mel
  12086670
• Ferrando AA, Neuberg DS, Staunton J, Loh ML, Huard C, Raimondi SC, Behm FG, Pui CH, Downing JR, Gilliland DG, Lander ES, Golub TR, Look AT.Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia.Cancer Cell 2002 F
  12086890
• Lessnick SL, Dacwag CS, Golub TR.The Ewing's sarcoma oncoprotein EWS/FLI induces a p53-dependent growth arrest in primary human fibroblasts.Cancer Cell 2002 May;1(4):393-401.
  12086853
• Ramaswamy S, Golub TR.DNA microarrays in clinical oncology.J Clin Oncol 2002 Apr 1;20(7):1932-41.
  11919254
• Kitareewan S, Pitha-Rowe I, Sekula D, Lowrey CH, Nemeth MJ, Golub TR, Freemantle SJ, Dmitrovsky E.UBE1L is a retinoid target that triggers PML/RARalpha degradation and apoptosis in acute promyelocytic leukemia.Proc Natl Acad Sci U S A 2002 Mar 19;99(6):38
  11891284
• Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP,
  11807556
• Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J, Neuberg DS, Lander ES, Aster JC, Golub TR.Diffuse large B-cell lymphoma outcome prediction by
  11786909
• Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR.Multiclass cancer diagnosis using tumor gene expression signatures.Proc Natl Acad Sci U S A 2001 De
  11742071
• Armstrong SA, Staunton JE, Silverman LB, Pieters R, den Boer ML, Minden MD, Sallan SE, Lander ES, Golub TR, Korsmeyer SJ.MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia.Nat Genet 2002 Jan;30(1):41-7.
  11731795
• Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M.Classification of human lung carcinomas by mRNA expressi
  11707567
• Golub TR.Genomic approaches to the pathogenesis of hematologic malignancy.Curr Opin Hematol 2001 Jul;8(4):252-61.
  11561164
• Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR.Chemosensitivity prediction by transcriptional profiling.Proc Natl Acad Sci U S A 2001 Sep 11;98(19):10787-92.
  11553813
• Yeang CH, Ramaswamy S, Tamayo P, Mukherjee S, Rifkin RM, Angelo M, Reich M, Lander E, Mesirov J, Golub T.Molecular classification of multiple tumor types.Bioinformatics 2001;17 Suppl 1:S316-22.
  11473023
• Johansen LM, Iwama A, Lodie TA, Sasaki K, Felsher DW, Golub TR, Tenen DG.c-Myc is a critical target for c/EBPalpha in granulopoiesis.Mol Cell Biol 2001 Jun;21(11):3789-806.
  11340171
• Golub TR.Genome-wide views of cancer.N Engl J Med 2001 Feb 22;344(8):601-2.
  11207357
• Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS.Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks.Proc Natl Acad Sci U S A 2000 Oct 24;97(22):12182-6.
  11027309
• Clark EA, Golub TR, Lander ES, Hynes RO.Genomic analysis of metastasis reveals an essential role for RhoC.Nature 2000 Aug 3;406(6795):532-5.
  10952316
• Coller HA, Grandori C, Tamayo P, Colbert T, Lander ES, Eisenman RN, Golub TR.Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion.Proc Natl Acad Sci U S A 2000 Mar 28
  10737792
• Dickson MA, Hahn WC, Ino Y, Ronfard V, Wu JY, Weinberg RA, Louis DN, Li FP, Rheinwald JG.Human keratinocytes that express hTERT and also bypass a p16(INK4a)-enforced mechanism that limits life span become immortal yet retain normal growth and differentiat
  10648628
• Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES.Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.Science 1999 Oct
  10521349
• Wang LC, Swat W, Fujiwara Y, Davidson L, Visvader J, Kuo F, Alt FW, Gilliland DG, Golub TR, Orkin SH.The TEL/ETV6 gene is required specifically for hematopoiesis in the bone marrow.Genes Dev 1998 Aug 1;12(15):2392-402.
  9694803
• Wang LC, Kuo F, Fujiwara Y, Gilliland DG, Golub TR, Orkin SH.Yolk sac angiogenic defect and intra-embryonic apoptosis in mice lacking the Ets-related factor TEL.EMBO J 1997 Jul 16;16(14):4374-83.
  9250681