2011 Publications

Research supported by Starr Cancer Consortium awards is reported in the following publications. The Starr Cancer Consortium is funded by the Starr Foundation.

Do Airway Epithelium Air-liquid Cultures Represent the In Vivo Airway Epithelium Transcriptome?

Authors: Dvorak A, Tilley AE, Shaykhiev R, Wang R, Crystal RG.

American Journal of Respiratory Cell Molecular Biology, 2011.

Aerobic glycolysis: meeting the metabolic requirements of cell proliferation.

Authors: Lunt SY, Vander Heiden MG.

Annual Review of Cell Developmental Biology, 2011.

Mirtrons: microRNA biogenesis via splicing.

Authors: Westholm JO, Lai EC.

Biochimie, 2011.

Haploinsufficiency for ribosomal protein genes causes selective activation of p53 in human erythroid progenitor cells.

Authors: Dutt S, Narla A, Lin K, Mullally A, Abayasekara N, Megerdichian C, Wilson FH, Currie T, Khanna-Gupta A, Berliner N, Kutok JL, Ebert BL.

Blood, 2011.

Common breast cancer susceptibility alleles are associated with tumor subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2.

Authors: Mulligan AM, Couch FJ, Barrowdale D, Domchek SM, Eccles D, et al.

Breast Cancer Research, 2011.

Reciprocal Feedback Regulation of PI3K and Androgen Receptor Signaling in PTEN-Deficient Prostate Cancer.

Authors: Carver BS, Chapinski C, Wongvipat J, Hieronymus H, Chen Y, Chandarlapaty S, Arora VK, Le C, Koutcher J, Scher H, Scardino PT, Rosen N, Sawyers CL.

Cancer Cell, 2011.

 
Authors: Chen M, Pratt CP, Zeeman ME, Schultz N, Taylor BS, O'Neill A, Castillo-Martin M, Nowak DG, Naguib A, Grace DM, Murn J, Navin N, Atwal GS, Sander C, Gerald WL, Cordon-Cardo C, Newton AC, Carver BS, Trotman LC.
 
Cancer Cell, 2011.
JAK2V617F-Mediated Phosphorylation of PRMT5 Downregulates Its Methyltransferase Activity and Promotes Myeloproliferation.

Authors: Liu F, Zhao X, Perna F, Wang L, Koppikar P, Abdel-Wahab O, Harr MW, Levine RL, Xu H, Tefferi A, Deblasio A, Hatlen M, Menendez S, Nimer SD.

Cancer Cell, 2011.

Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation.

Authors: Moran-Crusio K, Reavie L, Shih A, Abdel-Wahab O, Ndiaye-Lobry D, Lobry C, Figueroa ME, Vasanthakumar A, Patel J, Zhao X, Perna F, Pandey S, Madzo J, Song C, Dai Q, He C, Ibrahim S, Beran M, Zavadil J, Nimer SD, Melnick A, Godley LA, Aifantis I, Levine RL.

Cancer Cell, 2011.

Gammaherpesvirus and lymphoproliferative disorders in immunocompromised patients.

Author: Cesarman, E.

Cancer Letters, 2011.

Small RNA sequencing and functional characterization reveals microRNA-143 tumor suppressor activity in liposarcoma.

Authors: Ugras S, Brill ER, Jacobsen A, Hafner M, Socci N, Decarolis PL, Khanin R, O'Connor RB, Mihailovic A, Taylor BS, Sheridan R, Gimble J, Viale A, Crago A, Antonescu CR, Sander C, Tuschl T, Singer S.

Cancer Research, 2011.

Role for Dpy-30 in ES Cell-Fate Specification by Regulation of H3K4 Methylation within Bivalent Domains.

Authors: Jiang H, Shukla A, Wang X, Chen WY, Bernstein BE, Roeder RG.

Cell, 2011.

Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes.

Authors: Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, Di Virgilio M, Bothmer A, Nussenzweig A, Robbiani DF, Casellas R, Nussenzweig MC.

Cell, 2011.

The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma.

Authors: Oricchio E, Nanjangud G, Wolfe AL, Schatz JH, Mavrakis KJ, Jiang M, Liu X, Bruno J, Heguy A, Olshen AB, Socci ND, Teruya-Feldstein J, Weis-Garcia F, Tam W, Shaknovich R, Melnick A, Himanen JP, Chaganti RS, Wendel HG.

Cell, 2011.

Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions.

Authors: Ruthenburg AJ, Li H, Milne TA, Dewell S, McGinty RK, Yuen M, Ueberheide B, Dou Y, Muir TW, Patel DJ, Allis CD.

Cell, 2011.

A Poised Chromatin Platform for TGF-beta Access to Master Regulators.

Authors: Xi Q, Wang Z, Zaromytidou AI, Zhang XH, Chow-Tsang LF, Liu JX, Kim H, Barlas A, Manova-Todorova K, Kaartinen V, Studer L, Mark W, Patel DJ, Massague J.

Cell, 2011.

Targeted cancer therapy: what if the driver is just a messenger?

Authors: Schatz JH, Wendel HG.

Cell Cycle, 2011.

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines.

Authors: Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U, Cullen BR.

Cell Host and Microbe, 2011.

TET Family Proteins and Their Role in Stem Cell Differentiation and Transformation.

Authors: Cimmino, L; Abdel-Wahab, O; Levine, RL; Aifantis, I.

Cell Stem Cell, 2011.

Assessment of the prevalence of de novo mutations in the BRCA1 and BRCA2 genes.

Authors: Zhang, L; Fleischut, MH; Kohut, K; Spencer, S; Wong, K; Stadler, ZK; Kauff, ND; Offit, K; Robson, ME.

Clinical Genetics, 2011.

Control of microRNA biogenesis and transcription by cell signaling pathways.

Authors: Saj A, Lai EC.

Current Opinion in Genetics and Development, 2011.

Cerebellum development and medulloblastoma.

Authors: Roussel MF, Hatten ME.

Current Topics in Developmental Biology, 2011.

The role of Rho GTPase proteins in CNS neuronal migration.

Authors: Govek EE, Hatten ME, Van Aelst L.

Developmental Neurobiology, 2011.

Ubiquitylation and the Fanconi anemia pathway.

Authors: Garner E, Smogorzewska A.

FEBS Letters, 2011.

mRNA and protein levels of FUS, EWSR1, and TAF15 are upregulated in liposarcoma.

Authors: Spitzer JI, Ugras S, Runge S, Decarolis P, Antonescu C, Tuschl T, Singer S.

Genes, Chromosomes & Cancer, 2011.

Vive la différence: biogenesis and evolution of microRNAs in plants and animals.

Authors: Axtell MJ, Westholm JO, Lai EC.

Genome Biology, 2011.

Clinical implications of novel mutations in epigenetic modifiers in AML.

Authors: Abdel-Wahab O, Patel J, Levine RL.

Hematology/Oncology Clinics of North America, 2011.

Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers.

Authors: Im KM, et. al.

Human Genetics, 2011

Hydrogen-bonding catalysis and inhibition by simple solvents in the stereoselective kinetic epoxide-opening spirocyclization of glycal epoxides to form spiroketals.

Authors: Wurst JM, Liu G, Tan DS.

Journal of the American Chemical Society, 2011.

Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling.

Authors: Wagle N, Emery C, Berger MF, Davis MJ, Sawyer A, Pochanard P, Kehoe SM, Johannessen CM, Macconaill LE, Hahn WC, Meyerson M, Garraway LA.

Journal of Clinical Oncology, 2011.

Innate Immune Cells in Breast Cancer - From Villains to Heroes?

Authors: Kees T, Egeblad M.

Journal of Mammary Gland Biology and Neoplasia, 2011.

Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons.

Authors: Wang Z, Chatterjee D, Jeon HY, Akerman M, Vander Heiden MG,  Cantley LC,  Krainer AR.

Journal of Molecular Cell Biology, 2011.

miRNAs in human cancer.

Authors: Farazi TA, Spitzer JI, Morozov P, Tuschl T.

The Journal of Pathology, 2011.

Visualization of the interstitial cells of cajal (ICC) network in mice.

Authors: Chen Y, Shamu T, Chen H, Besmer P, Sawyers CL, Chi P.

Journal of Visualized Experiments, 2011.

Concomitant analysis of EZH2 and ASXL1 mutations in myelofibrosis, chronic myelomonocytic leukemia and blast-phase myeloproliferative neoplasms.

Authors: Abdel-Wahab O, Pardanani A, Patel J, Wadleigh M, Lasho T, Heguy A, Beran M, Gilliland DG, Levine RL, Tefferi A.

Leukemia, 2011.

DNMT3A mutational analysis in primary myelofibrosis, chronic myelomonocytic leukemia and advanced phases of myeloproliferative neoplasms.

Authors: Abdel-Wahab O, Pardanani A, Rampal R, Lasho TL, Levine RL, Tefferi A.

Leukemia, 2011.

Nucleosomal H2B ubiquitylation with purified factors.

Authors: Kim J, Roeder RG.

Methods, 2011.

Formulating a fluorogenic assay to evaluate S-adenosyl-L-methionine analogues as protein methyltransferase cofactors.

Authors: Wang R, Ibáñez G, Islam K, Zheng W, Blum G, Sengelaub C, Luo M.

Molecular BioSystems, 2011.

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability.

Authors: Mukherjee, N; Corcoran, DL; Nusbaum, JD; Reid, DW; Georgiev, S; Hafner, M; Ascano, M; Tuschl, T; Ohler, U; Keene, JD.

Molecular Cell, 2011.

PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression.

Authors: Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y.

Molecular Cell, 2011.

Alternative miRNA Biogenesis Pathways and the Interpretation of Core miRNA Pathway Mutants.

Authors: Yang, JS; Lai, EC.

Molecular Cell, 2011.

The Genomic Complexity of Primary Human Prostate Cancer.

Authors: 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.

Nature, 2011.

RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E).

Authors: Poulikakos PI, Persaud Y, Janakiraman M, Kong X, Ng C, Moriceau G, Shi H, Atefi M, Titz B, Gabay MT, Salton M, Dahlman KB, Tadi M, Wargo JA, Flaherty KT, Kelley MC, Misteli T, Chapman PB, Sosman JA, Graeber TG, Ribas A, Lo RS, Rosen N, Solit DB.

Nature, 2011.

PathSeq: software to identify or discover microbes by deep sequencing of human tissue.

Authors: Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M.

Nature Biotechnology, 2011.

Toolkit for evaluating genes required for proliferation and survival using tetracycline-regulated RNAi.

Authors: Zuber J, McJunkin K, Fellmann C, Dow LE, Taylor MJ, Hannon GJ, Lowe SW.

Nature Biotechnology, 2011.

Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction.

Authors: Fierz B, Chatterjee C, McGinty RK, Bar-Dagan M, Raleigh DP, Muir TW.

Nature Chemical Biology, 2011.

Imatinib potentiates antitumor T cell responses in gastrointestinal stromal tumor through the inhibition of Ido.

Authors: Balachandran, VP; Cavnar, MJ; Zeng, S; Bamboat, ZM; Ocuin, LM; Obaid, H; Sorenson, EC; Popow, R; Ariyan, C; Rossi, F; Besmer, P; Guo, TH; Antonescu, CR; Taguchi, T; Yuan, JD; Wolchok, JD; Allison, JP; DeMatteo, RP.

Nature Medicine, 2011.

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.

Authors: Adli, M; Bernstein, BE.

Nature Protocols, 2011.

Targeting cancer metabolism: a therapeutic window opens.

Author: Vander Heiden, MG.

Nature Reviews Drug Discovery, 2011.

Towards systematic functional characterization of cancer genomes.

Authors: Boehm JS, Hahn WC.

Nature Reviews. Genetics, 2011.

RNA targets of wild-type and mutant FET family proteins.

Authors: Hoell JI, Larsson E, Runge S, Nusbaum JD, Duggimpudi S, Farazi TA, Hafner M, Borkhardt A, Sander C, Tuschl T.

Nature Structural and Molecular Biology, 2011.

ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome.

Authors: Iwase, S; Xiang, B; Ghosh, S; Ren, T; Lewis, PW; Cochrane, JC; Allis, CD; Picketts, DJ; Patel, DJ; Li, HT; Shi, Y.

Nature Structural and Molecular Biology, 2011.

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs.

Authors: Rosenberg, BR, Hamilton, CE, Mwangi, MM, Dewell, S, Papavasiliou, FN.

Nature Structural and Molecular Biology, 2011.

Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex.

Authors: Tian Y, Simanshu DK, Ascano M, Diaz-Avalos R, Park AY, Juranek SA, Rice WJ, Yin Q, Robinson CV, Tuschl T, Patel DJ.

Nature Structural and Molecular Biology, 2011,

Clinical effect of point mutations in myelodysplastic syndromes.

Authors: Bejar R, Stevenson K, Abdel-Wahab O, Galili N, Nilsson B, Garcia-Manero G, Kantarjian H, Raza A, Levine RL, Neuberg D, Ebert BL.

The New England Journal of Medicine, 2011.

A Computational Framework Discovers New Copy Number Variants with Functional Importance.

Authors: Banerjee S, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F.

PLoS One, 2011.

DNA methylation of the first exon is tightly linked to transcriptional silencing.

Authors: Brenet F, Moh M, Funk P, Feierstein E, Viale AJ, Socci ND, Scandura JM.

PLoS One, 2011.

Recruited Cells Can Become Transformed and Overtake PDGF-Induced Murine Gliomas In Vivo during Tumor Progression.

Authors: Fomchenko EI, Dougherty JD, Helmy KY, Katz AM, Pietras A, Brennan C, Huse JT, Milosevic A, Holland EC.

PLoS One, 2011.

The human airway epithelial Basal cell transcriptome.

Authors: Hackett NR, Shaykhiev R, Walters MS, Wang R, Zwick RK, Ferris B, Witover B, Salit J, Crystal RG.

PLoS One, 2011.

Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer.

Authors: Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R.

PLoS One, 2011.

Function of leukemogenic mixed lineage leukemia 1 (MLL) fusion proteins through distinct partner protein complexes.

Authors: Biswas, D; Milne, TA; Basrur, V; Kim, J; Elenitoba-Johnson, KSJ; Allis, CD; Roeder, RG.

Proceedings of the National Academy of Sciences of the USA, 2011.

Genomic dissection of the epidermal growth factor receptor (EGFR)/PI3K pathway reveals frequent deletion of the EGFR phosphatase PTPRS in head and neck cancers.

Authors: Morris LG, Taylor BS, Bivona TG, Gong Y, Eng S, Brennan CW, Kaufman A, Kastenhuber ER, Banuchi VE, Singh B, Heguy A, Viale A, Mellinghoff IK, Huse J, Ganly I, Chan TA.

Proceedings of the National Academy of Sciences of the USA, 2011.

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries.

Authors: Hafner, M; Renwick, N; Brown, M; Mihailovic, A; Holoch, D; Lin, C; Pena, JTG; Nusbaum, JD; Morozov, P; Ludwig, J; Ojo, T; Luo, SJ; Schroth, G; Tuschl, T.

RNA, 2011.

A Drosophila genetic screen yields allelic series of core microRNA biogenesis factors and reveals post-developmental roles for microRNAs.

Authors: Smibert P, Bejarano F, Wang D, Garaulet DL, Yang JS, Martin R, Bortolamiol-Becet D, Robine N, Hiesinger PR, Lai EC.

RNA, 2011.

Widespread regulatory activity of vertebrate microRNA* species.

Authors: Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC.

RNA, 2011.

Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses.

Authors: Anastasiou D, Poulogiannis G, Asara JM, Boxer MB, Jiang JK, Shen M, Bellinger G, Sasaki AT, Locasale JW, Auld DS, Thomas CJ, Vander Heiden MG, Cantley LC.

Science, 2011.

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma.

Authors: Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence M, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortés ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio R, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Winckler W, Ardlie K, Gabriel SB, Meyerson M, Lander ES, Getz G, Golub TR, Garraway LA, Grandis JR.

Science, 2011.

The leukemogenicity of AML1-ETO is dependent on site-specific lysine acetylation.

Authors: Wang L, Gural A, Sun XJ, Zhao X, Perna F, Huang G, Hatlen MA, Vu L, Liu F, Xu H, Asai T, Xu H, Deblasio T, Menendez S, Voza F, Jiang Y, Cole PA, Zhang J, Melnick A, Roeder RG, Nimer SD.

Science, 2011.

Breast cancer methylomes establish an epigenomic foundation for metastasis.

Authors: Fang F, Turcan S, Rimner A, Kaufman A, Giri D, Morris LG, Shen R, Seshan V, Mo Q, Heguy A, Baylin SB, Ahuja N, Viale A, Massague J, Norton L, Vahdat LT, Moynahan ME, Chan TA.

Science Translational Medicine, 2011.

Foxo: in command of T lymphocyte homeostasis and tolerance.

Authors: Ouyang, WM; Li, MO.

Trends in Immunology, 2011.

Development and cancer of the cerebellum.

Authors: Hatten ME, Roussel MF.

Trends in Neurosciences, 2011.