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.

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.

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.

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, Massagu¨¦ J.

Cell, 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.

Restoration of C/EBPá in dedifferentiated liposarcoma induces G2/M cell cycle arrest and apoptosis.

Authors: Wu YV, Okada T, Decarolis P, Socci N, O'Connor R, Geha RC, Joy Somberg C, Antonescu C, 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.

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.

Authors: Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., Baselga, J., Liu, C., Shivdasani, R. A., Ogino, S., Birren, B. W., Huttenhower, C., Garrett, W. S., Meyerson, M.

Genome Research, 2011.

Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers.

Authors: Im KM, et. al.

Human Genetics, 2011

RAS Mutations Are Associated With the Development of Cutaneous Squamous Cell Tumors in Patients Treated With RAF Inhibitors.

Authors: Oberholzer PA, Kee D, Dziunycz P, Sucker A, Kamsukom N, Jones R, Roden C, Chalk CJ, Ardlie K, Palescandolo E, Piris A, Macconaill LE, Robert C, Hofbauer GF, McArthur GA, Schadendorf D, Garraway LA.

Journal of Clinical Oncology, 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.

miRNAs in human cancer.

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

The Journal of Pathology, 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.

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.

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.

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

Authors: Adli, M; Bernstein, BE.

Nature Protocols, 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.

Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring (V600E)BRAF.

Authors: Xing F, Persaud Y, Pratilas CA, Taylor BS, Janakiraman M, She QB, Gallardo H, Liu C, Merghoub T, Hefter B, Dolgalev I, Viale A, Heguy A, De Stanchina E, Cobrinik D, Bollag G, Wolchok J, Houghton A, Solit DB.

Oncogene, 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.

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.

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.

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 - A Publication of the RNA Society, 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.