Journal ArticleDOI
Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells
Ian J. Majewski,Matthew E. Ritchie,Belinda Phipson,Jason Corbin,Miha Pakusch,Anja Ebert,Meinrad Busslinger,Haruhiko Koseki,Yifang Hu,Gordon K. Smyth,Warren S. Alexander,Douglas J. Hilton,Marnie E. Blewitt +12 more
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TLDR
It is shown that mice with loss of function mutations in PRC2 components display enhanced HSC/progenitor population activity, whereas mutations that disrupt PRC1 or pleiohomeotic repressive complex are associated with HSC or progenitor cell defects.About:
This article is published in Blood.The article was published on 2010-08-05. It has received 131 citations till now. The article focuses on the topics: Progenitor cell & Stem cell.read more
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limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie,Belinda Phipson,Di Wu,Yifang Hu,Charity W. Law,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
Journal ArticleDOI
Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy.
Imran Siddiqui,Karin Schaeuble,Vijaykumar Chennupati,Silvia A. Fuertes Marraco,Sandra Calderon-Copete,Daniela Pais Ferreira,Santiago J. Carmona,Santiago J. Carmona,Santiago J. Carmona,Leonardo Scarpellino,David Gfeller,David Gfeller,David Gfeller,Sylvain Pradervand,Sanjiv A. Luther,Daniel E. Speiser,Werner Held +16 more
TL;DR: This work identified a subset of tumor‐reactive TILs bearing hallmarks of exhausted cells and central memory cells, including expression of the checkpoint protein PD‐1 and the transcription factor Tcf1 that promote tumor control in response to vaccination and checkpoint blockade immunotherapy.
Journal ArticleDOI
Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression
TL;DR: The robust empirical Bayes (RB) algorithm as mentioned in this paper improves the robust differential expression tests by robustifying the hyperparameter estimation procedure, which has the double benefit of reducing the chance that hypervariable genes will be spuriously identified as DE while increasing statistical power for the main body of genes.
Journal ArticleDOI
Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression
TL;DR: Simulations show that the robustified tests have similar performance to the original tests in the absence of outlier genes but have greater power and robustness when outliers are present, and the robust method correctly identifies and downweights genes associated with hidden covariates and detects more genes likely to be scientifically relevant to the experimental conditions.
Journal ArticleDOI
Aberrations of EZH2 in cancer
Andrew Chase,Nicholas C.P. Cross +1 more
TL;DR: 3-deazaneplanocin (DZNep) reduces EZH2 levels and H3K27 trimethylation, resulting in reduced cell proliferation in breast and prostate cancer cells in vitro, and synergistic effects are seen for combined treatment with DNA demethylating agents and histone deacetylation inhibitors, opening up the possibility of refined epigenetic treatments in the future.
References
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Journal ArticleDOI
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin
Ryan D. Morin,Nathalie A. Johnson,Tesa M. Severson,Andrew J. Mungall,Jianghong An,Rodrigo Goya,Paul Je,Merrill Boyle,Bruce Woolcock,Florian Kuchenbauer,Damian Yap,Humphries Rk,Obi L. Griffith,Sohrab P. Shah,Hao Zhu,Kimbara M,Shashkin P,Charlot Jf,Tcherpakov M,Richard Corbett,Angela K Y Tam,Richard Varhol,Duane E Smailus,Michelle Moksa,Yongjun Zhao,Allen Delaney,Hong Qian,Inanc Birol,Jacquie Schein,Richard A. Moore,Robert A. Holt,Douglas E. Horsman,Joseph M. Connors,Joseph M. Connors,Steven J.M. Jones,Samuel Aparicio,Martin Hirst,Randy D. Gascoyne,Marco A. Marra,Marco A. Marra +39 more
TL;DR: Recurrent somatic mutations affecting the polycomb-group oncogene EZH2, which encodes a histone methyltransferase responsible for trimethylating Lys27 of histone H3 (H3K27), are reported, consistent with the notion that EZh2 proteins with mutant Tyr641 have reduced enzymatic activity in vitro.
Journal ArticleDOI
Polycomb silencers control cell fate, development and cancer
TL;DR: New insights are discussed into the possible mechanisms by which PcGs regulate cellular identity, and how these functions might be relevant during tumorigenesis are speculated.
Journal ArticleDOI
Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions
TL;DR: The Polycomb group (PcG) proteins form chromatin-modifying complexes that are essential for embryonic development and stem cell renewal and are commonly deregulated in cancer are identified using genome-wide location analysis in human embryonic fibroblasts.
Journal ArticleDOI
Cloning and expression of murine thrombopoietin cDNA and stimulation of platelet production in vivo
Si Lok,Kenneth Kaushansky,Richard D. Holly,Joseph L. Kuijper,Catherine Lofton-Day,Oort Pieter J,Francis J. Grant,Mark D. Heipel,Steve K. Burkhead,Janet M. Kramer,L. Anne Bell,Cindy A. Sprecher,Hal Blumberg,Rebecca A. Johnson,Donna E. Prunkard,Andrew Ching,Shannon Mathewes,Mason C. Bailey,John W. Forstrom,Michele M. Buddle,Sherri G. Osborn,Simon J. Evans,Paul O. Sheppard,Scott R. Presnell,Patrick J. O'Hara,Fredrick S. Hagen,Gerald Juergen Roth,Donald C. Foster +27 more
TL;DR: The functional cloning of a murine complementary DNA encoding a ligand for the receptor encoded by the c-mpl proto-oncogene is reported, and results strongly suggest that theligand for c-Mpl is thrombopoietin.
Journal ArticleDOI
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
Manching Ku,Richard Koche,Richard Koche,Richard Koche,Esther Rheinbay,Esther Rheinbay,Esther Rheinbay,Eric M. Mendenhall,Eric M. Mendenhall,Mitsuhiro Endoh,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Aviva Presser,Aviva Presser,Chad Nusbaum,Xiaohui Xie,Andrew S. Chi,Andrew S. Chi,Mazhar Adli,Mazhar Adli,Simon Kasif,Leon M. Ptaszek,Chad A. Cowan,Eric S. Lander,Eric S. Lander,Haruhiko Koseki,Bradley E. Bernstein +26 more
TL;DR: It is proposed that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells.
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Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin
Ryan D. Morin,Nathalie A. Johnson,Tesa M. Severson,Andrew J. Mungall,Jianghong An,Rodrigo Goya,Paul Je,Merrill Boyle,Bruce Woolcock,Florian Kuchenbauer,Damian Yap,Humphries Rk,Obi L. Griffith,Sohrab P. Shah,Hao Zhu,Kimbara M,Shashkin P,Charlot Jf,Tcherpakov M,Richard Corbett,Angela K Y Tam,Richard Varhol,Duane E Smailus,Michelle Moksa,Yongjun Zhao,Allen Delaney,Hong Qian,Inanc Birol,Jacquie Schein,Richard A. Moore,Robert A. Holt,Douglas E. Horsman,Joseph M. Connors,Joseph M. Connors,Steven J.M. Jones,Samuel Aparicio,Martin Hirst,Randy D. Gascoyne,Marco A. Marra,Marco A. Marra +39 more
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