Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia

[1]  Ex vivo , 2020, Definitions.

[2]  M. Hafner,et al.  RNA-binding protein IGF2BP1 maintains leukemia stem cell properties by regulating HOXB4, MYB, and ALDH1A1. , 2019, Leukemia.

[3]  J. Flowers,et al.  Origins and geographic diversification of African rice (Oryza glaberrima) , 2018, bioRxiv.

[4]  M. Toribio,et al.  The NOTCH1/CD44 axis drives pathogenesis in a T cell acute lymphoblastic leukemia model , 2018, The Journal of clinical investigation.

[5]  M. Hirst,et al.  Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis , 2017, Journal of visualized experiments : JoVE.

[6]  Thawfeek M. Varusai,et al.  The Reactome Pathway Knowledgebase , 2017, Nucleic Acids Res..

[7]  Mikhail Shugay,et al.  Antigen receptor repertoire profiling from RNA-seq data , 2017, Nature Biotechnology.

[8]  J. Krosl,et al.  Committed Hemopoietic Progenitors, Not Stem Cells, are the Principal Responders to Hox Gene Transduction , 2017, bioRxiv.

[9]  Cheng Cheng,et al.  THE GENOMIC LANDSCAPE OF PEDIATRIC AND YOUNG ADULT T-LINEAGE ACUTE LYMPHOBLASTIC LEUKEMIA , 2017, Nature Genetics.

[10]  Peng Li,et al.  Current status and perspectives of patient-derived xenograft models in cancer research , 2017, Journal of Hematology & Oncology.

[11]  M. Hirst,et al.  Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility. , 2016, Cell reports.

[12]  Margaret A Goodell,et al.  Highly Efficient Genome Editing of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9. , 2016, Cell reports.

[13]  A. Ferrando,et al.  The genetics and mechanisms of T cell acute lymphoblastic leukaemia , 2016, Nature Reviews Cancer.

[14]  Donna Neuberg,et al.  The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. , 2016, Cancer cell.

[15]  L. Stein,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic Acids Res..

[16]  Daniel S. Day,et al.  Activation of proto-oncogenes by disruption of chromosome neighborhoods , 2015, Science.

[17]  D. Casero,et al.  LncRNA profiling of human lymphoid progenitors reveals transcriptional divergence of B and T lineages , 2015, Nature Immunology.

[18]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[19]  T. Fry,et al.  Murine Models of Acute Leukemia: Important Tools in Current Pediatric Leukemia Research , 2014, Front. Oncol..

[20]  M. V. D. van den Brink,et al.  Human proT-cells generated in vitro facilitate hematopoietic stem cell-derived T-lymphopoiesis in vivo and restore thymic architecture. , 2013, Blood.

[21]  R. Emerson,et al.  Using synthetic templates to design an unbiased multiplex PCR assay , 2013, Nature Communications.

[22]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[23]  G. Crooks,et al.  Critical Differences in Hematopoiesis and Lymphoid Development between Humans and Mice , 2013, Journal of Clinical Immunology.

[24]  R. Morgan,et al.  The role of HOX genes in normal hematopoiesis and acute leukemia , 2013, Leukemia.

[25]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[26]  J. Aster,et al.  Defined, serum-free conditions for in vitro culture of primary human T-ALL blasts , 2013, Leukemia.

[27]  J. Aster,et al.  PKCθ Regulates T-Cell Leukemia-Initiating Activity via Reactive Oxygen Species , 2012, Nature medicine.

[28]  Abel Licon,et al.  Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens , 2012, PloS one.

[29]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[30]  C. Desmarais,et al.  Ultra-sensitive detection of rare T cell clones. , 2012, Journal of immunological methods.

[31]  Kiran C. Bobba,et al.  The genetic basis of early T-cell precursor acute lymphoblastic leukaemia , 2012, Nature.

[32]  A. Trumpp,et al.  High-level IGF1R expression is required for leukemia-initiating cell activity in T-ALL and is supported by Notch signaling , 2011, The Journal of experimental medicine.

[33]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[34]  A. Gedman,et al.  Acute T-cell leukemias remain dependent on Notch signaling despite PTEN and INK4A/ARF loss. , 2009, Blood.

[35]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[36]  Abigail Wacher,et al.  Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. , 2009, Blood.

[37]  G. Smyth,et al.  ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays. , 2009, Journal of immunological methods.

[38]  J. Dick,et al.  Characterization in vitro and engraftment potential in vivo of human progenitor T cells generated from hematopoietic stem cells. , 2009, Blood.

[39]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[40]  Cheng Cheng,et al.  Early T-cell precursor leukaemia: a subtype of very high-risk acute lymphoblastic leukaemia. , 2009, The Lancet. Oncology.

[41]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[42]  D. Gifford,et al.  Tissue-specific transcriptional regulation has diverged significantly between human and mouse , 2007, Nature Genetics.

[43]  B. Blom,et al.  Development of human lymphoid cells. , 2006, Annual review of immunology.

[44]  A. Berns,et al.  Retroviral insertional mutagenesis: past, present and future , 2005, Oncogene.

[45]  E. Macintyre,et al.  CALM-AF10+ T-ALL expression profiles are characterized by overexpression of HOXA and BMI1 oncogenes , 2005, Leukemia.

[46]  F. Sigaux,et al.  HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL). , 2005, Blood.

[47]  P. Marynen,et al.  A new recurrent inversion, inv(7)(p15q34), leads to transcriptional activation of HOXA10 and HOXA11 in a subset of T-cell acute lymphoblastic leukemias , 2005, Leukemia.

[48]  Smaroula Dilioglou,et al.  Correction of multi-gene deficiency in vivo using a single 'self-cleaving' 2A peptide–based retroviral vector , 2004, Nature Biotechnology.

[49]  X. Shu,et al.  RAS oncogene mutations and outcome of therapy for childhood acute lymphoblastic leukemia , 2004, Leukemia.

[50]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[51]  Sean J Morrison,et al.  Bmi1, stem cells, and senescence regulation. , 2004, The Journal of clinical investigation.

[52]  M Hummel,et al.  Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: Report of the BIOMED-2 Concerted Action BMH4-CT98-3936 , 2003, Leukemia.

[53]  Robert A. Weinberg,et al.  Comparative Biology of Mouse versus Human Cells: Modelling Human Cancer in Mice O P I N I O N , 2022 .

[54]  S. Armstrong,et al.  Gene expression signatures in MLL-rearranged T-lineage and B-precursor acute leukemias: dominance of HOX dysregulation. , 2003, Blood.

[55]  S. Karlsson,et al.  Reduced Proliferative Capacity of Hematopoietic Stem Cells Deficient in Hoxb3 and Hoxb4 , 2003, Molecular and Cellular Biology.

[56]  E. Macintyre,et al.  Analysis of TCR, pT alpha, and RAG-1 in T-acute lymphoblastic leukemias improves understanding of early human T-lymphoid lineage commitment. , 2003, Blood.

[57]  G. Sauvageau,et al.  HOXB4-Induced Expansion of Adult Hematopoietic Stem Cells Ex Vivo , 2002, Cell.

[58]  R. DePinho,et al.  The oncogene and Polycomb-group gene bmi-1 regulates cell proliferation and senescence through the ink4a locus , 1999, Nature.

[59]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[60]  A. Hall,et al.  A comprehensive analysis of the CDKN2A gene in childhood acute lymphoblastic leukemia reveals genomic deletion, copy number neutral loss of heterozygosity, and association with specific cytogenetic subgroups. , 2009, Blood.

[61]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[62]  Andrew E. Jaffe,et al.  Bioinformatics Applications Note Gene Expression the Sva Package for Removing Batch Effects and Other Unwanted Variation in High-throughput Experiments , 2022 .