151
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Chung J, Riella LV, Maillard I. Targeting the Notch Pathway to Prevent Rejection. Am J Transplant 2016; 16:3079-3085. [PMID: 27037759 PMCID: PMC7017453 DOI: 10.1111/ajt.13816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 02/23/2016] [Accepted: 03/24/2016] [Indexed: 01/25/2023]
Abstract
Immune rejection is mediated by a complex interplay of cellular and humoral mechanisms. Current therapeutic strategies, which rely on global immunosuppression, can result in serious complications and are not completely effective. Notch signaling is a cell-to-cell communication pathway that plays an important role during T cell development and in the regulation of peripheral immune responses. Initial work, performed mainly through gain-of-function approaches, paradoxically identified Notch as an inducer of tolerance; however, recent studies using loss-of-function approaches in mouse models of transplant rejection and graft-versus-host disease have clarified an important role for Notch as a central mediator of T cell alloreactivity. Short-term inhibition of individual Notch ligands in the peritransplant period had long-lasting protective effects. In a vascularized heart allograft model, blockade of Delta-like Notch ligands dampened both cellular and humoral rejection. In this minireview, we summarize current knowledge about the role of Notch signaling during allograft rejection and provide an overarching mechanism through which Notch acts to promote T cell pathogenicity and allograft damage. We propose that targeting elements of the Notch pathway could provide a new therapeutic approach to prevent allograft rejection.
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Affiliation(s)
- J. Chung
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI,Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - L. V. Riella
- Schuster Transplantation Research Center, Harvard Medical School, Boston, MA,Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - I. Maillard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI,Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI,Corresponding author: Ivan Maillard,
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152
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153
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Verginelli F, Adesso L, Limon I, Alisi A, Gueguen M, Panera N, Giorda E, Raimondi L, Ciarapica R, Campese AF, Screpanti I, Stifani S, Kitajewski J, Miele L, Rota R, Locatelli F. Activation of an endothelial Notch1-Jagged1 circuit induces VCAM1 expression, an effect amplified by interleukin-1β. Oncotarget 2016; 6:43216-29. [PMID: 26646450 PMCID: PMC4791227 DOI: 10.18632/oncotarget.6456] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/21/2015] [Indexed: 01/13/2023] Open
Abstract
The Notch1 and Notch4 signaling pathways regulate endothelial cell homeostasis. Inflammatory cytokines induce the expression of endothelial adhesion molecules, including VCAM1, partly by downregulating Notch4 signaling. We investigated the role of endothelial Notch1 in this IL-1β-mediated process. Brief treatment with IL-1β upregulated endothelial VCAM1 and Notch ligand Jagged1. IL-1β decreased Notch1 mRNA levels, but levels of the active Notch1ICD protein remained constant. IL-1β-mediated VCAM1 induction was downregulated in endothelial cells subjected to pretreatment with a pharmacological inhibitor of the γ-secretase, which activates Notch receptors, producing NotchICD. It was also downregulated in cells in which Notch1 and/or Jagged1 were silenced.Conversely, the forced expression of Notch1ICD in naïve endothelial cells upregulated VCAM1 per se and amplified IL-1β-mediated VCAM1 induction. Jagged1 levels increased and Notch4 signaling was downregulated in parallel. Finally, Notch1ICD and Jagged1 expression was upregulated in the endothelium of the liver in a model of chronic liver inflammation.In conclusion, we describe here a cell-autonomous, pro-inflammatory endothelial Notch1-Jagged1 circuit (i) triggering the expression of VCAM1 even in the absence of inflammatory cytokines and (ii) enhancing the effects of IL-1β. Thus, IL-1β regulates Notch1 and Notch4 activity in opposite directions, consistent with a selective targeting of Notch1 in inflamed endothelium.
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Affiliation(s)
- Federica Verginelli
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Laura Adesso
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Isabelle Limon
- Department of Sorbonne Universités, UPMC University Paris 06, CNRS, UMR, IBPS, Paris, France
| | - Anna Alisi
- Liver Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Marie Gueguen
- Department of Sorbonne Universités, UPMC University Paris 06, CNRS, UMR, IBPS, Paris, France
| | - Nadia Panera
- Liver Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ezio Giorda
- Department of Unit of Flow Cytometry, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Lavinia Raimondi
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Roberta Ciarapica
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | - Stefano Stifani
- Center for Neuronal Survival, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Jan Kitajewski
- Departments of Pathology and Ob/Gyn, Columbia University Medical Center, New York, NY, USA
| | - Lucio Miele
- Department of Genetics and Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, New Orleans, LA, USA
| | - Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Dipartimento di Scienze Pediatriche, Università di Pavia, Pavia PV, Italy
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154
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Khandekar A, Springer S, Wang W, Hicks S, Weinheimer C, Diaz-Trelles R, Nerbonne JM, Rentschler S. Notch-Mediated Epigenetic Regulation of Voltage-Gated Potassium Currents. Circ Res 2016; 119:1324-1338. [PMID: 27697822 DOI: 10.1161/circresaha.116.309877] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 12/19/2022]
Abstract
RATIONALE Ventricular arrhythmias often arise from the Purkinje-myocyte junction and are a leading cause of sudden cardiac death. Notch activation reprograms cardiac myocytes to an induced Purkinje-like state characterized by prolonged action potential duration and expression of Purkinje-enriched genes. OBJECTIVE To understand the mechanism by which canonical Notch signaling causes action potential prolongation. METHODS AND RESULTS We find that endogenous Purkinje cells have reduced peak K+ current, Ito, and IK,slow when compared with ventricular myocytes. Consistent with partial reprogramming toward a Purkinje-like phenotype, Notch activation decreases peak outward K+ current density, as well as the outward K+ current components Ito,f and IK,slow. Gene expression studies in Notch-activated ventricles demonstrate upregulation of Purkinje-enriched genes Contactin-2 and Scn5a and downregulation of K+ channel subunit genes that contribute to Ito,f and IK,slow. In contrast, inactivation of Notch signaling results in increased cell size commensurate with increased K+ current amplitudes and mimics physiological hypertrophy. Notch-induced changes in K+ current density are regulated at least in part via transcriptional changes. Chromatin immunoprecipitation demonstrates dynamic RBP-J (recombination signal binding protein for immunoglobulin kappa J region) binding and loss of active histone marks on K+ channel subunit promoters with Notch activation, and similar transcriptional and epigenetic changes occur in a heart failure model. Interestingly, there is a differential response in Notch target gene expression and cellular electrophysiology in left versus right ventricular cardiac myocytes. CONCLUSIONS In summary, these findings demonstrate a novel mechanism for regulation of voltage-gated potassium currents in the setting of cardiac pathology and may provide a novel target for arrhythmia drug design.
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Affiliation(s)
- Aditi Khandekar
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Steven Springer
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Wei Wang
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Stephanie Hicks
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Carla Weinheimer
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Jeanne M Nerbonne
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Stacey Rentschler
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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155
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Sahni JM, Gayle SS, Bonk KLW, Vite LC, Yori JL, Webb B, Ramos EK, Seachrist DD, Landis MD, Chang JC, Bradner JE, Keri RA. Bromodomain and Extraterminal Protein Inhibition Blocks Growth of Triple-negative Breast Cancers through the Suppression of Aurora Kinases. J Biol Chem 2016; 291:23756-23768. [PMID: 27650498 DOI: 10.1074/jbc.m116.738666] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 12/15/2022] Open
Abstract
Bromodomain and extraterminal (BET) proteins are epigenetic "readers" that recognize acetylated histones and mark areas of the genome for transcription. BRD4, a BET family member protein, has been implicated in a number of types of cancer, and BET protein inhibitors (BETi) are efficacious in many preclinical cancer models. However, the drivers of response to BETi vary depending on tumor type, and little is known regarding the target genes conveying BETi activity in triple-negative breast cancer (TNBC). Here, we show that BETi repress growth of multiple in vitro and in vivo models of TNBC by inducing two terminal responses: apoptosis and senescence. Unlike in other cancers, response to BETi in TNBC is not dependent upon suppression of MYC Instead, both end points are preceded by the appearance of polyploid cells caused by the suppression of Aurora kinases A and B (AURKA/B), which are critical mediators of mitosis. In addition, AURKA/B inhibitors phenocopy the effects of BETi. These results indicate that Aurora kinases play an important role in the growth suppressive activity of BETi in TNBC. Elucidating the mechanism of response to BETi in TNBC should 1) facilitate the prediction of how distinct TNBC tumors will respond to BETi and 2) inform the rational design of drug combination therapies.
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Affiliation(s)
| | | | | | | | | | - Bryan Webb
- From the Departments of Pharmacology and
| | | | | | - Melissa D Landis
- the Methodist Cancer Center, Houston Methodist Hospital, Houston, Texas 77030, and
| | - Jenny C Chang
- the Methodist Cancer Center, Houston Methodist Hospital, Houston, Texas 77030, and
| | - James E Bradner
- the Dana-Farber Cancer Institute, Boston, Massachusetts 02115
| | - Ruth A Keri
- From the Departments of Pharmacology and .,Genetics and Genome Sciences and General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio 44106
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156
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DEPTOR is a direct NOTCH1 target that promotes cell proliferation and survival in T-cell leukemia. Oncogene 2016; 36:1038-1047. [PMID: 27593934 DOI: 10.1038/onc.2016.275] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022]
Abstract
Aberrant activation of NOTCH1 signaling plays a vital role in the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL). Yet the molecular events downstream of NOTCH1 that drive T-cell leukemogenesis remain incompletely understood. Starting from genome-wide gene-expression profiling to seek important NOTCH1 transcriptional targets, we identified DEP-domain containing mTOR-interacting protein (DEPTOR), which was previously shown to be important in multiple myeloma but remains functionally unclear in other hematological malignancies. Mechanistically, we demonstrated NOTCH1 directly bound to and activated the human DEPTOR promoter in T-ALL cells. DEPTOR depletion abolished cellular proliferation, attenuated glycolytic metabolism and enhanced cell death, while ectopically expressed DEPTOR significantly promoted cell growth and glycolysis. We further showed that DEPTOR depletion inhibited while its overexpression enhanced AKT activation in T-ALL cells. Importantly, AKT inhibition completely abrogated DEPTOR-mediated cell growth advantages. Moreover, DEPTOR depletion in a human T-ALL xenograft model significantly delayed T-ALL onset and caused a substantial decrease of AKT activation in leukemic blasts. We thus reveal a novel mechanism involved in NOTCH1-driven leukemogenesis, identifying the transcriptional control of DEPTOR and its regulation of AKT as additional key elements of the leukemogenic program activated by NOTCH1.
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157
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Ntziachristos P, Abdel-Wahab O, Aifantis I. Emerging concepts of epigenetic dysregulation in hematological malignancies. Nat Immunol 2016; 17:1016-24. [PMID: 27478938 PMCID: PMC5134743 DOI: 10.1038/ni.3517] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
The past decade brought a revolution in understanding of the structure, topology and disease-inducing lesions of RNA and DNA, fueled by unprecedented progress in next-generation sequencing. This technological revolution has also affected understanding of the epigenome and has provided unique opportunities for the analysis of DNA and histone modifications, as well as the first map of the non-protein-coding genome and three-dimensional (3D) chromosomal interactions. Overall, these advances have facilitated studies that combine genetic, transcriptomics and epigenomics data to address a wide range of issues ranging from understanding the role of the epigenome in development to targeting the transcription of noncoding genes in human cancer. Here we describe recent insights into epigenetic dysregulation characteristic of the malignant differentiation of blood stem cells based on studies of alterations that affect epigenetic complexes, enhancers, chromatin, long noncoding RNAs (lncRNAs), RNA splicing, nuclear topology and the 3D conformation of chromatin.
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Affiliation(s)
- Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Iannis Aifantis
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, New York, USA
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158
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Abstract
The highly conserved Notch signalling pathway functions in many different developmental and homeostatic processes, which raises the question of how this pathway can achieve such diverse outcomes. With a direct route from the membrane to the nucleus, the Notch pathway has fewer opportunities for regulation than do many other signalling pathways, yet it generates exquisitely patterned structures, including sensory hair cells and branched arterial networks. More confusingly, its activity promotes tissue growth and cancers in some circumstances but cell death and tumour suppression in others. Many different regulatory mechanisms help to shape the activity of the Notch pathway, generating functional outputs that are appropriate for each context. These mechanisms include the receptor-ligand landscape, the tissue topology, the nuclear environment and the connectivity of the regulatory networks.
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Affiliation(s)
- Sarah J Bray
- Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
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159
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Abstract
T cell acute lymphoblastic leukaemia (T-ALL) is an aggressive haematological malignancy derived from early T cell progenitors. In recent years genomic and transcriptomic studies have uncovered major oncogenic and tumour suppressor pathways involved in T-ALL transformation and identified distinct biological groups associated with prognosis. An increased understanding of T-ALL biology has already translated into new prognostic biomarkers and improved animal models of leukaemia and has opened opportunities for the development of targeted therapies for the treatment of this disease. In this Review we examine our current understanding of the molecular mechanisms of T-ALL and recent developments in the translation of these results to the clinic.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pathology, Columbia University Medical Center, New York, New York 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
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160
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Abstract
The Notch signaling pathway plays fundamental roles in diverse developmental processes. Studies of the basic biology of Notch function have provided insights into how its dysfunction contributes to multi-systemic diseases and cancer. In addition, our understanding of Notch signaling in maintaining stem/progenitor cell populations is revealing new avenues for rekindling regeneration. The Notch IX meeting, which was held in Athens, Greece in October 2015, brought together scientists working on different model systems and studying Notch signaling in various contexts. Here, we provide a summary of the key points that were presented at the meeting. Although we focus on the molecular mechanisms that determine Notch signaling and its role in development, we also cover talks describing roles for Notch in adulthood. Together, the talks revealed how interactions between adjacent cells mediated by Notch regulate development and physiology at multiple levels.
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Affiliation(s)
- Ajay Chitnis
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Building 6B, Room 3B-315, Bethesda, MD 20892, USA
| | - Laure Balle-Cuif
- Paris-Saclay Institute for Neuroscience (Neuro-PSI), UMR 9197, CNRS - Université Paris-Sud, Avenue de la Terrasse, Bldg 5, 91190 Gif-sur-Yvette, France
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161
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Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment. Nat Immunol 2016; 17:956-65. [PMID: 27376470 PMCID: PMC4955789 DOI: 10.1038/ni.3514] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/14/2016] [Indexed: 12/28/2022]
Abstract
During T cell development, multipotent progenitors relinquish competence for other fates and commit to the T cell lineage by turning on the transcription factor Bcl11b. To clarify lineage commitment mechanisms, we followed developing T cells at single-cell level using Bcl11b knock-in fluorescent reporter mice. Notch signaling and Notch-activated transcription factors collaborate to activate Bcl11b expression, irrespective of Notch-dependent proliferation. These inputs work via three distinct, asynchronous mechanisms: an early locus poising function dependent on TCF-1 and GATA-3; a stochastic permissivity function dependent on Notch signaling; and a separate amplitude-control function dependent on Runx1, a factor already present in multipotent progenitors. Despite all being necessary for Bcl11b activation, these inputs act in a stage specific manner, providing a multi-tiered mechanism for developmental gene regulation.
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162
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Kalchschmidt JS, Bashford-Rogers R, Paschos K, Gillman ACT, Styles CT, Kellam P, Allday MJ. Epstein-Barr virus nuclear protein EBNA3C directly induces expression of AID and somatic mutations in B cells. J Exp Med 2016; 213:921-8. [PMID: 27217538 PMCID: PMC4886369 DOI: 10.1084/jem.20160120] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022] Open
Abstract
Allday and collaborators demonstrate that the EBV transcription factor and oncoprotein EBNA3C directly induces the expression of AID and somatic mutations in B cells, providing a mechanism linking infection and lymphoma induction. Activation-induced cytidine deaminase (AID), the enzyme responsible for induction of sequence variation in immunoglobulins (Igs) during the process of somatic hypermutation (SHM) and also Ig class switching, can have a potent mutator phenotype in the development of lymphoma. Using various Epstein-Barr virus (EBV) recombinants, we provide definitive evidence that the viral nuclear protein EBNA3C is essential in EBV-infected primary B cells for the induction of AID mRNA and protein. Using lymphoblastoid cell lines (LCLs) established with EBV recombinants conditional for EBNA3C function, this was confirmed, and it was shown that transactivation of the AID gene (AICDA) is associated with EBNA3C binding to highly conserved regulatory elements located proximal to and upstream of the AICDA transcription start site. EBNA3C binding initiated epigenetic changes to chromatin at specific sites across the AICDA locus. Deep sequencing of cDNA corresponding to the IgH V-D-J region from the conditional LCL was used to formally show that SHM is activated by functional EBNA3C and induction of AID. These data, showing the direct targeting and induction of functional AID by EBNA3C, suggest a novel role for EBV in the etiology of B cell cancers, including endemic Burkitt lymphoma.
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Affiliation(s)
- Jens S Kalchschmidt
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | | | - Kostas Paschos
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | - Adam C T Gillman
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | - Christine T Styles
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, England, UK
| | - Martin J Allday
- Molecular Virology, Department of Medicine, Imperial College London, London W2 1PG, England, UK
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163
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Knoechel B, Bhatt A, Pan L, Pedamallu CS, Severson E, Gutierrez A, Dorfman DM, Kuo FC, Kluk M, Kung AL, Zweidler-McKay P, Meyerson M, Blacklow SC, DeAngelo DJ, Aster JC. Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the γ-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case. Cold Spring Harb Mol Case Stud 2016; 1:a000539. [PMID: 27148573 PMCID: PMC4850884 DOI: 10.1101/mcs.a000539] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Notch pathway antagonists such as γ-secretase inhibitors (GSIs) are being tested in diverse cancers, but exceptional responses have yet to be reported. We describe the case of a patient with relapsed/refractory early T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) who achieved a complete hematologic response following treatment with the GSI BMS-906024. Whole-exome sequencing of leukemic blasts revealed heterozygous gain-of-function driver mutations in NOTCH1, CSF3R, and PTPN11, and a homozygous/hemizygous loss-of-function mutation in DNMT3A. The three gain-of-function mutations were absent from remission marrow cells, but the DNMT3A mutation persisted in heterozygous form in remission marrow, consistent with an origin for the patient's ETP-ALL from clonal hematopoiesis. Ex vivo culture of ETP-ALL blasts confirmed high levels of activated NOTCH1 that were repressed by GSI treatment, and RNA-seq documented that GSIs downregulated multiple known Notch target genes. Surprisingly, one potential target gene that was unaffected by GSIs was MYC, a key Notch target in GSI-sensitive T-ALL of cortical T-cell type. H3K27ac super-enhancer landscapes near MYC showed a pattern previously reported in acute myeloid leukemia (AML) that is sensitive to BRD4 inhibitors, and in line with this ETP-ALL blasts downregulated MYC in response to the BRD4 inhibitor JQ1. To our knowledge, this is the first example of complete response of a Notch-mutated ETP-ALL to a Notch antagonist and is also the first description of chromatin landscapes associated with ETP-ALL. Our experience suggests that additional attempts to target Notch in Notch-mutated ETP-ALL are merited.
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Affiliation(s)
- Birgit Knoechel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ami Bhatt
- Departments of Medicine and Genetics, Stanford University, Stanford, California 95305, USA
| | - Li Pan
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Chandra S Pedamallu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;; Broad Institute of MIT and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Eric Severson
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - David M Dorfman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Frank C Kuo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Michael Kluk
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | - Patrick Zweidler-McKay
- Department of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA;; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA;; Broad Institute of MIT and Harvard University, Cambridge, Massachusetts 02142, USA
| | - Stephen C Blacklow
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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164
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Xu Y, Guo W, Li P, Zhang Y, Zhao M, Fan Z, Zhao Z, Yan J. Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression. PLoS Genet 2016; 12:e1005992. [PMID: 27135601 PMCID: PMC4852938 DOI: 10.1371/journal.pgen.1005992] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/27/2016] [Indexed: 01/08/2023] Open
Abstract
Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes in vivo. As genome-wide transcription is organized under the high-order chromosome structure, it is largely uncharted how circadian gene expression is influenced by chromosome architecture. We focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. Using circular chromosome conformation capture sequencing, we systematically examined the interacting loci of a Bmal1-bound super-enhancer upstream of a clock gene Nr1d1 in mouse liver. These interactions are largely stable in the circadian cycle and cohesin binding sites are enriched in the interactome. Global analysis showed that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites are associated with high circadian rhythmicity of transcription. A model integrating the effects of cohesin and CTCF markedly improved the mechanistic understanding of circadian gene expression. Further experiments in cohesin knockout cells demonstrated that cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. This study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.
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Affiliation(s)
- Yichi Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Weimin Guo
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Meng Zhao
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zenghua Fan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
| | - Jun Yan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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165
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MEK and PI3K-AKT inhibitors synergistically block activated IL7 receptor signaling in T-cell acute lymphoblastic leukemia. Leukemia 2016; 30:1832-43. [PMID: 27174491 PMCID: PMC5240021 DOI: 10.1038/leu.2016.83] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/02/2016] [Accepted: 03/14/2016] [Indexed: 02/06/2023]
Abstract
We identified mutations in the IL7Ra gene or in genes encoding the downstream signaling molecules JAK1, JAK3, STAT5B, N-RAS, K-RAS, NF1, AKT and PTEN in 49% of patients with pediatric T-cell acute lymphoblastic leukemia (T-ALL). Strikingly, these mutations (except RAS/NF1) were mutually exclusive, suggesting that they each cause the aberrant activation of a common downstream target. Expressing these mutant signaling molecules—but not their wild-type counterparts—rendered Ba/F3 cells independent of IL3 by activating the RAS-MEK-ERK and PI3K-AKT pathways. Interestingly, cells expressing either IL7Ra or JAK mutants are sensitive to JAK inhibitors, but respond less robustly to inhibitors of the downstream RAS-MEK-ERK and PI3K-AKT-mTOR pathways, indicating that inhibiting only one downstream pathway is not sufficient. Here, we show that inhibiting both the MEK and PI3K-AKT pathways synergistically prevents the proliferation of BaF3 cells expressing mutant IL7Ra, JAK and RAS. Furthermore, combined inhibition of MEK and PI3K/AKT was cytotoxic to samples obtained from 6 out of 11 primary T-ALL patients, including 1 patient who had no mutations in the IL7R signaling pathway. Taken together, these results suggest that the potent cytotoxic effects of inhibiting both MEK and PI3K/AKT should be investigated further as a therapeutic option using leukemia xenograft models.
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166
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Crabtree JS, Singleton CS, Miele L. Notch Signaling in Neuroendocrine Tumors. Front Oncol 2016; 6:94. [PMID: 27148486 PMCID: PMC4830836 DOI: 10.3389/fonc.2016.00094] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/31/2016] [Indexed: 12/12/2022] Open
Abstract
Carcinoids and neuroendocrine tumors (NETs) are a heterogeneous group of tumors that arise from the neuroendocrine cells of the GI tract, endocrine pancreas, and the respiratory system. NETs remain significantly understudied with respect to molecular mechanisms of pathogenesis, particularly the role of cell fate signaling systems such as Notch. The abundance of literature on the Notch pathway is a testament to its complexity in different cellular environments. Notch receptors can function as oncogenes in some contexts and tumor suppressors in others. The genetic heterogeneity of NETs suggests that to fully understand the roles and the potential therapeutic implications of Notch signaling in NETs, a comprehensive analysis of Notch expression patterns and potential roles across all NET subtypes is required.
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Affiliation(s)
- Judy S Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA; Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Ciera S Singleton
- Department of Genetics, Louisiana State University Health Sciences Center , New Orleans, LA , USA
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA; Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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167
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EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1. PLoS Pathog 2016; 12:e1005339. [PMID: 26752713 PMCID: PMC4709166 DOI: 10.1371/journal.ppat.1005339] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/21/2015] [Indexed: 01/08/2023] Open
Abstract
Epstein-Barr Virus (EBV) transforms resting B-lymphocytes into proliferating lymphoblasts to establish latent infections that can give rise to malignancies. We show here that EBV-encoded transcriptional regulator EBNA2 drives the cooperative and combinatorial genome-wide binding of two master regulators of B-cell fate, namely EBF1 and RBP-jκ. Previous studies suggest that these B-cell factors are statically bound to target gene promoters. In contrast, we found that EBNA2 induces the formation of new binding for both RBP-jκ and EBF1, many of which are in close physical proximity in the cellular and viral genome. These newly induced binding sites co-occupied by EBNA2-EBF1-RBP-jκ correlate strongly with transcriptional activation of linked genes that are important for B-lymphoblast function. Conditional expression or repression of EBNA2 leads to a rapid alteration in RBP-jκ and EBF1 binding. Biochemical and shRNA depletion studies provide evidence for cooperative assembly at co-occupied sites. These findings reveal that EBNA2 facilitate combinatorial interactions to induce new patterns of transcription factor occupancy and gene programming necessary to drive B-lymphoblast growth and survival. Epstein-Barr Virus (EBV) reprograms host cell transcription through multiple mechanisms. Here, we show that EBV-encoded transcriptional co-activator EBNA2 drives the formation of new chromosome binding sites for host cell factors RBP-jκ and EBF1. The formation of these new sites is EBNA2-dependent. These newly formed sites have overlapping or neighboring consensus binding sites for these factors, but are only co-occupied in the presence of EBNA2. Newly formed, co-occupied binding sites are highly enriched at promoter and enhancer regulatory elements of genes activated by EBV and required for B-cell proliferation and survival. These findings indicate that EBNA2 drives cooperative and combinatorial transcription factor interactions on chromosomal DNA. We suggest that models depicting the static binding of master regulatory transcription factors to consensus binding sites be revised, and that co-activators, like EBNA2, induce dynamic and combinatorial selection of genome-wide binding sites to alter gene regulation.
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168
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Khan A, Zhang X. dbSUPER: a database of super-enhancers in mouse and human genome. Nucleic Acids Res 2016; 44:D164-71. [PMID: 26438538 PMCID: PMC4702767 DOI: 10.1093/nar/gkv1002] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/10/2015] [Accepted: 09/23/2015] [Indexed: 01/02/2023] Open
Abstract
Super-enhancers are clusters of transcriptional enhancers that drive cell-type-specific gene expression and are crucial to cell identity. Many disease-associated sequence variations are enriched in super-enhancer regions of disease-relevant cell types. Thus, super-enhancers can be used as potential biomarkers for disease diagnosis and therapeutics. Current studies have identified super-enhancers in more than 100 cell types and demonstrated their functional importance. However, a centralized resource to integrate all these findings is not currently available. We developed dbSUPER (http://bioinfo.au.tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further studies related to transcriptional control of cell identity and disease. dbSUPER provides a responsive and user-friendly web interface to facilitate efficient and comprehensive search and browsing. The data can be easily sent to Galaxy instances, GREAT and Cistrome web-servers for downstream analysis, and can also be visualized in the UCSC genome browser where custom tracks can be added automatically. The data can be downloaded and exported in variety of formats. Furthermore, dbSUPER lists genes associated with super-enhancers and also links to external databases such as GeneCards, UniProt and Entrez. dbSUPER also provides an overlap analysis tool to annotate user-defined regions. We believe dbSUPER is a valuable resource for the biology and genetic research communities.
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Affiliation(s)
- Aziz Khan
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China School of Life Sciences, Tsinghua University, Beijing 100084, China
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169
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170
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Pinnell N, Yan R, Cho HJ, Keeley T, Murai MJ, Liu Y, Alarcon AS, Qin J, Wang Q, Kuick R, Elenitoba-Johnson KSJ, Maillard I, Samuelson LC, Cierpicki T, Chiang MY. The PIAS-like Coactivator Zmiz1 Is a Direct and Selective Cofactor of Notch1 in T Cell Development and Leukemia. Immunity 2015; 43:870-83. [PMID: 26522984 PMCID: PMC4654973 DOI: 10.1016/j.immuni.2015.10.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/30/2015] [Accepted: 07/31/2015] [Indexed: 01/17/2023]
Abstract
Pan-NOTCH inhibitors are poorly tolerated in clinical trials because NOTCH signals are crucial for intestinal homeostasis. These inhibitors might also promote cancer because NOTCH can act as a tumor suppressor. We previously reported that the PIAS-like coactivator ZMIZ1 is frequently co-expressed with activated NOTCH1 in T cell acute lymphoblastic leukemia (T-ALL). Here, we show that similar to Notch1, Zmiz1 was important for T cell development and controlled the expression of certain Notch target genes, such as Myc. However, unlike Notch, Zmiz1 had no major role in intestinal homeostasis or myeloid suppression. Deletion of Zmiz1 impaired the initiation and maintenance of Notch-induced T-ALL. Zmiz1 directly interacted with Notch1 via a tetratricopeptide repeat domain at a special class of Notch-regulatory sites. In contrast to the Notch cofactor Maml, which is nonselective, Zmiz1 was selective. Thus, targeting the NOTCH1-ZMIZ1 interaction might combat leukemic growth while avoiding the intolerable toxicities of NOTCH inhibitors.
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Affiliation(s)
- Nancy Pinnell
- Cancer Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ran Yan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Theresa Keeley
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcelo J Murai
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yiran Liu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amparo Serna Alarcon
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason Qin
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qing Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rork Kuick
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ivan Maillard
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Linda C Samuelson
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark Y Chiang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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171
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Jiang P, Wang H, Li W, Zang C, Li B, Wong YJ, Meyer C, Liu JS, Aster JC, Liu XS. Network analysis of gene essentiality in functional genomics experiments. Genome Biol 2015; 16:239. [PMID: 26518695 PMCID: PMC4627418 DOI: 10.1186/s13059-015-0808-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/20/2015] [Indexed: 12/18/2022] Open
Abstract
Many genomic techniques have been developed to study gene essentiality genome-wide, such as CRISPR and shRNA screens. Our analyses of public CRISPR screens suggest protein interaction networks, when integrated with gene expression or histone marks, are highly predictive of gene essentiality. Meanwhile, the quality of CRISPR and shRNA screen results can be significantly enhanced through network neighbor information. We also found network neighbor information to be very informative on prioritizing ChIP-seq target genes and survival indicator genes from tumor profiling. Thus, our study provides a general method for gene essentiality analysis in functional genomic experiments ( http://nest.dfci.harvard.edu ).
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Affiliation(s)
- Peng Jiang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Hongfang Wang
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Wei Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Chongzhi Zang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Bo Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Yinling J Wong
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Cliff Meyer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, 200092, China
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA. .,School of Life Science and Technology, Tongji University, Shanghai, MA, 02138, USA.
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172
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González AJ, Setty M, Leslie CS. Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation. Nat Genet 2015; 47:1249-59. [PMID: 26390058 PMCID: PMC4626279 DOI: 10.1038/ng.3402] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/19/2015] [Indexed: 12/23/2022]
Abstract
We carried out an integrative analysis of enhancer landscape and gene expression dynamics during hematopoietic differentiation using DNase-seq, histone mark ChIP-seq and RNA sequencing to model how the early establishment of enhancers and regulatory locus complexity govern gene expression changes at cell state transitions. We found that high-complexity genes-those with a large total number of DNase-mapped enhancers across the lineage-differ architecturally and functionally from low-complexity genes, achieve larger expression changes and are enriched for both cell type-specific and transition enhancers, which are established in hematopoietic stem and progenitor cells and maintained in one differentiated cell fate but lost in others. We then developed a quantitative model to accurately predict gene expression changes from the DNA sequence content and lineage history of active enhancers. Our method suggests a new mechanistic role for PU.1 at transition peaks during B cell specification and can be used to correct assignments of enhancers to genes.
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Affiliation(s)
- Alvaro J González
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Manu Setty
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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173
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Peirs S, Van der Meulen J, Van de Walle I, Taghon T, Speleman F, Poppe B, Van Vlierberghe P. Epigenetics in T-cell acute lymphoblastic leukemia. Immunol Rev 2015; 263:50-67. [PMID: 25510271 DOI: 10.1111/imr.12237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Normal T-cell development is a strictly regulated process in which hematopoietic progenitor cells migrate from the bone marrow to the thymus and differentiate from early T-cell progenitors toward mature and functional T cells. During this maturation process, cooperation between a variety of oncogenes and tumor suppressors can drive immature thymocytes into uncontrolled clonal expansion and cause T-cell acute lymphoblastic leukemia (T-ALL). Despite improved insights in T-ALL disease biology and comprehensive characterization of its genetic landscape, clinical care remained largely similar over the past decades and still consists of high-dose multi-agent chemotherapy potentially followed by hematopoietic stem cell transplantation. Even with such aggressive treatment regimens, which are often associated with considerable side effects, clinical outcome is still extremely poor in a significant subset of T-ALL patients as a result of therapy resistance or hematological relapses. Recent genetic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in T-ALL, suggesting that epigenetic homeostasis is critically required in restraining tumor development in the T-cell lineage. In this review, we provide an overview of the epigenetic regulators that could be implicated in T-ALL disease biology and speculate how the epigenetic landscape of T-ALL could trigger the development of epigenetic-based therapies to further improve the treatment of human T-ALL.
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Affiliation(s)
- Sofie Peirs
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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174
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Witte S, O'Shea JJ, Vahedi G. Super-enhancers: Asset management in immune cell genomes. Trends Immunol 2015; 36:519-26. [PMID: 26277449 DOI: 10.1016/j.it.2015.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 12/29/2022]
Abstract
Super-enhancers (SEs) are regions of the genome consisting of clusters of regulatory elements bound with very high amounts of transcription factors, and this architecture appears to be the hallmark of genes and noncoding RNAs linked with cell identity. Recent studies have identified SEs in CD4(+) T cells and have further linked these regions to single nucleotide polymorphisms (SNPs) associated with immune-mediated disorders, pointing to an important role for these structures in the T cell differentiation and function. Here we review the features that define SEs, and discuss their function within the broader understanding of the mechanisms that define immune cell identity and function. We propose that SEs present crucial regulatory hubs, coordinating intrinsic and extrinsic differentiation signals, and argue that delineating these regions will provide important insight into the factors and mechanisms that define immune cell identity.
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Affiliation(s)
- Steven Witte
- Lymphocyte Cell Biology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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175
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Hass MR, Liow HH, Chen X, Sharma A, Inoue YU, Inoue T, Reeb A, Martens A, Fulbright M, Raju S, Stevens M, Boyle S, Park JS, Weirauch MT, Brent MR, Kopan R. SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers. Mol Cell 2015; 59:685-97. [PMID: 26257285 DOI: 10.1016/j.molcel.2015.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/11/2015] [Accepted: 07/02/2015] [Indexed: 12/20/2022]
Abstract
We developed Split DamID (SpDamID), a protein complementation version of DamID, to mark genomic DNA bound in vivo by interacting or juxtapositioned transcription factors. Inactive halves of DAM (DNA adenine methyltransferase) were fused to protein pairs to be queried. Either direct interaction between proteins or proximity enabled DAM reconstitution and methylation of adenine in GATC. Inducible SpDamID was used to analyze Notch-mediated transcriptional activation. We demonstrate that Notch complexes label RBP sites broadly across the genome and show that a subset of these complexes that recruit MAML and p300 undergo changes in chromatin accessibility in response to Notch signaling. SpDamID differentiates between monomeric and dimeric binding, thereby allowing for identification of half-site motifs used by Notch dimers. Motif enrichment of Notch enhancers coupled with SpDamID reveals co-targeting of regulatory sequences by Notch and Runx1. SpDamID represents a sensitive and powerful tool that enables dynamic analysis of combinatorial protein-DNA transactions at a genome-wide level.
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Affiliation(s)
- Matthew R Hass
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Hien-Haw Liow
- Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO 63108, USA
| | - Xiaoting Chen
- School of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA; Center for Autoimmune Genomics and Etiology (CAGE) and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ankur Sharma
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Ashley Reeb
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Andrew Martens
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Mary Fulbright
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Saravanan Raju
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Michael Stevens
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Scott Boyle
- Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA
| | - Joo-Seop Park
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Pediatric Urology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Autoimmune Genomics and Etiology (CAGE) and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael R Brent
- Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO 63108, USA
| | - Raphael Kopan
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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176
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Takebe N, Miele L, Harris PJ, Jeong W, Bando H, Kahn M, Yang SX, Ivy SP. Targeting Notch, Hedgehog, and Wnt pathways in cancer stem cells: clinical update. Nat Rev Clin Oncol 2015; 12:445-64. [PMID: 25850553 PMCID: PMC4520755 DOI: 10.1038/nrclinonc.2015.61] [Citation(s) in RCA: 924] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the past decade, cancer stem cells (CSCs) have been increasingly identified in many malignancies. Although the origin and plasticity of these cells remain controversial, tumour heterogeneity and the presence of small populations of cells with stem-like characteristics is established in most malignancies. CSCs display many features of embryonic or tissue stem cells, and typically demonstrate persistent activation of one or more highly conserved signal transduction pathways involved in development and tissue homeostasis, including the Notch, Hedgehog (HH), and Wnt pathways. CSCs generally have slow growth rates and are resistant to chemotherapy and/or radiotherapy. Thus, new treatment strategies targeting these pathways to control stem-cell replication, survival and differentiation are under development. Herein, we provide an update on the latest advances in the clinical development of such approaches, and discuss strategies for overcoming CSC-associated primary or acquired resistance to cancer treatment. Given the crosstalk between the different embryonic developmental signalling pathways, as well as other pathways, designing clinical trials that target CSCs with rational combinations of agents to inhibit possible compensatory escape mechanisms could be of particular importance. We also share our views on the future directions for targeting CSCs to advance the clinical development of these classes of agents.
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Affiliation(s)
- Naoko Takebe
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Lucio Miele
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Pamela Jo Harris
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Woondong Jeong
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Hideaki Bando
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Michael Kahn
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - Sherry X. Yang
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
| | - S. Percy Ivy
- Investigational Drug Branch, Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institute of Health, 9609 Medical Center Drive MSC9739, Bethesda, MD 20852, USA (N.T., P.J.H., S.P.I.). Stanley Scott Cancer Center, Louisiana State University Health Sciences Center and Louisiana Cancer Research Consortium, USA (L.M.). Cancer Therapy and Research Center, University of Texas, USA (W.J.). Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Japan (H.B.). Norris Comprehensive Cancer Research Center, University of Southern California, USA (M.K.). National Clinical Target Validation Laboratory, Division of Cancer Treatment and Diagnosis, National Cancer Institute, USA (S.X.Y.)
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Durinck K, Goossens S, Peirs S, Wallaert A, Van Loocke W, Matthijssens F, Pieters T, Milani G, Lammens T, Rondou P, Van Roy N, De Moerloose B, Benoit Y, Haigh J, Speleman F, Poppe B, Van Vlierberghe P. Novel biological insights in T-cell acute lymphoblastic leukemia. Exp Hematol 2015; 43:625-39. [PMID: 26123366 DOI: 10.1016/j.exphem.2015.05.017] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 05/24/2015] [Indexed: 01/07/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer that accounts for about 15% of pediatric and 25% of adult acute lymphoblastic leukemia (ALL) cases. It is considered as a paradigm for the multistep nature of cancer initiation and progression. Genetic and epigenetic reprogramming events, which transform T-cell precursors into malignant T-ALL lymphoblasts, have been extensively characterized over the past decade. Despite our comprehensive understanding of the genomic landscape of human T-ALL, leukemia patients are still treated by high-dose multiagent chemotherapy, potentially followed by hematopoietic stem cell transplantation. Even with such aggressive treatment regimens, which are often associated with considerable acute and long-term side effects, about 15% of pediatric and 40% of adult T-ALL patients still relapse, owing to acquired therapy resistance, and present with very dismal survival perspectives. Unfortunately, the molecular mechanisms by which residual T-ALL tumor cells survive chemotherapy and act as a reservoir for leukemic progression and hematologic relapse remain poorly understood. Nevertheless, it is expected that enhanced molecular understanding of T-ALL disease biology will ultimately facilitate a targeted therapy driven approach that can reduce chemotherapy-associated toxicities and improve survival of refractory T-ALL patients through personalized salvage therapy. In this review, we summarize recent biological insights into the molecular pathogenesis of T-ALL and speculate how the genetic landscape of T-ALL could trigger the development of novel therapeutic strategies for the treatment of human T-ALL.
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Affiliation(s)
- Kaat Durinck
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | - Steven Goossens
- Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Unit for Molecular Oncology, VIB Inflammation Research Center, Ghent, Belgium; Mammalian Functional Genetics Laboratory, Division of Blood Cancers, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Sofie Peirs
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | - Annelynn Wallaert
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | - Wouter Van Loocke
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | | | - Tim Pieters
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium; Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Unit for Molecular Oncology, VIB Inflammation Research Center, Ghent, Belgium
| | - Gloria Milani
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | - Tim Lammens
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Pieter Rondou
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | - Nadine Van Roy
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Yves Benoit
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Jody Haigh
- Mammalian Functional Genetics Laboratory, Division of Blood Cancers, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Frank Speleman
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Department for Pediatrics, Ghent, Belgium
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178
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Durinck K, Van Loocke W, Van der Meulen J, Van de Walle I, Ongenaert M, Rondou P, Wallaert A, de Bock CE, Van Roy N, Poppe B, Cools J, Soulier J, Taghon T, Speleman F, Van Vlierberghe P. Characterization of the genome-wide TLX1 binding profile in T-cell acute lymphoblastic leukemia. Leukemia 2015; 29:2317-27. [PMID: 26108691 DOI: 10.1038/leu.2015.162] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/15/2015] [Accepted: 06/09/2015] [Indexed: 01/27/2023]
Abstract
The TLX1 transcription factor is critically involved in the multi-step pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) and often cooperates with NOTCH1 activation during malignant T-cell transformation. However, the exact molecular mechanism by which these T-cell specific oncogenes cooperate during transformation remains to be established. Here, we used chromatin immunoprecipitation followed by sequencing to establish the genome-wide binding pattern of TLX1 in human T-ALL. This integrative genomics approach showed that ectopic TLX1 expression drives repression of T cell-specific enhancers and mediates an unexpected transcriptional antagonism with NOTCH1 at critical target genes, including IL7R and NOTCH3. These phenomena coordinately trigger a TLX1-driven pre-leukemic phenotype in human thymic precursor cells, reminiscent of the thymus regression observed in murine TLX1 tumor models, and create a strong genetic pressure for acquiring activating NOTCH1 mutations as a prerequisite for full leukemic transformation. In conclusion, our results uncover a functional antagonism between cooperative oncogenes during the earliest phases of tumor development and provide novel insights in the multi-step pathogenesis of TLX1-driven human leukemia.
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Affiliation(s)
- K Durinck
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - W Van Loocke
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - J Van der Meulen
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - I Van de Walle
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - M Ongenaert
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - P Rondou
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - A Wallaert
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - C E de Bock
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - N Van Roy
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - B Poppe
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - J Cools
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - J Soulier
- Genome Rearrangements and Cancer Laboratory, U944 INSERM, University Paris Diderot and Hematology Laboratory, Saint-Louis Hospital, Paris, France
| | - T Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | - F Speleman
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - P Van Vlierberghe
- Center for Medical Genetics, Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
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179
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Skalska L, Stojnic R, Li J, Fischer B, Cerda-Moya G, Sakai H, Tajbakhsh S, Russell S, Adryan B, Bray SJ. Chromatin signatures at Notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation. EMBO J 2015; 34:1889-904. [PMID: 26069324 DOI: 10.15252/embj.201489923] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 05/13/2015] [Indexed: 12/23/2022] Open
Abstract
The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target selection and gene activation in each context. To investigate the influence of chromatin organisation and dynamics on the response to Notch signalling, we partitioned Drosophila chromatin using histone modifications and established the preferred chromatin conditions for binding of Su(H), the Notch pathway transcription factor. By manipulating activity of a co-operating factor, Lozenge/Runx, we showed that it can help facilitate these conditions. While many histone modifications were unchanged by Su(H) binding or Notch activation, we detected rapid changes in acetylation of H3K56 at Notch-regulated enhancers. This modification extended over large regions, required the histone acetyl-transferase CBP and was independent of transcription. Such rapid changes in H3K56 acetylation appear to be a conserved indicator of enhancer activation as they also occurred at the mammalian Notch-regulated Hey1 gene and at Drosophila ecdysone-regulated genes. This intriguing example of a core histone modification increasing over short timescales may therefore underpin changes in chromatin accessibility needed to promote transcription following signalling activation.
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Affiliation(s)
- Lenka Skalska
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Robert Stojnic
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Jinghua Li
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Bettina Fischer
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gustavo Cerda-Moya
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Hiroshi Sakai
- Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
| | - Shahragim Tajbakhsh
- Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
| | - Steven Russell
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK Department of Genetics, University of Cambridge, Cambridge, UK
| | - Boris Adryan
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK Department of Genetics, University of Cambridge, Cambridge, UK
| | - Sarah J Bray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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180
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Dicer1 imparts essential survival cues in Notch-driven T-ALL via miR-21-mediated tumor suppressor Pdcd4 repression. Blood 2015; 126:993-1004. [PMID: 25979949 DOI: 10.1182/blood-2014-12-618892] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 05/07/2015] [Indexed: 02/07/2023] Open
Abstract
The modulatory function of individual microRNAs (miRNAs) in Notch-driven T-cell acute lymphoblastic leukemias (T-ALLs) has recently been established. Although protumorigenic and tumor-suppressive miRNAs are implicated in disease onset in murine models of Notch-driven T-cell leukemia, whether Dicer1-processed miRNAs are essential for Notch-driven T-ALL is currently unknown. Here we used conditional and inducible genetic loss-of-function approaches to test whether the development and maintenance of Notch-driven T-ALL was dependent on Dicer1 function. Mice with specific inactivation of both Dicer1 alleles in the T-cell lineage did not develop Notch-driven T-ALL. In contrast, loss of 1 functional Dicer1 allele did not significantly perturb T-ALL onset and tumor progression. Inducible inactivation of Dicer1 in early stage polyclonal T-ALL cells was sufficient to abrogate T-ALL progression in leukemic mice, whereas late-stage monoclonal T-ALL cells were counterselected against loss of Dicer1. Lineage-tracing experiments revealed that Dicer1 deficiency led to the induction of apoptosis in T-ALL cells, whereas cell cycle progression remained unaltered. Through microarray-based miRNA profiling, we identified miR-21 as a previously unrecognized miRNA deregulated in both mouse and human T-ALL. Herein, we demonstrate that miR-21 regulates T-ALL cell survival via repression of the tumor suppressor Pdcd4.
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181
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Mathieu M, Duval F, Daudelin JF, Labrecque N. The Notch signaling pathway controls short-lived effector CD8+ T cell differentiation but is dispensable for memory generation. THE JOURNAL OF IMMUNOLOGY 2015; 194:5654-62. [PMID: 25972473 DOI: 10.4049/jimmunol.1402837] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/19/2015] [Indexed: 11/19/2022]
Abstract
Following an infection, naive CD8(+) T cells expand and differentiate into two main populations of effectors: short-lived effector cells (SLECs) and memory precursor effector cells (MPECs). There is limited understanding of the molecular mechanism and cellular processes governing this cell fate. Notch is a key regulator of cell fate decision relevant in many immunological pathways. In this study, we add to the role of Notch in cell fate decision and demonstrate that the Notch signaling pathway controls the MPEC/SLEC differentiation choice following both Listeria infection and dendritic cell immunization of mice. Although fewer SLECs were generated, Notch deficiency did not alter the rate of memory CD8(+) T cell generation. Moreover, we reveal that the Notch signaling pathway plays a context-dependent role for optimal cytokine production by effector CD8(+) T cells. Together, our results unravel critical functions for the Notch signaling pathway during effector CD8(+) T cell differentiation.
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Affiliation(s)
- Mélissa Mathieu
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada; Department of Microbiology, Infectiology and Immunology, University of Montreal, Montreal, Quebec H3T 1J4, Canada; and
| | - Frédéric Duval
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada; Department of Microbiology, Infectiology and Immunology, University of Montreal, Montreal, Quebec H3T 1J4, Canada; and
| | | | - Nathalie Labrecque
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada; Department of Microbiology, Infectiology and Immunology, University of Montreal, Montreal, Quebec H3T 1J4, Canada; and Department of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada
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182
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Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin 2015; 8:16. [PMID: 25984238 PMCID: PMC4432502 DOI: 10.1186/s13072-015-0009-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background Regulated gene expression controls organismal development, and variation in regulatory patterns has been implicated in complex traits. Thus accurate prediction of enhancers is important for further understanding of these processes. Genome-wide measurement of epigenetic features, such as histone modifications and occupancy by transcription factors, is improving enhancer predictions, but the contribution of these features to prediction accuracy is not known. Given the importance of the hematopoietic transcription factor TAL1 for erythroid gene activation, we predicted candidate enhancers based on genomic occupancy by TAL1 and measured their activity. Contributions of multiple features to enhancer prediction were evaluated based on the results of these and other studies. Results TAL1-bound DNA segments were active enhancers at a high rate both in transient transfections of cultured cells (39 of 79, or 56%) and transgenic mice (43 of 66, or 65%). The level of binding signal for TAL1 or GATA1 did not help distinguish TAL1-bound DNA segments as active versus inactive enhancers, nor did the density of regulation-related histone modifications. A meta-analysis of results from this and other studies (273 tested predicted enhancers) showed that the presence of TAL1, GATA1, EP300, SMAD1, H3K4 methylation, H3K27ac, and CAGE tags at DNase hypersensitive sites gave the most accurate predictors of enhancer activity, with a success rate over 80% and a median threefold increase in activity. Chromatin accessibility assays and the histone modifications H3K4me1 and H3K27ac were sensitive for finding enhancers, but they have high false positive rates unless transcription factor occupancy is also included. Conclusions Occupancy by key transcription factors such as TAL1, GATA1, SMAD1, and EP300, along with evidence of transcription, improves the accuracy of enhancer predictions based on epigenetic features. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0009-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nergiz Dogan
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA
| | - Weisheng Wu
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA ; Bioinformatics Core, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218 USA
| | - Christapher S Morrissey
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA
| | - Kuan-Bei Chen
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA
| | - Aaron Stonestrom
- Division of Hematology, The Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104 USA ; Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104 USA
| | - Maria Long
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA
| | - Cheryl A Keller
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA
| | - Yong Cheng
- Department of Genetics, Mail Stop-5120, Stanford University, Stanford, CA 94305 USA
| | - Deepti Jain
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA
| | - Axel Visel
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 84-171, Berkeley, CA 94720 USA ; DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Len A Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 84-171, Berkeley, CA 94720 USA ; DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104 USA ; Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104 USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA
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183
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Wang H, Zang C, Liu XS, Aster JC. The role of Notch receptors in transcriptional regulation. J Cell Physiol 2015; 230:982-8. [PMID: 25418913 DOI: 10.1002/jcp.24872] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/19/2014] [Indexed: 12/22/2022]
Abstract
Notch signaling has pleiotropic context-specific functions that have essential roles in many processes, including embryonic development and maintenance and homeostasis of adult tissues. Aberrant Notch signaling (both hyper- and hypoactive) is implicated in a number of human developmental disorders and many cancers. Notch receptor signaling is mediated by tightly regulated proteolytic cleavages that lead to the assembly of a nuclear Notch transcription complex, which drives the expression of downstream target genes and thereby executes Notch's functions. Thus, understanding regulation of gene expression by Notch is central to deciphering how Notch carries out its many activities. Here, we summarize the recent findings pertaining to the complex interplay between the Notch transcriptional complex and interacting factors involved in transcriptional regulation, including co-activators, cooperating transcription factors, and chromatin regulators, and discuss emerging data pertaining to the role of Notch-regulated noncoding RNAs in transcription.
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Affiliation(s)
- Hongfang Wang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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184
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Schwanbeck R. The role of epigenetic mechanisms in Notch signaling during development. J Cell Physiol 2015; 230:969-81. [PMID: 25336183 DOI: 10.1002/jcp.24851] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 10/16/2014] [Indexed: 12/16/2022]
Abstract
The Notch pathway is a highly conserved cell-cell communication pathway in metazoan involved in numerous processes during embryogenesis, development, and adult organisms. Ligand-receptor interaction of Notch components on adjacent cells facilitates controlled sequential proteolytic cleavage resulting in the nuclear translocation of the intracellular domain of Notch (NICD). There it binds to the Notch effector protein RBP-J, displaces a corepressor complex and enables the induction of target genes by recruitment of coactivators in a cell-context dependent manner. Both, the gene-specific repression and the context dependent activation require an intense communication with the underlying chromatin of the regulatory regions. Since the epigenetic landscape determines the function of the genome, processes like cell fate decision, differentiation, and self-renewal depend on chromatin structure and its remodeling during development. In this review, structural features enabling the Notch pathway to read these epigenetic marks by proteins interacting with RBP-J/Notch will be discussed. Furthermore, mechanisms of the Notch pathway to write and erase chromatin marks like histone acetylation and methylation are depicted as well as ATP-dependent chromatin remodeling during the activation of target genes. An additional fine-tuning of transcriptional regulation upon Notch activation seems to be controlled by the commitment of miRNAs. Since cells within an organism have to react to environmental changes, and developmental and differentiation cues in a proper manner, different signaling pathways have to crosstalk to each other. The chromatin status may represent one major platform to integrate these different pathways including the canonical Notch signaling.
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Affiliation(s)
- Ralf Schwanbeck
- Institute of Biochemistry, Medical Faculty, University of Kiel, Kiel, Germany
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185
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Hnisz D, Schuijers J, Lin CY, Weintraub AS, Abraham BJ, Lee TI, Bradner JE, Young RA. Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Mol Cell 2015; 58:362-70. [PMID: 25801169 DOI: 10.1016/j.molcel.2015.02.014] [Citation(s) in RCA: 353] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/17/2014] [Accepted: 02/05/2015] [Indexed: 12/19/2022]
Abstract
Super-enhancers and stretch enhancers (SEs) drive expression of genes that play prominent roles in normal and disease cells, but the functional importance of these clustered enhancer elements is poorly understood, so it is not clear why genes key to cell identity have evolved regulation by such elements. Here, we show that SEs consist of functional constituent units that concentrate multiple developmental signaling pathways at key pluripotency genes in embryonic stem cells and confer enhanced responsiveness to signaling of their associated genes. Cancer cells frequently acquire SEs at genes that promote tumorigenesis, and we show that these genes are especially sensitive to perturbation of oncogenic signaling pathways. Super-enhancers thus provide a platform for signaling pathways to regulate genes that control cell identity during development and tumorigenesis.
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Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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186
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Krishnamoorthy V, Carr T, de Pooter RF, Emanuelle AO, Akinola EO, Gounari F, Kee BL. Repression of Ccr9 transcription in mouse T lymphocyte progenitors by the Notch signaling pathway. THE JOURNAL OF IMMUNOLOGY 2015; 194:3191-200. [PMID: 25710912 DOI: 10.4049/jimmunol.1402443] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The chemokine receptor CCR9 controls the immigration of multipotent hematopoietic progenitor cells into the thymus to sustain T cell development. Postimmigration, thymocytes downregulate CCR9 and migrate toward the subcapsular zone where they recombine their TCR β-chain and γ-chain gene loci. CCR9 is subsequently upregulated and participates in the localization of thymocytes during their selection for self-tolerant receptor specificities. Although the dynamic regulation of CCR9 is essential for early T cell development, the mechanisms controlling CCR9 expression have not been determined. In this article, we show that key regulators of T cell development, Notch1 and the E protein transcription factors E2A and HEB, coordinately control the expression of Ccr9. E2A and HEB bind at two putative enhancers upstream of Ccr9 and positively regulate CCR9 expression at multiple stages of T cell development. In contrast, the canonical Notch signaling pathway prevents the recruitment of p300 to the putative Ccr9 enhancers, resulting in decreased acetylation of histone H3 and a failure to recruit RNA polymerase II to the Ccr9 promoter. Although Notch signaling modestly modulates the binding of E proteins to one of the two Ccr9 enhancers, we found that Notch signaling represses Ccr9 in T cell lymphoma lines in which Ccr9 transcription is independent of E protein function. Our data support the hypothesis that activation of Notch1 has a dominant-negative effect on Ccr9 transcription and that Notch1 and E proteins control the dynamic expression of Ccr9 during T cell development.
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Affiliation(s)
- Veena Krishnamoorthy
- Committee on Molecular Pathogenesis and Molecular Medicine, The University of Chicago, Chicago, IL 60637
| | - Tiffany Carr
- Committee on Immunology, The University of Chicago, Chicago, IL 60637
| | - Renee F de Pooter
- Committee on Immunology, The University of Chicago, Chicago, IL 60637
| | | | | | - Fotini Gounari
- Committee on Immunology, The University of Chicago, Chicago, IL 60637; Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, IL 60637; and
| | - Barbara L Kee
- Committee on Molecular Pathogenesis and Molecular Medicine, The University of Chicago, Chicago, IL 60637; Committee on Immunology, The University of Chicago, Chicago, IL 60637; Department of Pathology, The University of Chicago, Chicago, IL 60637
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187
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Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, Aifantis I. Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell 2015; 158:593-606. [PMID: 25083870 DOI: 10.1016/j.cell.2014.05.049] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 03/23/2014] [Accepted: 05/16/2014] [Indexed: 12/24/2022]
Abstract
Notch signaling is a key developmental pathway that is subject to frequent genetic and epigenetic perturbations in many different human tumors. Here we investigate whether long noncoding RNA (lncRNA) genes, in addition to mRNAs, are key downstream targets of oncogenic Notch1 in human T cell acute lymphoblastic leukemia (T-ALL). By integrating transcriptome profiles with chromatin state maps, we have uncovered many previously unreported T-ALL-specific lncRNA genes, a fraction of which are directly controlled by the Notch1/Rpbjκ activator complex. Finally we have shown that one specific Notch-regulated lncRNA, LUNAR1, is required for efficient T-ALL growth in vitro and in vivo due to its ability to enhance IGF1R mRNA expression and sustain IGF1 signaling. These results confirm that lncRNAs are important downstream targets of the Notch signaling pathway, and additionally they are key regulators of the oncogenic state in T-ALL.
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Affiliation(s)
- Thomas Trimarchi
- Howard Hughes Medical Institute, Laura and Isaac Perlmutter Cancer Center, and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Erhan Bilal
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA
| | - Panagiotis Ntziachristos
- Howard Hughes Medical Institute, Laura and Isaac Perlmutter Cancer Center, and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Giulia Fabbri
- Institute for Cancer Genetics and the Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics and the Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Center for Health Informatics and Bioinformatics, NYU School of Medicine, 227 East 30(th) Street, New York, NY 10016, USA.
| | - Iannis Aifantis
- Howard Hughes Medical Institute, Laura and Isaac Perlmutter Cancer Center, and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, 550 First Avenue, New York, NY 10016, USA.
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188
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Laky K, Evans S, Perez-Diez A, Fowlkes BJ. Notch signaling regulates antigen sensitivity of naive CD4+ T cells by tuning co-stimulation. Immunity 2015; 42:80-94. [PMID: 25607460 PMCID: PMC4314725 DOI: 10.1016/j.immuni.2014.12.027] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/24/2014] [Indexed: 10/24/2022]
Abstract
Adaptive immune responses begin when naive CD4(+) T cells engage peptide+major histocompatibility complex class II and co-stimulatory molecules on antigen-presenting cells (APCs). Notch signaling can influence effector functions in differentiated CD4(+) T helper and T regulatory cells. Whether and how ligand-induced Notch signaling influences the initial priming of CD4(+) T cells has not been addressed. We have found that Delta Like Ligand 4 (DLL4)-induced Notch signaling potentiates phosphatidylinositol 3-OH kinase (PI3K)-dependent signaling downstream of the T cell receptor+CD28, allowing naive CD4(+) T cells to respond to lower doses of antigen. In vitro, DLL4-deficient APCs were less efficient stimulators of CD4(+) T cell activation, metabolism, proliferation, and cytokine secretion. With deletion of DLL4 from CD11c(+) APCs in vivo, these deficits translated to an impaired ability to mount an effective CD4(+)-dependent anti-tumor response. These data implicate Notch signaling as an important regulator of adaptive immune responses.
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MESH Headings
- Animals
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- CD28 Antigens/metabolism
- CD4-Positive T-Lymphocytes/immunology
- Carcinoma/immunology
- Cell Proliferation
- Cells, Cultured
- Cytokines/metabolism
- Female
- Intracellular Signaling Peptides and Proteins/metabolism
- Lymphocyte Activation/genetics
- Male
- Membrane Proteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Neoplasm Transplantation
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Receptor Cross-Talk
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Notch/genetics
- Receptors, Notch/immunology
- Receptors, Notch/metabolism
- Signal Transduction/genetics
- Tumor Burden/genetics
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Affiliation(s)
- Karen Laky
- T Cell Development Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sharron Evans
- T Cell Development Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ainhoa Perez-Diez
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - B J Fowlkes
- T Cell Development Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
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189
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Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proc Natl Acad Sci U S A 2014; 111:E4946-53. [PMID: 25369933 DOI: 10.1073/pnas.1407079111] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Notch is needed for T-cell development and is a common oncogenic driver in T-cell acute lymphoblastic leukemia. The protooncogene c-Myc (Myc) is a critical target of Notch in normal and malignant pre-T cells, but how Notch regulates Myc is unknown. Here, we identify a distal enhancer located >1 Mb 3' of human and murine Myc that binds Notch transcription complexes and physically interacts with the Myc proximal promoter. The Notch1 binding element in this region activates reporter genes in a Notch-dependent, cell-context-specific fashion that requires a conserved Notch complex binding site. Acute changes in Notch activation produce rapid changes in H3K27 acetylation across the entire enhancer (a region spanning >600 kb) that correlate with Myc expression. This broad Notch-influenced region comprises an enhancer region containing multiple domains, recognizable as discrete H3K27 acetylation peaks. Leukemia cells selected for resistance to Notch inhibitors express Myc despite epigenetic silencing of enhancer domains near the Notch transcription complex binding sites. Notch-independent expression of Myc in resistant cells is highly sensitive to inhibitors of bromodomain containing 4 (Brd4), a change in drug sensitivity that is accompanied by preferential association of the Myc promoter with more 3' enhancer domains that are strongly dependent on Brd4 for function. These findings indicate that altered long-range enhancer activity can mediate resistance to targeted therapies and provide a mechanistic rationale for combined targeting of Notch and Brd4 in leukemia.
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190
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Durinck K, Wallaert A, Van de Walle I, Van Loocke W, Volders PJ, Vanhauwaert S, Geerdens E, Benoit Y, Van Roy N, Poppe B, Soulier J, Cools J, Mestdagh P, Vandesompele J, Rondou P, Van Vlierberghe P, Taghon T, Speleman F. The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia. Haematologica 2014; 99:1808-16. [PMID: 25344525 DOI: 10.3324/haematol.2014.115683] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting a role as an essential driver for this gene in T-cell acute lymphoblastic leukemia oncogenesis. In this study, we aimed to establish a comprehensive compendium of the long non-coding RNA transcriptome under control of Notch signaling. For this purpose, we measured the transcriptional response of all protein coding genes and long non-coding RNAs upon pharmacological Notch inhibition in the human T-cell acute lymphoblastic leukemia cell line CUTLL1 using RNA-sequencing. Similar Notch dependent profiles were established for normal human CD34(+) thymic T-cell progenitors exposed to Notch signaling activity in vivo. In addition, we generated long non-coding RNA expression profiles (array data) from ex vivo isolated Notch active CD34(+) and Notch inactive CD4(+)CD8(+) thymocytes and from a primary cohort of 15 T-cell acute lymphoblastic leukemia patients with known NOTCH1 mutation status. Integration of these expression datasets with publicly available Notch1 ChIP-sequencing data resulted in the identification of long non-coding RNAs directly regulated by Notch activity in normal and malignant T cells. Given the central role of Notch in T-cell acute lymphoblastic leukemia oncogenesis, these data pave the way for the development of novel therapeutic strategies that target hyperactive Notch signaling in human T-cell acute lymphoblastic leukemia.
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Affiliation(s)
- Kaat Durinck
- Center for Medical Genetics, Ghent University, Belgium;
| | | | - Inge Van de Walle
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
| | | | | | | | - Ellen Geerdens
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Yves Benoit
- Center for Medical Genetics, Ghent University, Belgium
| | | | - Bruce Poppe
- Center for Medical Genetics, Ghent University, Belgium
| | - Jean Soulier
- Genome Rearrangements and Cancer Laboratory, U944 INSERM, University Paris Diderot and Hematology Laboratory, Saint-Louis Hospital, Paris, France
| | - Jan Cools
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | | | | | - Pieter Rondou
- Center for Medical Genetics, Ghent University, Belgium
| | | | - Tom Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
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191
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Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 2014; 159:374-387. [PMID: 25303531 PMCID: PMC4197132 DOI: 10.1016/j.cell.2014.09.030] [Citation(s) in RCA: 640] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/18/2014] [Accepted: 09/15/2014] [Indexed: 12/31/2022]
Abstract
The pluripotent state of embryonic stem cells (ESCs) is produced by active transcription of genes that control cell identity and repression of genes encoding lineage-specifying developmental regulators. Here, we use ESC cohesin ChIA-PET data to identify the local chromosomal structures at both active and repressed genes across the genome. The results produce a map of enhancer-promoter interactions and reveal that super-enhancer-driven genes generally occur within chromosome structures that are formed by the looping of two interacting CTCF sites co-occupied by cohesin. These looped structures form insulated neighborhoods whose integrity is important for proper expression of local genes. We also find that repressed genes encoding lineage-specifying developmental regulators occur within insulated neighborhoods. These results provide insights into the relationship between transcriptional control of cell identity genes and control of local chromosome structure.
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Affiliation(s)
- Jill M Dowen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Computational and Systems Biology Program
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Gang Ren
- Systems Biology Center, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
- College of Animal Science and Technology, Northwest A&F University, Xi'An, P. R. China
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Lyndon N Zhang
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Jurian Schujiers
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Keji Zhao
- Systems Biology Center, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
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192
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Stoeck A, Lejnine S, Truong A, Pan L, Wang H, Zang C, Yuan J, Ware C, MacLean J, Garrett-Engele PW, Kluk M, Laskey J, Haines BB, Moskaluk C, Zawel L, Fawell S, Gilliland G, Zhang T, Kremer BE, Knoechel B, Bernstein BE, Pear WS, Liu XS, Aster JC, Sathyanarayanan S. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discov 2014; 4:1154-67. [PMID: 25104330 DOI: 10.1158/2159-8290.cd-13-0830] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
UNLABELLED Next-generation sequencing was used to identify Notch mutations in a large collection of diverse solid tumors. NOTCH1 and NOTCH2 rearrangements leading to constitutive receptor activation were confined to triple-negative breast cancers (TNBC; 6 of 66 tumors). TNBC cell lines with NOTCH1 rearrangements associated with high levels of activated NOTCH1 (N1-ICD) were sensitive to the gamma-secretase inhibitor (GSI) MRK-003, both alone and in combination with paclitaxel, in vitro and in vivo, whereas cell lines with NOTCH2 rearrangements were resistant to GSI. Immunohistochemical staining of N1-ICD in TNBC xenografts correlated with responsiveness, and expression levels of the direct Notch target gene HES4 correlated with outcome in patients with TNBC. Activating NOTCH1 point mutations were also identified in other solid tumors, including adenoid cystic carcinoma (ACC). Notably, ACC primary tumor xenografts with activating NOTCH1 mutations and high N1-ICD levels were sensitive to GSI, whereas N1-ICD-low tumors without NOTCH1 mutations were resistant. SIGNIFICANCE NOTCH1 mutations, immunohistochemical staining for activated NOTCH1, and HES4 expression are biomarkers that can be used to identify solid tumors that are likely to respond to GSI-based therapies.
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MESH Headings
- Amyloid Precursor Protein Secretases/antagonists & inhibitors
- Animals
- Antineoplastic Agents/administration & dosage
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Apoptosis/genetics
- Biomarkers
- Carcinoma, Adenoid Cystic/drug therapy
- Carcinoma, Adenoid Cystic/genetics
- Carcinoma, Adenoid Cystic/metabolism
- Cell Line, Tumor
- Cellular Senescence/drug effects
- Cyclic S-Oxides/pharmacology
- Disease Models, Animal
- Drug Resistance, Neoplasm/genetics
- Exome
- Female
- Gene Expression Regulation, Neoplastic
- Gene Rearrangement
- Genes, myc
- High-Throughput Nucleotide Sequencing
- Humans
- Models, Molecular
- Mutation
- Prognosis
- Protease Inhibitors/administration & dosage
- Protease Inhibitors/pharmacology
- Protein Conformation
- Protein Interaction Domains and Motifs
- Receptors, Notch/antagonists & inhibitors
- Receptors, Notch/chemistry
- Receptors, Notch/genetics
- Receptors, Notch/metabolism
- Signal Transduction/drug effects
- Thiadiazoles/pharmacology
- Treatment Outcome
- Triple Negative Breast Neoplasms/drug therapy
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
| | | | | | - Li Pan
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hongfang Wang
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Chongzhi Zang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jing Yuan
- Merck Research Laboratory, Boston, Massachusetts
| | - Chris Ware
- Merck Research Laboratory, Boston, Massachusetts
| | - John MacLean
- Merck Research Laboratory, Boston, Massachusetts
| | | | - Michael Kluk
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jason Laskey
- Merck Research Laboratory, Boston, Massachusetts
| | | | - Christopher Moskaluk
- Department of Medicine and Digestive Health Research Center, University of Virginia, Charlottesville, Virginia
| | - Leigh Zawel
- Merck Research Laboratory, Boston, Massachusetts
| | | | | | | | - Brandon E Kremer
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Birgit Knoechel
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Warren S Pear
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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