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Geng T, Yang D, Lin T, Harrison AG, Wang B, Cao Z, Torrance B, Fan Z, Wang K, Wang Y, Yang L, Haynes L, Cheng G, Vella AT, Flavell RA, Pereira JP, Fikrig E, Wang P. UBXN3B is crucial for B lymphopoiesis. EBioMedicine 2024; 106:105248. [PMID: 39018756 PMCID: PMC11287013 DOI: 10.1016/j.ebiom.2024.105248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/29/2024] [Accepted: 07/02/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND The ubiquitin regulatory X (UBX) domain-containing proteins (UBXNs) are putative adaptors for ubiquitin ligases and valosin-containing protein; however, their in vivo physiological functions remain poorly characterised. We recently showed that UBXN3B is essential for activating innate immunity to DNA viruses and controlling DNA/RNA virus infection. Herein, we investigate its role in adaptive immunity. METHODS We evaluated the antibody responses to multiple viruses and pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza in tamoxifen-inducible global and constitutive B cell-specific Ubxn3b knockout mice; quantified various immune populations, B lineage progenitors/precursors, B cell receptor (BCR) signalling and apoptosis by flow cytometry, immunoblotting and immunofluorescence microscopy. We also performed bone marrow transfer, single-cell and bulk RNA sequencing. FINDINGS Both global and B cell-specific Ubxn3b knockout mice present a marked reduction in small precursor B-II (>60%), immature (>70%) and mature B (>95%) cell numbers. Transfer of wildtype bone marrow to irradiated global Ubxn3b knockouts restores normal B lymphopoiesis, while reverse transplantation does not. The mature B population shrinks rapidly with apoptosis and higher pro and activated caspase-3 protein levels were observed following induction of Ubxn3b knockout. Mechanistically, Ubxn3b deficiency leads to impaired pre-BCR signalling and cell cycle arrest. Ubxn3b knockout mice are highly vulnerable to respiratory viruses, with increased viral loads and prolonged immunopathology in the lung, and reduced production of virus-specific IgM/IgG. INTERPRETATION UBXN3B is essential for B lymphopoiesis by maintaining constitutive pre-BCR signalling and cell survival in a cell-intrinsic manner. FUNDING United States National Institutes of Health grants, R01AI132526 and R21AI155820.
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Affiliation(s)
- Tingting Geng
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Duomeng Yang
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Tao Lin
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Andrew G Harrison
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Binsheng Wang
- Center on Aging and Department of Genetics and Genome Sciences, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Ziming Cao
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Blake Torrance
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Zhichao Fan
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Kepeng Wang
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Yanlin Wang
- Department of Medicine, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Long Yang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Laura Haynes
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Gong Cheng
- Department of Basic Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Anthony T Vella
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Joao P Pereira
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Erol Fikrig
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Penghua Wang
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, 06030, USA.
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2
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Bogush D, Schramm J, Ding Y, He B, Singh C, Sharma A, Tukaramrao DB, Iyer S, Desai D, Nalesnik G, Hengst J, Bhalodia R, Gowda C, Dovat S. Signaling pathways and regulation of gene expression in hematopoietic cells. Adv Biol Regul 2023; 88:100942. [PMID: 36621151 DOI: 10.1016/j.jbior.2022.100942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Cellular functions are regulated by signal transduction pathway networks consisting of protein-modifying enzymes that control the activity of many downstream proteins. Protein kinases and phosphatases regulate gene expression by reversible phosphorylation of transcriptional factors, which are their direct substrates. Casein kinase II (CK2) is a serine/threonine kinase that phosphorylates a large number of proteins that have critical roles in cellular proliferation, metabolism and survival. Altered function of CK2 has been associated with malignant transformation, immunological disorders and other types of diseases. Protein phosphatase 1 (PP1) is a serine/threonine phosphatase, which regulates the phosphorylation status of many proteins that are essential for cellular functions. IKAROS is a DNA-binding protein, which functions as a regulator of gene transcription in hematopoietic cells. CK2 directly phosphorylates IKAROS at multiple phosphosites which determines IKAROS activity as a regulator of gene expression. PP1 binds to IKAROS via the PP1-consensus recognition site and dephosphorylates serine/threonine residues that are phosphorylated by CK2. Thus, the interplay between CK2 and PP1 signaling pathways have opposing effects on the phosphorylation status of their mutual substrate - IKAROS. This review summarizes the effects of CK2 and PP1 on IKAROS role in regulation of gene expression and its function as a tumor suppressor in leukemia.
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Affiliation(s)
- Daniel Bogush
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Joseph Schramm
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Yali Ding
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Bing He
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chingakham Singh
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Arati Sharma
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | | | - Soumya Iyer
- University of Chicago, Chicago, IL, 60637, USA
| | - Dhimant Desai
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Gregory Nalesnik
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Jeremy Hengst
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Riya Bhalodia
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chandrika Gowda
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
| | - Sinisa Dovat
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
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3
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Swargiary P, Boruah N, Singh CS, Chatterjee A. Genome-wide analysis of DNaseI hypersensitivity unveils open chromatin associated with histone H3 modifications after areca nut with lime exposure. Mutagenesis 2022; 37:182-190. [DOI: 10.1093/mutage/geac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Research over the years revealed that precocious anaphase, securin overexpression, and genome instability in both target and nontarget cells are significantly associated with the increased risk of areca nut (AN) and lime-induced oral, esophageal, and gastric cancers. Further, hyperphosphorylation of Rb and histone H3 epigenetic modifications both globally and in the promoter region of the securin gene were demonstrated after AN + lime exposure. This study aims whether the extract of raw AN + lime relaxes chromatin structure which further facilitates the histone H3 epigenetic modifications during the initial phase of carcinogenesis. Three groups of mice (10 in each group) were used. The treated group consumed 1 mg/day/mice of AN extract with lime ad libitum in the drinking water for 60 days. The dose was increased by 1 mg every 60 days. Isolated nuclei were digested with DNaseI and 2 kb and below DNA was eluted from the agarose gel, purified and PCR amplified by using securin and GAPDH primers. Securin and E2F1 expression, pRb phosphorylation, and histone epigenetic modifications were analyzed by immunohistochemistry. The number of DNA fragments within 2 kb in size after DNaseI treatment was higher significantly in AN + lime exposed tissue samples than in the untreated one. The PCR result showed that the number of fragments bearing securin gene promoter and GAPDH gene was significantly higher in AN + lime exposed DNaseI-treated samples. Immunohistochemistry data revealed increased Rb hyperphosphorylation, upregulation of E2F1, and securin in the AN + lime-treated samples. Increased trimethylation of histone H3 lysine 4 and acetylation of H3 lysine 9 and 18 were observed globally in the treated samples. Therefore, the results of this study have led to the hypothesis that AN + lime exposure relaxes the chromatin, changes the epigenetic landscape, and deregulates the Rb–E2F1 circuit which might be involved in the upregulation of securin and some other proto-oncogenes that might play an important role in the initial phases of AN + lime mediated carcinogenesis.
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Affiliation(s)
- Pooja Swargiary
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
| | - Nabamita Boruah
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
| | - Chongtham Sovachandra Singh
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
| | - Anupam Chatterjee
- Molecular Genetics Laboratory, Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, Meghalaya 793022 , India
- Department of Biotechnology, Royal School of Biosciences, The Assam Royal Global University , Guwahati, Assam 781035 , India
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The Pleiotropy of PAX5 Gene Products and Function. Int J Mol Sci 2022; 23:ijms231710095. [PMID: 36077495 PMCID: PMC9456430 DOI: 10.3390/ijms231710095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
PAX5, a member of the Paired Box (PAX) transcription factor family, is an essential factor for B-lineage identity during lymphoid differentiation. Mechanistically, PAX5 controls gene expression profiles, which are pivotal to cellular processes such as viability, proliferation, and differentiation. Given its crucial function in B-cell development, PAX5 aberrant expression also correlates with hallmark cancer processes leading to hematological and other types of cancer lesions. Despite the well-established association of PAX5 in the development, maintenance, and progression of cancer disease, the use of PAX5 as a cancer biomarker or therapeutic target has yet to be implemented. This may be partly due to the assortment of PAX5 expressed products, which layers the complexity of their function and role in various regulatory networks and biological processes. In this review, we provide an overview of the reported data describing PAX5 products, their regulation, and function in cellular processes, cellular biology, and neoplasm.
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5
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Coda DM, Patel H, Gori I, Gaarenstroom TE, Song OR, Howell M, Hill CS. A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses. J Cell Sci 2022; 135:jcs259972. [PMID: 35302162 PMCID: PMC9080556 DOI: 10.1242/jcs.259972] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
SMAD2, an effector of the NODAL/Activin signalling pathway, regulates developmental processes by sensing distinct chromatin states and interacting with different transcriptional partners. However, the network of factors that controls SMAD2 chromatin binding and shapes its transcriptional programme over time is poorly characterised. Here, we combine ATAC-seq with computational footprinting to identify temporal changes in chromatin accessibility and transcription factor activity upon NODAL/Activin signalling. We show that SMAD2 binding induces chromatin opening genome wide. We discover footprints for FOXI3, FOXO3 and ZIC3 at the SMAD2-bound enhancers of the early response genes, Pmepa1 and Wnt3, respectively, and demonstrate their functionality. Finally, we determine a mechanism by which NODAL/Activin signalling induces delayed gene expression, by uncovering a self-enabling transcriptional cascade whereby activated SMADs, together with ZIC3, induce the expression of Wnt3. The resultant activated WNT pathway then acts together with the NODAL/Activin pathway to regulate expression of delayed target genes in prolonged NODAL/Activin signalling conditions. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Davide M. Coda
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Tessa E. Gaarenstroom
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ok-Ryul Song
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Caroline S. Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
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6
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Tachibana H, Daino K, Ishikawa A, Morioka T, Shang Y, Ogawa M, Matsuura A, Shimada Y, Kakinuma S. Genomic profile of radiation-induced early-onset mouse B-cell lymphoma recapitulates features of Philadelphia chromosome-like acute lymphoblastic leukemia in humans. Carcinogenesis 2022; 43:693-703. [PMID: 35395675 DOI: 10.1093/carcin/bgac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/22/2022] [Accepted: 04/04/2022] [Indexed: 11/12/2022] Open
Abstract
Epidemiological studies have revealed a radiation-related increase in the risk of developing acute lymphoblastic leukemia (ALL). Our recent study revealed early induction and increased risk of precursor B-cell (pB) lymphomas in mice after radiation exposure. However, the genomic landscape of radiation-induced B-cell lymphomas remains unclear. To identify the relevant genetic alterations in mice, whole-exome sequencing was performed on both early-onset and late-onset B-cell lymphomas that developed spontaneously or after gamma-irradiation. In addition to multiple driver mutations, the data revealed that interstitial deletion of chromosome 4, including Pax5, and missense mutations in Jak3 are unique genomic alterations in radiation-induced, early-onset B-cell lymphomas. RNA sequencing revealed a pB-cell-type gene-expression profile with no involvement of known fusion genes for human ALLs in the early-onset B-cell lymphomas. Activation of Jak3/Stat5 signaling in early-onset B-cell lymphomas was validated using western capillary electrophoresis. Those features were similar to those of Philadelphia chromosome-like ALL. Our data suggest a critical role for Pax5 loss-of-function mutations in initiating B-cell leukemogenesis coupled with activation of Jak3/Stat5 signaling as a basis for the rapid development of radiation-induced pB-ALL. These molecular signatures for radiation-induced cancers will inform both risk assessment and potential targeted therapies for pB-ALL.
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Affiliation(s)
- Hirotaka Tachibana
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan.,Department of Biology, Graduate School of Science, Chiba University; Chiba, Japan
| | - Kazuhiro Daino
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan
| | - Atsuko Ishikawa
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan
| | - Takamitsu Morioka
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan
| | - Yi Shang
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan
| | - Mari Ogawa
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan
| | - Akira Matsuura
- Department of Biology, Graduate School of Science, Chiba University; Chiba, Japan
| | - Yoshiya Shimada
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan.,Chief director, Institute for Environmental Sciences; Aomori, Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, Quantum Medical Science Directorate, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology (QST); Chiba, Japan
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7
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Umemoto T, Johansson A, Ahmad SAI, Hashimoto M, Kubota S, Kikuchi K, Odaka H, Era T, Kurotaki D, Sashida G, Suda T. ATP citrate lyase controls hematopoietic stem cell fate and supports bone marrow regeneration. EMBO J 2022; 41:e109463. [PMID: 35229328 PMCID: PMC9016348 DOI: 10.15252/embj.2021109463] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
In order to support bone marrow regeneration after myeloablation, hematopoietic stem cells (HSCs) actively divide to provide both stem and progenitor cells. However, the mechanisms regulating HSC function and cell fate choice during hematopoietic recovery remain unclear. We herein provide novel insights into HSC regulation during regeneration by focusing on mitochondrial metabolism and ATP citrate lyase (ACLY). After 5-fluorouracil-induced myeloablation, HSCs highly expressing endothelial protein C receptor (EPCRhigh ) were enriched within the stem cell fraction at the expense of more proliferative EPCRLow HSCs. These EPCRHigh HSCs were initially more primitive than EPCRLow HSCs and enabled stem cell expansion by enhancing histone acetylation, due to increased activity of ACLY in the early phase of hematopoietic regeneration. In the late phase of recovery, HSCs enhanced differentiation potential by increasing the accessibility of cis-regulatory elements in progenitor cell-related genes, such as CD48. In conditions of reduced mitochondrial metabolism and ACLY activity, these HSCs maintained stem cell phenotypes, while ACLY-dependent histone acetylation promoted differentiation into CD48+ progenitor cells. Collectively, these results indicate that the dynamic control of ACLY-dependent metabolism and epigenetic alterations is essential for HSC regulation during hematopoietic regeneration.
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Affiliation(s)
- Terumasa Umemoto
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Alban Johansson
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Shah Adil Ishtiyaq Ahmad
- Laboratory of Hematopoietic Stem Cell EngineeringInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Michihiro Hashimoto
- Laboratory of Stem Cell RegulationInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Sho Kubota
- Laboratory of Transcriptional Regulation in LeukemogenesisInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Kenta Kikuchi
- Laboratory of Chromatin Organization in Immune Cell DevelopmentInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Haruki Odaka
- Department of Cell ModulationInstitute of Molecular Embryology and GeneticsKumamoto UniversityKumamotoJapan
| | - Takumi Era
- Department of Cell ModulationInstitute of Molecular Embryology and GeneticsKumamoto UniversityKumamotoJapan
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell DevelopmentInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in LeukemogenesisInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | - Toshio Suda
- Laboratory of Stem Cell RegulationInternational Research Center for Medical SciencesKumamoto UniversityKumamotoJapan,Cancer Science Institute of SingaporeNational University of SingaporeSingapore CitySingapore
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8
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Tcf1 and Lef1 provide constant supervision to mature CD8 + T cell identity and function by organizing genomic architecture. Nat Commun 2021; 12:5863. [PMID: 34615872 PMCID: PMC8494933 DOI: 10.1038/s41467-021-26159-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 09/17/2021] [Indexed: 02/01/2023] Open
Abstract
T cell identity is established during thymic development, but how it is maintained in the periphery remains unknown. Here we show that ablating Tcf1 and Lef1 transcription factors in mature CD8+ T cells aberrantly induces genes from non-T cell lineages. Using high-throughput chromosome-conformation-capture sequencing, we demonstrate that Tcf1/Lef1 are important for maintaining three-dimensional genome organization at multiple scales in CD8+ T cells. Comprehensive network analyses coupled with genome-wide profiling of chromatin accessibility and Tcf1 occupancy show the direct impact of Tcf1/Lef1 on the T cell genome is to promote formation of extensively interconnected hubs through enforcing chromatin interaction and accessibility. The integrative mechanisms utilized by Tcf1/Lef1 underlie activation of T cell identity genes and repression of non-T lineage genes, conferring fine control of various T cell functionalities. These findings suggest that Tcf1/Lef1 control global genome organization and help form intricate chromatin-interacting hubs to facilitate promoter-enhancer/silencer contact, hence providing constant supervision of CD8+ T cell identity and function. How CD8+ T cell identity is maintained after exit from the thymus is not fully established. Here the authors use multiomics approaches including Hi-C to show that Tcf1 and Lef1 prevent aberrant expression of lineage-inappropriate genes by organizing three-dimensional genomic architecture in CD8+ T cells.
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9
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Wang L, Wang E, Prado Balcazar J, Wu Z, Xiang K, Wang Y, Huang Q, Negrete M, Chen K, Li W, Fu Y, Dohlman A, Mines R, Zhang L, Kobayashi Y, Chen T, Shi G, Shen JP, Kopetz S, Tata PR, Moreno V, Gersbach C, Crawford G, Hsu D, Huang E, Bu P, Shen X. Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004673. [PMID: 34378358 PMCID: PMC8498885 DOI: 10.1002/advs.202004673] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Colorectal cancer (CRC) metastasizes mainly to the liver, which accounts for the majority of CRC-related deaths. Here it is shown that metastatic cells undergo specific chromatin remodeling in the liver. Hepatic growth factor (HGF) induces phosphorylation of PU.1, a pioneer factor, which in turn binds and opens chromatin regions of downstream effector genes. PU.1 increases histone acetylation at the DPP4 locus. Precise epigenetic silencing by CRISPR/dCas9KRAB or CRISPR/dCas9HDAC revealed that individual PU.1-remodeled regulatory elements collectively modulate DPP4 expression and liver metastasis growth. Genetic silencing or pharmacological inhibition of each factor along this chromatin remodeling axis strongly suppressed liver metastasis. Therefore, microenvironment-induced epimutation is an important mechanism for metastatic tumor cells to grow in their new niche. This study presents a potential strategy to target chromatin remodeling in metastatic cancer and the promise of repurposing drugs to treat metastasis.
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Affiliation(s)
- Lihua Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Ergang Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | | | - Zhenzhen Wu
- Key Laboratory of RNA BiologyKey Laboratory of Protein and Peptide PharmaceuticalInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Kun Xiang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Yi Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Qiang Huang
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Marcos Negrete
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Kai‐Yuan Chen
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Wei Li
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Yujie Fu
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Anders Dohlman
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Robert Mines
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Liwen Zhang
- Key Laboratory of RNA BiologyKey Laboratory of Protein and Peptide PharmaceuticalInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yoshihiko Kobayashi
- Department of Cell BiologyRegeneration NextDuke University School of MedicineDurhamNC27710USA
| | - Tianyi Chen
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Guizhi Shi
- Laboratory Animal Research CenterInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
| | - John Paul Shen
- Department of Gastrointestinal Medical OncologyMD AndersonDurhamNC77030USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical OncologyMD AndersonDurhamNC77030USA
| | - Purushothama Rao Tata
- Department of Cell BiologyRegeneration NextDuke University School of MedicineDurhamNC27710USA
| | - Victor Moreno
- Department of Clinical SciencesUniversity of BarcelonaBarcelona08193Spain
- Prevention and Control ProgramCatalan Institute of Oncology‐IDIBELLCIBERESPBarcelonaE08907Spain
| | - Charles Gersbach
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
| | - Gregory Crawford
- Department of PediatricsDuke University School of MedicineDurhamNC27710USA
| | - David Hsu
- Department of MedicineDuke University School of MedicineDurhamNC27710USA
| | - Emina Huang
- Department of Cancer Biology and Colorectal SurgeryLerner Research Institute, Cleveland ClinicClevelandOH44195USA
| | - Pengcheng Bu
- Key Laboratory of RNA BiologyKey Laboratory of Protein and Peptide PharmaceuticalInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Center for Excellence in BiomacromoleculesChinese Academy of SciencesBeijing100101China
| | - Xiling Shen
- Department of Biomedical EngineeringDuke UniversityDurhamNC27708USA
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10
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Activated B Cells and Plasma Cells Are Resistant to Radiation Therapy. Int J Radiat Oncol Biol Phys 2021; 112:514-528. [PMID: 34474108 DOI: 10.1016/j.ijrobp.2021.08.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE B cells play a key role in outcomes of cancer patients and responses to checkpoint blockade immunotherapies. However, the effect of radiation therapy on B cell populations is poorly understood. Here we characterize the effects of radiation on the development, survival, and phenotype of physiological B-cell subsets. METHODS AND MATERIALS Naïve and immunized tumor bearing and nontumor bearing mice were treated with large-field or focal stereotactic radiation and distinct B-cell subsets of varying developmental stages were analyzed by flow cytometry and real-time reverse transcription polymerase chain reaction. RESULTS We first report that focal stereotactic radiation is highly superior to large-field radiation at inducing tumor infiltration of B cells, CD8+ T cells, and macrophages. We observed that radiation affects B cell development in the bone marrow, increasing frequencies of early pro-B cells and late pro-B cells while inducing upregulation of programmed cell death protein 1. We then demonstrate that class switched B cells and plasma cells are highly resistant to radiation therapy compared with naïve B cells and upregulate activation markers programmed cell death 1 ligand 2 and major histocompatibility complex class II) after radiation. Mechanistically, radiation upregulates Xbp1 and Bcl6 in plasma cells, conferring radioresistance. Furthermore, using an immunization approach, we demonstrate that radiation enhances activation-induced cytidine deaminase mediated class switching and somatic hypermutation in primed B cells. CONCLUSIONS These data demonstrate that stereotactic radiation is superior to large-field radiation at inducing infiltration of immune cells into tumors and that plasma cells and class switched B cells are highly resistant to radiation therapy. These results represent the most comprehensive analysis of the effects of radiation on B cells to date and identify novel mechanisms by which radiation modulates immune cells within the tumor microenvironment.
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11
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Geng T, Yang D, Lin T, Harrison AG, Wang B, Torrance B, Wang K, Wang Y, Yang L, Haynes L, Cheng G, Vella AT, Fikrig E, Wang P. An Essential Role of UBXN3B in B Lymphopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34462748 DOI: 10.1101/2021.03.04.433919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hematopoiesis is finely regulated to enable timely production of the right numbers and types of mature immune cells to maintain tissue homeostasis. Dysregulated hematopoiesis may compromise antiviral immunity and/or exacerbate immunopathogenesis. Herein, we report an essential role of UBXN3B in maintenance of hematopoietic homeostasis and restriction of immunopathogenesis during respiratory viral infection. Ubxn3b deficient ( Ubxn3b -/- ) mice are highly vulnerable to SARS-CoV-2 and influenza A infection, characterized by more severe lung immunopathology, lower virus-specific IgG, significantly fewer B cells, but more myeloid cells than Ubxn3b +/+ littermates. This aberrant immune compartmentalization is recapitulated in uninfected Ubxn3b -/- mice. Mechanistically, UBXN3B controls precursor B-I (pre-BI) transition to pre-BII and subsequent proliferation in a cell-intrinsic manner, by maintaining BLNK protein stability and pre-BCR signaling. These results reveal an essential role of UBXN3B for the early stage of B cell development.
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12
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Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways. Cancers (Basel) 2021; 13:cancers13174250. [PMID: 34503064 PMCID: PMC8428231 DOI: 10.3390/cancers13174250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Melanoma, an aggressive form of skin cancer, is frequently associated with drug resistance in the advanced stages. For instance, frequently resistance is observed in sequential treatment of melanoma with targeted therapy and immunotherapy. In this research, the authors investigated whether potential transcriptional mechanisms and pathways associated with PD-L1 protein expression could underlie targeted therapy drug resistance in melanoma. The authors found a PD-L1 expression transcriptional pattern underlies resistance to targeted therapy in a subgroup of melanomas. These melanomas were markedly dedifferentiated, as compared to melanomas that were not drug resistant. Understanding changes in transcription and molecular pathways that lead to drug resistance could allow researchers to develop interventions to prevent drug resistance from occurring in melanoma, which could also be relevant to other cancer types. Abstract Melanoma is the most aggressive type of skin cancer, with increasing incidence worldwide. Advances in targeted therapy and immunotherapy have improved the survival of melanoma patients experiencing recurrent disease, but unfortunately treatment resistance frequently reduces patient survival. Resistance to targeted therapy is associated with transcriptomic changes and has also been shown to be accompanied by increased expression of programmed death ligand 1 (PD-L1), a potent inhibitor of immune response. Intrinsic upregulation of PD-L1 is associated with genome-wide DNA hypomethylation and widespread alterations in gene expression in melanoma cell lines. However, an in-depth analysis of the transcriptomic landscape of melanoma cells with intrinsically upregulated PD-L1 expression is lacking. To determine the transcriptomic landscape of intrinsically upregulated PD-L1 expression in melanoma, we investigated transcriptomes in melanomas with constitutive versus inducible PD-L1 expression (referred to as PD-L1CON and PD-L1IND). RNA-Seq analysis was performed on seven PD-L1CON melanoma cell lines and ten melanoma cell lines with low inducible PD-L1IND expression. We observed that PD-L1CON melanoma cells had a reprogrammed transcriptome with a characteristic pattern of dedifferentiated gene expression, together with active interferon (IFN) and tumour necrosis factor (TNF) signalling pathways. Furthermore, we identified key transcription factors that were also differentially expressed in PD-L1CON versus PD-L1IND melanoma cell lines. Overall, our studies describe transcriptomic reprogramming of melanomas with PD-L1CON expression.
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13
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Zenere A, Rundquist O, Gustafsson M, Altafini C. Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs. Bioinformatics 2021; 38:173-178. [PMID: 34383882 PMCID: PMC8696094 DOI: 10.1093/bioinformatics/btab577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 07/04/2021] [Accepted: 08/10/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The simultaneous availability of ATAC-seq and RNA-seq experiments allows to obtain a more in-depth knowledge on the regulatory mechanisms occurring in gene regulatory networks. In this article, we highlight and analyze two novel aspects that leverage on the possibility of pairing RNA-seq and ATAC-seq data. Namely we investigate the causality of the relationships between transcription factors, chromatin and target genes and the internal consistency between the two omics, here measured in terms of structural balance in the sample correlations along elementary length-3 cycles. RESULTS We propose a framework that uses the a priori knowledge on the data to infer elementary causal regulatory motifs (namely chains and forks) in the network. It is based on the notions of conditional independence and partial correlation, and can be applied to both longitudinal and non-longitudinal data. Our analysis highlights a strong connection between the causal regulatory motifs that are selected by the data and the structural balance of the underlying sample correlation graphs: strikingly, >97% of the selected regulatory motifs belong to a balanced subgraph. This result shows that internal consistency, as measured by structural balance, is close to a necessary condition for 3-node regulatory motifs to satisfy causality rules. AVAILABILITY AND IMPLEMENTATION The analysis was carried out in MATLAB and the code can be found at https://github.com/albertozenere/Multi-omics-elementary-regulatory-motifs. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alberto Zenere
- Division of Automatic Control, Department of Electrical Engineering, Linköping University, SE-58183 Linköping, Sweden
| | - Olof Rundquist
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, SE-58183 Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, SE-58183 Linköping, Sweden
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14
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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15
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Li J, Li L, Sun X, Deng T, Huang G, Li X, Xie Z, Zhou Z. Role of Tet2 in Regulating Adaptive and Innate Immunity. Front Cell Dev Biol 2021; 9:665897. [PMID: 34222235 PMCID: PMC8247589 DOI: 10.3389/fcell.2021.665897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
Accumulated evidence indicates that epigenetic modifications play central roles in gene expression regulation and participate in developing many autoimmune and autoinflammatory diseases. Mechanistically, epigenetic modifications act as a bridge between environmental and cellular factors and susceptibility genes. DNA methylation is a critical epigenetic modification that is regulated by ten-eleven translocation (TET) enzymes. Accumulating evidence has revealed that TET family proteins function as gene regulators and antitumor drug targets mainly because of their ability to oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Recently, the effect of Tet2, an essential TET protein, on the development of autoimmune diseases has been explored. In this review, we summarize the current understanding of Tet2 in immune response regulation, clarify the mechanisms of Tet2 in B and T cell differentiation and function, and discuss the opposing effects of Tet2 on inflammatory gene expression in the immune system to provide new potential therapeutic targets for related diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoxiao Sun
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Tuo Deng
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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16
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Burlet B, Ramla S, Fournier C, Abrey-Recalde MJ, Sauter C, Chrétien ML, Rossi C, Duffourd Y, Ragot S, Buriller C, Tournier B, Chapusot C, Nadal N, Racine J, Guy J, Bailly F, Martin L, Casasnovas O, Bastie JN, Caillot D, Albuisson J, Broccardo C, Thieblemont C, Delva L, Maynadié M, Aucagne R, Callanan MB. Identification of novel, clonally stable, somatic mutations targeting transcription factors PAX5 and NKX2-3, the epigenetic regulator LRIF1, and BRAF in a case of atypical B-cell chronic lymphocytic leukemia harboring a t(14;18)(q32;q21). Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005934. [PMID: 33608382 PMCID: PMC7903887 DOI: 10.1101/mcs.a005934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/06/2021] [Indexed: 12/15/2022] Open
Abstract
Diagnosis of B-cell chronic lymphocytic leukemia (B-CLL) is usually straightforward, involving clinical, immunophenotypic (Matutes score), and (immuno)genetic analyses (to refine patient prognosis for treatment). CLL cases with atypical presentation (e.g., Matutes ≤ 3) are also encountered, and for these diseases, biology and prognostic impact are less clear. Here we report the genomic characterization of a case of atypical B-CLL in a 70-yr-old male patient; B-CLL cells showed a Matutes score of 3, chromosomal translocation t(14;18)(q32;q21) (BCL2/IGH), mutated IGHV, deletion 17p, and mutations in BCL2, NOTCH1 (subclonal), and TP53 (subclonal). Quite strikingly, a novel PAX5 mutation that was predicted to be loss of function was also seen. Exome sequencing identified, in addition, a potentially actionable BRAF mutation, together with novel somatic mutations affecting the homeobox transcription factor NKX2-3, known to control B-lymphocyte development and homing, and the epigenetic regulator LRIF1, which is implicated in chromatin compaction and gene silencing. Neither NKX2-3 nor LRIF1 mutations, predicted to be loss of function, have previously been reported in B-CLL. Sequencing confirmed the presence of these mutations together with BCL2, NOTCH1, and BRAF mutations, with the t(14;18)(q32;q21) translocation, in the initial diagnostic sample obtained 12 yr prior. This is suggestive of a role for these novel mutations in B-CLL initiation and stable clonal evolution, including upon treatment withdrawal. This case extends the spectrum of atypical B-CLL with t(14;18)(q32;q21) and highlights the value of more global precision genomics for patient follow-up and treatment in these patients.
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Affiliation(s)
- Bénédicte Burlet
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Selim Ramla
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Cyril Fournier
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Maria Jimena Abrey-Recalde
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Camille Sauter
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Marie-Lorraine Chrétien
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Cédric Rossi
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Yannis Duffourd
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Sylviane Ragot
- Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Céline Buriller
- Genetics Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Benjamin Tournier
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Caroline Chapusot
- Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Nathalie Nadal
- Genetics Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Jessica Racine
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Julien Guy
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - François Bailly
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Laurent Martin
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Olivier Casasnovas
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Jean-Noël Bastie
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Denis Caillot
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Juliette Albuisson
- Oncogenetics laboratory, Centre George François Leclerc, 21079 Dijon, France
| | - Cyril Broccardo
- Centre de Recherches en Cancérologie de Toulouse, Inserm UMR1037, Université de Toulouse III - Paul Sabatier, 31037 Toulouse, France
| | - Catherine Thieblemont
- Department of Hemato-oncology, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.,Université de Paris, NF-kappaB, Différenciation et Cancer, 75006 Paris, France
| | - Laurent Delva
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Marc Maynadié
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France.,Registre des hémopathies malignes de Côte d'Or, University of Burgundy, Faculty of Medicine, 21079 Dijon, France
| | - Romain Aucagne
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Mary B Callanan
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
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17
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Tanaka S, Ise W, Inoue T, Ito A, Ono C, Shima Y, Sakakibara S, Nakayama M, Fujii K, Miura I, Sharif J, Koseki H, Koni PA, Raman I, Li QZ, Kubo M, Fujiki K, Nakato R, Shirahige K, Araki H, Miura F, Ito T, Kawakami E, Baba Y, Kurosaki T. Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity. Nat Immunol 2020; 21:950-961. [PMID: 32572241 DOI: 10.1038/s41590-020-0700-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
A contribution of epigenetic modifications to B cell tolerance has been proposed but not directly tested. Here we report that deficiency of ten-eleven translocation (Tet) DNA demethylase family members Tet2 and Tet3 in B cells led to hyperactivation of B and T cells, autoantibody production and lupus-like disease in mice. Mechanistically, in the absence of Tet2 and Tet3, downregulation of CD86, which normally occurs following chronic exposure of self-reactive B cells to self-antigen, did not take place. The importance of dysregulated CD86 expression in Tet2- and Tet3-deficient B cells was further demonstrated by the restriction, albeit not complete, on aberrant T and B cell activation following anti-CD86 blockade. Tet2- and Tet3-deficient B cells had decreased accumulation of histone deacetylase 1 (HDAC1) and HDAC2 at the Cd86 locus. Thus, our findings suggest that Tet2- and Tet3-mediated chromatin modification participates in repression of CD86 on chronically stimulated self-reactive B cells, which contributes, at least in part, to preventing autoimmunity.
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Affiliation(s)
- Shinya Tanaka
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan.,Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda, Japan
| | - Wataru Ise
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Ayako Ito
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Chisato Ono
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihito Shima
- Laboratory of Thermo-Therapeutics for Vascular Dysfunction, Osaka University, Suita, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kentaro Fujii
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Ikuo Miura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Jafar Sharif
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | | | - Indu Raman
- Microarray Core Facility, Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Quan-Zhen Li
- Microarray Core Facility, Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masato Kubo
- Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda, Japan.,Laboratory for Cytokine Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsunori Fujiki
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Ryuichiro Nakato
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiromitsu Araki
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eiryo Kawakami
- Medical Sciences Innovation Hub Program, RIKEN, Yokohama, Japan.,Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshihiro Baba
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan. .,Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan. .,Laboratory of Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
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18
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Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1. Nat Commun 2020; 11:402. [PMID: 31964861 PMCID: PMC6972792 DOI: 10.1038/s41467-019-13960-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/10/2019] [Indexed: 12/21/2022] Open
Abstract
Establishing gene regulatory networks during differentiation or reprogramming requires master or pioneer transcription factors (TFs) such as PU.1, a prototype master TF of hematopoietic lineage differentiation. To systematically determine molecular features that control its activity, here we analyze DNA-binding in vitro and genome-wide in vivo across different cell types with native or ectopic PU.1 expression. Although PU.1, in contrast to classical pioneer factors, is unable to access nucleosomal target sites in vitro, ectopic induction of PU.1 leads to the extensive remodeling of chromatin and redistribution of partner TFs. De novo chromatin access, stable binding, and redistribution of partner TFs both require PU.1's N-terminal acidic activation domain and its ability to recruit SWI/SNF remodeling complexes, suggesting that the latter may collect and distribute co-associated TFs in conjunction with the non-classical pioneer TF PU.1.
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19
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Sanz I, Wei C, Jenks SA, Cashman KS, Tipton C, Woodruff MC, Hom J, Lee FEH. Challenges and Opportunities for Consistent Classification of Human B Cell and Plasma Cell Populations. Front Immunol 2019; 10:2458. [PMID: 31681331 PMCID: PMC6813733 DOI: 10.3389/fimmu.2019.02458] [Citation(s) in RCA: 306] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022] Open
Abstract
The increasingly recognized role of different types of B cells and plasma cells in protective and pathogenic immune responses combined with technological advances have generated a plethora of information regarding the heterogeneity of this human immune compartment. Unfortunately, the lack of a consistent classification of human B cells also creates significant imprecision on the adjudication of different phenotypes to well-defined populations. Additional confusion in the field stems from: the use of non-discriminatory, overlapping markers to define some populations, the extrapolation of mouse concepts to humans, and the assignation of functional significance to populations often defined by insufficient surface markers. In this review, we shall discuss the current understanding of human B cell heterogeneity and define major parental populations and associated subsets while discussing their functional significance. We shall also identify current challenges and opportunities. It stands to reason that a unified approach will not only permit comparison of separate studies but also improve our ability to define deviations from normative values and to create a clean framework for the identification, functional significance, and disease association with new populations.
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Affiliation(s)
- Ignacio Sanz
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Chungwen Wei
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Scott A Jenks
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Kevin S Cashman
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Christopher Tipton
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Matthew C Woodruff
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Jennifer Hom
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, United States
| | - F Eun-Hyung Lee
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, United States.,Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Emory University, Atlanta, GA, United States
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20
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Gowda C, Song C, Ding Y, Iyer S, Dhanyamraju PK, McGrath M, Bamme Y, Soliman M, Kane S, Payne JL, Dovat S. Cellular signaling and epigenetic regulation of gene expression in leukemia. Adv Biol Regul 2019; 75:100665. [PMID: 31623972 PMCID: PMC7239353 DOI: 10.1016/j.jbior.2019.100665] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022]
Abstract
Alterations in normal regulation of gene expression is one of the key features of hematopoietic malignancies. In order to gain insight into the mechanisms that regulate gene expression in these diseases, we dissected the role of the Ikaros protein in leukemia. Ikaros is a DNA-binding, zinc finger protein that functions as a transcriptional regulator and a tumor suppressor in leukemia. The use of ChIP-seq, RNA-seq, and ATAC-seq—coupled with functional experiments—revealed that Ikaros regulates both the global epigenomic landscape and epigenetic signature at promoter regions of its target genes. Casein kinase II (CK2), an oncogenic kinase that is overexpressed in leukemia, directly phosphorylates Ikaros at multiple, evolutionarily-conserved residues. Phosphorylation of Ikaros impairs the protein's ability to regulate both the transcription of its target genes and global epigenetic landscape in leukemia. Treatment of leukemia cells with a specific inhibitor of CK2 restores Ikaros function, resulting in cytotoxicity of leukemia cells. Here, we review the mechanisms through which the CK2-Ikaros signaling axis regulates the global epigenomic landscape and expression of genes that control cellular proliferation in leukemia.
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Affiliation(s)
- Chandrika Gowda
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Chunhua Song
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yali Ding
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Mary McGrath
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Yevgeniya Bamme
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Mario Soliman
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Shriya Kane
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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21
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Ru B, Sun J, Kang Q, Tong Y, Zhang J. A framework for identifying dysregulated chromatin regulators as master regulators in human cancer. Bioinformatics 2019; 35:1805-1812. [PMID: 30358822 DOI: 10.1093/bioinformatics/bty836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 10/24/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Chromatin regulators (CRs) are frequently dysregulated to reprogram the epigenetic landscape of the cancer genome. However, the underpinnings of the dysregulation of CRs and their downstream effectors remain to be elucidated. RESULTS Here, we designed an integrated framework based on multi-omics data to identify candidate master regulatory CRs affected by genomic alterations across eight cancer types in The Cancer Genome Atlas. Most of them showed consistent activated or repressed (i.e. oncogenic or tumor-suppressive) roles in cancer initiation and progression. In order to further explore the insight mechanism of the dysregulated CRs, we developed an R package ModReg based on differential connectivity to identify CRs as modulators of transcription factors (TFs) involved in tumorigenesis. Our analysis revealed that the connectivity between TFs and their target genes (TGs) tended to be disrupted in the patients who had a high expression of oncogenic CRs or low-expression of tumor-suppressive CRs. As a proof-of-principle study, 14 (82.4%) of the top-ranked 17 driver CRs in liver cancer were able to be validated by literature mining or experiments including shRNA knockdown and dCas9-based epigenetic editing. Moreover, we confirmed that CR SIRT7 physically interacted with TF NFE2L2, and positively modulated the transcriptional program of NFE2L2 by affecting ∼64% of its TGs. AVAILABILITY AND IMPLEMENTATION ModReg is freely accessible at http://cis.hku.hk/software/ModReg.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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22
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Ding Y, Zhang B, Payne JL, Song C, Ge Z, Gowda C, Iyer S, Dhanyamraju PK, Dorsam G, Reeves ME, Desai D, Huang S, Payne KJ, Yue F, Dovat S. Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity. Leukemia 2019; 33:2720-2731. [PMID: 31073152 PMCID: PMC6842075 DOI: 10.1038/s41375-019-0474-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Ikaros encodes a transcription factor that functions as a tumor suppressor in T-cell acute lymphoblastic leukemia (T-ALL). The mechanisms through which Ikaros regulates gene expression and cellular proliferation in T-ALL are unknown. Re-introduction of Ikaros into Ikaros-null T-ALL cells resulted in cessation of cellular proliferation and induction of T-cell differentiation. We performed dynamic, global, epigenomic and gene expression analyses to determine the mechanisms of Ikaros tumor suppressor activity. Our results identified novel Ikaros functions in the epigenetic regulation of gene expression: Ikaros directly regulates de novo formation and depletion of enhancers, de novo formation of active enhancers and activation of poised enhancers; Ikaros directly induces the formation of super-enhancers; and Ikaros demonstrates pioneering activity by directly regulating chromatin accessibility. Dynamic analyses demonstrate the long-lasting effects of Ikaros DNA binding on enhancer activation, de novo formation of enhancers and super-enhancers, and chromatin accessibility. Our results establish that Ikaros’ tumor suppressor function occurs via global regulation of the enhancer and super-enhancer landscape and through pioneering activity. Expression analysis identified a large number of novel signaling pathways that are directly regulated by Ikaros and Ikaros-induced enhancers, and that are responsible for the cessation of proliferation and induction of T-cell differentiation in T-ALL cells.
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Affiliation(s)
- Yali Ding
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Bo Zhang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jonathon L Payne
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA.,Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Chunhua Song
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital Southeast University, Institute of Hematology Southeast University, 210009, Nanjing, China
| | - Chandrika Gowda
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Soumya Iyer
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Pavan K Dhanyamraju
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Glenn Dorsam
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Mark E Reeves
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Dhimant Desai
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suming Huang
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kimberly J Payne
- Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Sinisa Dovat
- Depatment of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
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23
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The E3 ubiquitin ligase Itch is required for B-cell development. Sci Rep 2019; 9:421. [PMID: 30674954 PMCID: PMC6344599 DOI: 10.1038/s41598-018-36844-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/12/2018] [Indexed: 11/20/2022] Open
Abstract
The E3 ubiquitin ligase Itch interacts with Foxo1 and targets it for ubiquitination and degradation during follicular helper T-cell differentiation, whereas the transcription factor Foxo1 plays a critical role in B-cell development. Thus, we proposed that Itch mediates B-cell differentiation. Unexpectedly, we found that Itch deficiency downregulated Foxo1 expression in B cells. Itch cKO (conditional knock out in B cells) mice had fewer pro-B cells in the bone marrow, more small resting IgM−IgD−B cells in the periphery, and lower B-cell numbers in the lymph nodes through decreased Foxo1-mediated IL-7Rα, RAG, and CD62L expression, respectively. Importantly, Itch deficiency reduced Foxo1 mRNA expression by up-regulating JunB-mediated miR-182. Finally, Foxo1 negatively regulated JunB expression by up-regulating Itch. Thus, we have identified a novel regulatory axis between Itch and Foxo1 in B cells, suggesting that Itch is essential for B-cell development.
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24
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Mandal M, Maienschein-Cline M, Maffucci P, Veselits M, Kennedy DE, McLean KC, Okoreeh MK, Karki S, Cunningham-Rundles C, Clark MR. BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis. Nat Commun 2018; 9:3888. [PMID: 30250168 PMCID: PMC6155124 DOI: 10.1038/s41467-018-06165-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/20/2018] [Indexed: 12/30/2022] Open
Abstract
Transcription factor (TF) networks determine cell fate in hematopoiesis. However, how TFs cooperate with other regulatory mechanisms to instruct transcription remains poorly understood. Here we show that in small pre-B cells, the lineage restricted epigenetic reader BRWD1 closes early development enhancers and opens the enhancers of late B lymphopoiesis to TF binding. BRWD1 regulates over 7000 genes to repress proliferative and induce differentiation programs. However, BRWD1 does not regulate the expression of TFs required for B lymphopoiesis. Hypogammaglobulinemia patients with BRWD1 mutations have B-cell transcriptional profiles and enhancer landscapes similar to those observed in Brwd1-/- mice. These data indicate that, in both mice and humans, BRWD1 is a master orchestrator of enhancer accessibility that cooperates with TF networks to drive late B-cell development. B-cell development is tightly regulated by transcription programs that are coordinated by transcription factors (TF) and locus accessibility. Here the authors show that, in mice and humans, the epigenetic reader BRWD1 inhibits and promotes the accessibility of enhancers for early and late B lymphopoiesis, respectively.
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Affiliation(s)
- Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA.
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Patrick Maffucci
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret Veselits
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Domenick E Kennedy
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Kaitlin C McLean
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Michael K Okoreeh
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Sophiya Karki
- Department of Research Biology, Genentech, South San Francisco, California, USA
| | - Charlotte Cunningham-Rundles
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA.
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25
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Comprehensive profiling of transcriptional networks specific for lactogenic differentiation of HC11 mammary epithelial stem-like cells. Sci Rep 2018; 8:11777. [PMID: 30082875 PMCID: PMC6079013 DOI: 10.1038/s41598-018-30122-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/13/2018] [Indexed: 12/31/2022] Open
Abstract
The development of mammary gland as a lactogenic tissue is a highly coordinated multistep process. The epithelial cells of lactiferous tubules undergo profound changes during the developmental window of puberty, pregnancy, and lactation. Several hormones including estrogen, progesterone, glucocorticoids and prolactin act in concert, and orchestrate the development of mammary gland. Understanding the gene regulatory networks that coordinate proliferation and differentiation of HC11 Mammary Epithelial stem-like Cells (MEC) under the influence of lactogenic hormones is critical for elucidating the mechanism of lactogenesis in detail. In this study, we analyzed transcriptome profiles of undifferentiated MEC (normal) and compared them with Murine Embryonic Stem Cells (ESC) using next-generation mRNA sequencing. Further, we analyzed the transcriptome output during lactogenic differentiation of MEC following treatment with glucocorticoids (primed state) and both glucocorticoids and prolactin together (prolactin state). We established stage-specific gene regulatory networks in ESC and MEC (normal, priming and prolactin states). We validated the top up-and downregulated genes in each stage of differentiation of MEC by RT-PCR and found that they are comparable with that of RNA-seq data. HC11 MEC display decreased expression of Pou5f1 and Sox2, which is crucial for the differentiation of MEC, which otherwise ensure pluripotency to ESC. Cited4 is induced during priming and is involved in milk secretion. MEC upon exposure to both glucocorticoids and prolactin undergo terminal differentiation, which is associated with the expression of several genes, including Xbp1 and Cbp that are required for cell growth and differentiation. Our study also identified differential expression of transcription factors and epigenetic regulators in each stage of lactogenic differentiation. We also analyzed the transcriptome data for the pathways that are selectively activated during lactogenic differentiation. Further, we found that selective expression of chromatin modulators (Dnmt3l, Chd9) in response to glucocorticoids suggests a highly coordinated stage-specific lactogenic differentiation of MEC.
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26
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Zhu C, Chen G, Zhao Y, Gao XM, Wang J. Regulation of the Development and Function of B Cells by ZBTB Transcription Factors. Front Immunol 2018; 9:580. [PMID: 29616049 PMCID: PMC5869932 DOI: 10.3389/fimmu.2018.00580] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/07/2018] [Indexed: 12/20/2022] Open
Abstract
The large ZBTB family comprises a diverse group of transcriptional factors. Several ZBTB proteins have emerged as critical factors that regulate the lineage commitment, differentiation, and function of lymphoid cells as well as many other developmental events. For instance, dysfunctions of ZBTB20 or ZBTB24 have been linked to multisystem failures in humans. Within the B-cell lineage, BCL6, ZBTB7A, ZBTB17, and ZBTB1 regulate the development/differentiation of B cells in both bone marrow and peripheral lymphoid organs, while ZBTB20 and ZBTB32 seem to mainly impact the maintenance of terminal plasma cells. Given the importance of B cells in the prevention and treatment of infectious or autoimmune disorders, we herein summarize the roles of seven ZBTB family members (BCL6, ZBTB7A, ZBTB17, ZBTB20, ZBTB32, ZBTB1, and ZBTB24) in the development, differentiation, and function of B cells as well as the underlying molecular mechanisms.
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Affiliation(s)
- Can Zhu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ge Chen
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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27
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Charting the dynamic epigenome during B-cell development. Semin Cancer Biol 2017; 51:139-148. [PMID: 28851627 DOI: 10.1016/j.semcancer.2017.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023]
Abstract
The epigenetic landscape undergoes a widespread modulation during embryonic development and cell differentiation. Within the hematopoietic system, B cells are perhaps the cell lineage with a more dynamic DNA methylome during their maturation process, which involves approximately one third of all the CpG sites of the genome. Although each B-cell maturation step displays its own DNA methylation fingerprint, the DNA methylome is more extensively modified in particular maturation transitions. These changes are gradually accumulated in specific chromatin environments as cell differentiation progresses and reflect different features and functional states of B cells. Promoters and enhancers of B-cell transcription factors acquire activation-related epigenetic marks and are sequentially expressed in particular maturation windows. These transcription factors further reconfigure the epigenetic marks and activity state of their target sites to regulate the expression of genes related to B-cell functions. Together with this observation, extensive DNA methylation changes in areas outside gene regulatory elements such as hypomethylation of heterochromatic regions and hypermethylation of CpG-rich regions, also take place in mature B cells, which intriguingly have been described as hallmarks of cancer. This process starts in germinal center B cells, a highly proliferative cell type, and becomes particularly apparent in long-lived cells such as memory and plasma cells. Overall, the characterization of the DNA methylome during B-cell differentiation not only provides insights into the complex epigenetic network of regulatory elements that mediate the maturation process but also suggests that late B cells also passively accumulate epigenetic changes related to cell proliferation and longevity.
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28
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Grebbin BM, Schulte D. PBX1 as Pioneer Factor: A Case Still Open. Front Cell Dev Biol 2017; 5:9. [PMID: 28261581 PMCID: PMC5306212 DOI: 10.3389/fcell.2017.00009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/31/2017] [Indexed: 12/19/2022] Open
Abstract
Pioneer factors are proteins that can recognize their target sites in barely accessible chromatin and initiate a cascade of events that allows for later transcriptional activation of the respective genes. Pioneer factors are therefore particularly well-suited to initiate cell fate changes. To date, only a small number of pioneer factors have been identified and studied in depth, such as FOXD3/FOXA1, OCT4, or SOX2. Interestingly, several recent studies reported that the PBC transcription factor PBX1 can access transcriptionally inactive genomic loci. Here, we summarize the evidence linking PBX1 with transcriptional pioneer functions, suggest potential mechanisms involved and discuss open questions to be resolved.
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Affiliation(s)
- Britta M Grebbin
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, J. W. Goethe University Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, J. W. Goethe University Frankfurt, Germany
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29
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Ehsani R, Bahrami S, Drabløs F. Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function. BMC Bioinformatics 2016; 17:459. [PMID: 27842491 PMCID: PMC5109715 DOI: 10.1186/s12859-016-1349-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 11/10/2016] [Indexed: 12/15/2022] Open
Abstract
Background Transcription factors are key proteins in the regulation of gene transcription. An important step in this process is the opening of chromatin in order to make genomic regions available for transcription. Data on DNase I hypersensitivity has previously been used to label a subset of transcription factors as Pioneers, Settlers and Migrants to describe their potential role in this process. These labels represent an interesting hypothesis on gene regulation and possibly a useful approach for data analysis, and therefore we wanted to expand the set of labeled transcription factors to include as many known factors as possible. We have used a well-annotated dataset of 1175 transcription factors as input to supervised machine learning methods, using the subset with previously assigned labels as training set. We then used the final classifier to label the additional transcription factors according to their potential role as Pioneers, Settlers and Migrants. The full set of labeled transcription factors was used to investigate associated properties and functions of each class, including an analysis of interaction data for transcription factors based on DNA co-binding and protein-protein interactions. We also used the assigned labels to analyze a previously published set of gene lists associated with a time course experiment on cell differentiation. Results The analysis showed that the classification of transcription factors with respect to their potential role in chromatin opening largely was determined by how they bind to DNA. Each subclass of transcription factors was enriched for properties that seemed to characterize the subclass relative to its role in gene regulation, with very general functions for Pioneers, whereas Migrants to a larger extent were associated with specific processes. Further analysis showed that the expanded classification is a useful resource for analyzing other datasets on transcription factors with respect to their potential role in gene regulation. The analysis of transcription factor interaction data showed complementary differences between the subclasses, where transcription factors labeled as Pioneers often interact with other transcription factors through DNA co-binding, whereas Migrants to a larger extent use protein-protein interactions. The analysis of time course data on cell differentiation indicated a shift in the regulatory program associated with Pioneer-like transcription factors during differentiation. Conclusions The expanded classification is an interesting resource for analyzing data on gene regulation, as illustrated here on transcription factor interaction data and data from a time course experiment. The potential regulatory function of transcription factors seems largely to be determined by how they bind DNA, but is also influenced by how they interact with each other through cooperativity and protein-protein interactions. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1349-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rezvan Ehsani
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, PO Box 8905, NO-7491, Trondheim, Norway.,Department of Mathematics, University of Zabol, Zabol, Iran
| | - Shahram Bahrami
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, PO Box 8905, NO-7491, Trondheim, Norway.,St. Olavs Hospital, Trondheim University Hospital, NO-7006, Trondheim, Norway
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, PO Box 8905, NO-7491, Trondheim, Norway.
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30
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Montecino-Rodriguez E, Fice M, Casero D, Berent-Maoz B, Barber CL, Dorshkind K. Distinct Genetic Networks Orchestrate the Emergence of Specific Waves of Fetal and Adult B-1 and B-2 Development. Immunity 2016; 45:527-539. [PMID: 27566938 DOI: 10.1016/j.immuni.2016.07.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/13/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
B cell development is often depicted as a linear process initiating in the fetus and continuing postnatally. Using a PU.1 hypomorphic mouse model, we found that B-1 and B-2 lymphopoiesis occurred in distinct fetal and adult waves differentially dependent on the Sfpi1 14 kB upstream regulatory element. The initial wave of fetal B-1 development was absent in PU.1 hypomorphic mice, while subsequent fetal and adult waves emerged. In contrast, B-2 lymphopoiesis occurred in distinct fetal and adult waves. Whole-transcriptome profiling of fetal and adult B cell progenitors supported the existence of three waves of B-1 and two waves of B-2 development and revealed that the network of transcription factors governing B lineage specification and commitment was highly divergent between B-1 and B-2 progenitors. These findings support the view that the B-1 and B-2 lineages are distinct and provide a genetic basis for layering of immune system development.
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Affiliation(s)
- Encarnacion Montecino-Rodriguez
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Fice
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David Casero
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Beata Berent-Maoz
- Department of Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chad L Barber
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360, USA
| | - Kenneth Dorshkind
- Department of Pathology and Laboratory Medicine, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Al Dallal S, Wolton K, Hentges KE. Zfp521 promotes B-cell viability and cyclin D1 gene expression in a B cell culture system. Leuk Res 2016; 46:10-7. [PMID: 27107743 PMCID: PMC4910839 DOI: 10.1016/j.leukres.2016.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/13/2016] [Accepted: 03/31/2016] [Indexed: 12/16/2022]
Abstract
Knockdown of Zfp521 in BCL1 cell culture reduces viability and promotes apoptosis. Genes expressed in B cells are down-regulated in cells with Zfp521 knockdown. Cyclin D1 expression is increased in mouse tumors with Zfp521 over-expression.
Leukemia arises due to the dysregulated proliferation of hematopoietic progenitor cells. Errors in the multi-step commitment process result in excessive numbers of immature lymphocytes, causing malignant disease. Genes involved in the differentiation of lymphocytes are often associated with leukemia. One such gene, Zfp521, has been found to cause B-cell leukemia in mice when over-expressed. The role of Zfp521 in B-cell differentiation, and the mechanisms by which it leads to leukemic transformation, are unclear. In this study we report that Zfp521 knockdown causes apoptosis in a B-cell culture system and promotes down-regulation of genes acting at late stages of B-cell differentiation. We identify Pax5 and cyclin D1 as Zfp521 target genes, and suggest that excessive B-cell proliferation observed in mice with retroviral insertions near the Zfp521 gene is due to an up-regulation of cyclin D1 in B-cells. Overall, these results suggest links between dysregulated Zfp521 and B-cell survival.
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Affiliation(s)
- Salma Al Dallal
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Kathryn Wolton
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Kathryn E Hentges
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
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ZNF423 and ZNF521: EBF1 Antagonists of Potential Relevance in B-Lymphoid Malignancies. BIOMED RESEARCH INTERNATIONAL 2015; 2015:165238. [PMID: 26788497 PMCID: PMC4695665 DOI: 10.1155/2015/165238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/25/2015] [Indexed: 12/26/2022]
Abstract
The development of the B-lymphoid cell lineage is tightly controlled by the concerted action of a network of transcriptional and epigenetic regulators. EBF1, a central component of this network, is essential for B-lymphoid specification and commitment as well as for the maintenance of the B-cell identity. Genetic alterations causing loss of function of these B-lymphopoiesis regulators have been implicated in the pathogenesis of B-lymphoid malignancies, with particular regard to B-cell acute lymphoblastic leukaemias (B-ALLs), where their presence is frequently detected. The activity of the B-cell regulatory network may also be disrupted by the aberrant expression of inhibitory molecules. In particular, two multi-zinc finger transcription cofactors named ZNF423 and ZNF521 have been characterised as potent inhibitors of EBF1 and are emerging as potentially relevant contributors to the development of B-cell leukaemias. Here we will briefly review the current knowledge of these factors and discuss the importance of their functional cross talk with EBF1 in the development of B-cell malignancies.
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Kuzmich AI, Tyulkina DV, Vinogradova TV, Sverdlov ED. Pioneer transcription factors in normal development and carcinogenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:636-43. [DOI: 10.1134/s1068162015060084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Enhancer repertoires are reshaped independently of early priming and heterochromatin dynamics during B cell differentiation. Nat Commun 2015; 6:8324. [PMID: 26477271 PMCID: PMC4633987 DOI: 10.1038/ncomms9324] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 08/11/2015] [Indexed: 02/06/2023] Open
Abstract
A widely accepted model posits that activation of enhancers during differentiation goes through a priming step prior to lineage commitment. To investigate the chronology of enhancer repertoire establishment during hematopoiesis, we monitored epigenome dynamics during three developmental stages representing hematopoietic stem cells, B-cell progenitors and mature B-cells. We find that only a minority of enhancers primed in stem cells or progenitors become active at later stages. Furthermore, most enhancers active in differentiated cells were not primed in earlier stages. Thus, the enhancer repertoire is reshaped dynamically during B-cell differentiation and enhancer priming in early stages does not appear to be an obligate step for enhancer activation. Furthermore, our data reveal that heterochromatin and Polycomb-mediated silencing have only a minor contribution in shaping enhancer repertoires during cell differentiation. Together, our data revisit the prevalent model about epigenetic reprogramming during hematopoiesis and give insights into the formation of gene regulatory networks. Enhancers in differentiated haematopoietic cells are generally believed to be primed prior to lineage commitment. Here, the authors show that early priming and Polycomb group mediated silencing have minor roles in shaping the enhancer repertoire in differentiated B cells and that most active enhancers are generated de novo.
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Epigenetic Control of B Cell Development and B-Cell-Related Immune Disorders. Clin Rev Allergy Immunol 2015; 50:301-11. [DOI: 10.1007/s12016-015-8494-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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36
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Ignatieva EV, Podkolodnaya OA, Orlov YL, Vasiliev GV, Kolchanov NA. Regulatory genomics: Combined experimental and computational approaches. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415040067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Roy AL, Roeder RG. Chromatin and transcriptional tango on the immune dance floor. Front Immunol 2015; 5:631. [PMID: 25566246 PMCID: PMC4266087 DOI: 10.3389/fimmu.2014.00631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 11/25/2014] [Indexed: 11/22/2022] Open
Affiliation(s)
- Ananda L Roy
- Programs in Immunology and Genetics, Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine , Boston, MA , USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University , New York, NY , USA
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