1
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Hitomi Y, Nakamura M. The Genetics of Primary Biliary Cholangitis: A GWAS and Post-GWAS Update. Genes (Basel) 2023; 14:405. [PMID: 36833332 PMCID: PMC9957238 DOI: 10.3390/genes14020405] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which the small intrahepatic bile ducts are destroyed by autoimmune reactions. Among autoimmune diseases, which are polygenic complex traits caused by the combined contribution of genetic and environmental factors, PBC exhibits the strongest involvement of genetic heritability in disease development. As at December 2022, genome-wide association studies (GWASs) and associated meta-analyses identified approximately 70 PBC susceptibility gene loci in various populations, including those of European and East Asian descent. However, the molecular mechanisms through which these susceptibility loci affect the pathogenesis of PBC are not fully understood. This study provides an overview of current data regarding the genetic factors of PBC as well as post-GWAS approaches to identifying primary functional variants and effector genes in disease-susceptibility loci. Possible mechanisms of these genetic factors in the development of PBC are also discussed, focusing on four major disease pathways identified by in silico gene set analyses, namely, (1) antigen presentation by human leukocyte antigens, (2) interleukin-12-related pathways, (3) cellular responses to tumor necrosis factor, and (4) B cell activation, maturation, and differentiation pathways.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, 2-1001-1 Kubara, Omura 856-8562, Japan
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
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2
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Kong IY, Trezise S, Light A, Todorovski I, Arnau GM, Gadipally S, Yoannidis D, Simpson KJ, Dong X, Whitehead L, Tempany JC, Farchione AJ, Sheikh AA, Groom JR, Rogers KL, Herold MJ, Bryant VL, Ritchie ME, Willis SN, Johnstone RW, Hodgkin PD, Nutt SL, Vervoort SJ, Hawkins ED. Epigenetic modulators of B cell fate identified through coupled phenotype-transcriptome analysis. Cell Death Differ 2022; 29:2519-2530. [PMID: 35831623 PMCID: PMC9751284 DOI: 10.1038/s41418-022-01037-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 01/31/2023] Open
Abstract
High-throughput methodologies are the cornerstone of screening approaches to identify novel compounds that regulate immune cell function. To identify novel targeted therapeutics to treat immune disorders and haematological malignancies, there is a need to integrate functional cellular information with the molecular mechanisms that regulate changes in immune cell phenotype. We facilitate this goal by combining quantitative methods for dissecting complex simultaneous cell phenotypic effects with genomic analysis. This combination strategy we term Multiplexed Analysis of Cells sequencing (MAC-seq), a modified version of Digital RNA with perturbation of Genes (DRUGseq). We applied MAC-seq to screen compounds that target the epigenetic machinery of B cells and assess altered humoral immunity by measuring changes in proliferation, survival, differentiation and transcription. This approach revealed that polycomb repressive complex 2 (PRC2) inhibitors promote antibody secreting cell (ASC) differentiation in both murine and human B cells in vitro. This is further validated using T cell-dependent immunization in mice. Functional dissection of downstream effectors of PRC2 using arrayed CRISPR screening uncovered novel regulators of B cell differentiation, including Mybl1, Myof, Gas7 and Atoh8. Together, our findings demonstrate that integrated phenotype-transcriptome analyses can be effectively combined with drug screening approaches to uncover the molecular circuitry that drives lymphocyte fate decisions.
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Affiliation(s)
- Isabella Y. Kong
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Stephanie Trezise
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Amanda Light
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Izabela Todorovski
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, 3000 VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC Australia
| | - Gisela Mir Arnau
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, 3000 VIC Australia
| | - Sreeja Gadipally
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, 3000 VIC Australia
| | - David Yoannidis
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, 3000 VIC Australia
| | - Kaylene J. Simpson
- grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC Australia ,grid.1055.10000000403978434Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Xueyi Dong
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Lachlan Whitehead
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Jessica C. Tempany
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Anthony J. Farchione
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Amania A. Sheikh
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia
| | - Joanna R. Groom
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Kelly L. Rogers
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Marco J. Herold
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Vanessa L. Bryant
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Matthew E. Ritchie
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Simon N. Willis
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Ricky W. Johnstone
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, 3000 VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC Australia
| | - Philip D. Hodgkin
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Stephen L. Nutt
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
| | - Stephin J. Vervoort
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia ,grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, 3000 VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC Australia
| | - Edwin D. Hawkins
- grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052 VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, 3010 VIC Australia
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3
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Anderson KJ, Ósvaldsdóttir ÁB, Atzinger B, Traustadóttir GÁ, Jensen KN, Lárusdóttir AE, Bergthórsson JT, Hardardóttir I, Magnúsdóttir E. The BLIMP1-EZH2 nexus in a non-Hodgkin lymphoma. Oncogene 2020; 39:5138-5151. [PMID: 32533097 DOI: 10.1038/s41388-020-1347-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 01/12/2023]
Abstract
Waldenström's macroglobulinemia (WM) is a non-Hodgkin lymphoma, resulting in antibody-secreting lymphoplasmacytic cells in the bone marrow and pathologies resulting from high levels of monoclonal immunoglobulin M (IgM) in the blood. Despite the key role for BLIMP1 in plasma cell maturation and antibody secretion, its potential effect on WM cell biology has not yet been explored. Here we provide evidence of a crucial role for BLIMP1 in the survival of cells from WM cell line models and further demonstrate that BLIMP1 is necessary for the expression of the histone methyltransferase EZH2 in both WM and multiple myeloma cell lines. The effect of BLIMP1 on EZH2 levels is post-translational, at least partially through the regulation of proteasomal targeting of EZH2. Chromatin immunoprecipitation analysis and transcriptome profiling suggest that the two factors co-operate in regulating genes involved in cancer cell immune evasion. Co-cultures of natural killer cells and cells from a WM cell line further suggest that both factors participate in immune evasion by promoting escape from natural killer cell-mediated cytotoxicity. Together, the interplay of BLIMP1 and EZH2 plays a vital role in promoting the survival of WM cell lines, suggesting a role for the two factors in Waldenström's macroglobulinaemia.
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Affiliation(s)
- Kimberley Jade Anderson
- Department of Anatomy, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavik, Iceland.,Department of Biomedical Science, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland
| | - Árný Björg Ósvaldsdóttir
- Department of Anatomy, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavik, Iceland.,Department of Biomedical Science, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland
| | - Birgit Atzinger
- Department of Anatomy, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavik, Iceland.,Department of Biomedical Science, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland
| | - Gunnhildur Ásta Traustadóttir
- Department of Anatomy, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavik, Iceland.,The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland
| | - Kirstine Nolling Jensen
- The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, Vatnsmýrarvegur 16, University of Iceland, 101, Reykjavík, Iceland.,Department of Immunology, Landspitali-The National University Hospital of Iceland, Hringbraut, 101, Reykjavík, Iceland
| | - Aðalheiður Elín Lárusdóttir
- Department of Anatomy, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavik, Iceland.,Department of Biomedical Science, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland
| | - Jón Thór Bergthórsson
- Department of Biomedical Science, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,Department of Laboratory Haematology, Landspitali-The National University Hospital of Iceland, Hringbraut, 101, Reykjavík, Iceland
| | - Ingibjörg Hardardóttir
- The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, Vatnsmýrarvegur 16, University of Iceland, 101, Reykjavík, Iceland.,Department of Immunology, Landspitali-The National University Hospital of Iceland, Hringbraut, 101, Reykjavík, Iceland
| | - Erna Magnúsdóttir
- Department of Anatomy, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavik, Iceland. .,Department of Biomedical Science, Faculty of Medicine, University of Iceland, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland. .,The University of Iceland Biomedical Center, Vatnsmýrarvegur 16, 101, Reykjavík, Iceland.
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4
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Levels MJ, Fehres CM, van Baarsen LG, van Uden NO, Germar K, O'Toole TG, Blijdorp IC, Semmelink JF, Doorenspleet ME, Bakker AQ, Krasavin M, Tomilin A, Brouard S, Spits H, Baeten DL, Yeremenko NG. BOB.1 controls memory B-cell fate in the germinal center reaction. J Autoimmun 2019; 101:131-144. [DOI: 10.1016/j.jaut.2019.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 11/30/2022]
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5
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Bertrand E, Jouy N, Manier S, Fouquet G, Guidez S, Boyle E, Noel S, Tomowiak C, Herbaux C, Schraen S, Preudhomme C, Quesnel B, Poulain S, Leleu X. Role of IRF4 in resistance to immunomodulatory (IMid) compounds ® in Waldenström's macroglobulinemia. Oncotarget 2017; 8:112917-112927. [PMID: 29348877 PMCID: PMC5762562 DOI: 10.18632/oncotarget.22872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/17/2017] [Indexed: 12/05/2022] Open
Abstract
Background Immunomodulatory drugs, IMid compounds, are active in Waldenström's macroglobulinemia (WM), although in a lesser extent than multiple myeloma, where it was initially developed. We hypothesized WM tumour cells might develop mechanisms of resistance, and sought to identify and describe these mechanisms. Material and Method MM and WM-derived cell lines, and Waldenström's CD19+ cells were treated using both lenalidomide and pomalidomide. Stable CRBN expressing cells were generated. Results WM-derived cells were resistant to IMid compounds. We demonstrated a modulation of the downstream targets of IRF4, despite low expression of cereblon, and hypothesized IRF4 was the cause for resistance to IMid compounds. We ruled out the role of various IRF4 regulatory mechanisms, and other pathways activating WM tumor cells, such as B cell activators. Conclusion This study demonstrated that mechanisms of resistance to IMid compounds could be not related to cereblon. IRF4 was identified as the potential mechanism of resistance to lenalidomide and pomalidomide in WM. It potentially explains the lesser activity observed in the clinic in WM. Interestingly, some WM patients benefited strongly to lenalidomide and pomalidomide, and future studies will have to describe the indirect mechanisms of IMid compounds in WM, possibly related to an immune-mediated process.
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Affiliation(s)
- Elisabeth Bertrand
- Univ. Lille, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, JPARC - Centre de Recherche Jean-Pierre AUBERT, Neurosciences et Cancer, Lille, France.,Inserm, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, Factors of Persistence of Leukemic Cells Team, Lille, France
| | - Nathalie Jouy
- Univ. Lille, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, JPARC - Centre de Recherche Jean-Pierre AUBERT, Neurosciences et Cancer, Lille, France.,Plateau de Cytométrie, BioImaging Center Lille Nord de France, BICeL Campus Hospitalo-Universitaire, Lille, France
| | - Salomon Manier
- Univ. Lille, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, JPARC - Centre de Recherche Jean-Pierre AUBERT, Neurosciences et Cancer, Lille, France.,Inserm, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, Lille, France.,Service des Maladies du Sang, CHU, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, Factors of Persistence of Leukemic Cells Team, Lille, France
| | | | - Stéphanie Guidez
- Service d'Hématologie et Thérapie Cellulaire, Hôpital La Milétrie, et Faculté de Médecine, CHU, Poitiers, France.,CIC Inserm 1402, CHU, Poitiers, France
| | - Eileen Boyle
- Service des Maladies du Sang, CHU, Lille, France
| | | | - Cécile Tomowiak
- Service d'Hématologie et Thérapie Cellulaire, Hôpital La Milétrie, et Faculté de Médecine, CHU, Poitiers, France.,CIC Inserm 1402, CHU, Poitiers, France
| | | | - Susanna Schraen
- Laboratoire d'Hématologie, Centre de Biologie et Pathologie, CHU, Lille, France
| | - Claude Preudhomme
- Univ. Lille, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, JPARC - Centre de Recherche Jean-Pierre AUBERT, Neurosciences et Cancer, Lille, France.,Inserm, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, Factors of Persistence of Leukemic Cells Team, Lille, France.,Laboratoire d'Hématologie, Centre de Biologie et Pathologie, CHU, Lille, France
| | - Bruno Quesnel
- Univ. Lille, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, JPARC - Centre de Recherche Jean-Pierre AUBERT, Neurosciences et Cancer, Lille, France.,Inserm, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, Lille, France.,Service des Maladies du Sang, CHU, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, Factors of Persistence of Leukemic Cells Team, Lille, France
| | - Stéphanie Poulain
- Univ. Lille, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, JPARC - Centre de Recherche Jean-Pierre AUBERT, Neurosciences et Cancer, Lille, France.,Inserm, UMR-S 1172, Factors of Persistence of Leukemic Cells Team, Lille, France.,Institut pour la Recherche sur le Cancer de Lille, Factors of Persistence of Leukemic Cells Team, Lille, France.,Laboratoire d'Hématologie, Centre de Biologie et Pathologie, CHU, Lille, France
| | - Xavier Leleu
- Service d'Hématologie et Thérapie Cellulaire, Hôpital La Milétrie, et Faculté de Médecine, CHU, Poitiers, France.,CIC Inserm 1402, CHU, Poitiers, France
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6
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Solomon LA, Batista CR, DeKoter RP. Lenalidomide modulates gene expression in human ABC-DLBCL cells by regulating IKAROS interaction with an intronic control region of SPIB. Exp Hematol 2017; 56:46-57.e1. [DOI: 10.1016/j.exphem.2017.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 11/16/2022]
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7
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The Transcriptional Network Structure of a Myeloid Cell: A Computational Approach. Int J Genomics 2017; 2017:4858173. [PMID: 29119102 PMCID: PMC5651161 DOI: 10.1155/2017/4858173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 07/28/2017] [Accepted: 08/09/2017] [Indexed: 01/24/2023] Open
Abstract
Understanding the general principles underlying genetic regulation in eukaryotes is an incomplete and challenging endeavor. The lack of experimental information regarding the regulation of the whole set of transcription factors and their targets in different cell types is one of the main reasons to this incompleteness. So far, there is a small set of curated known interactions between transcription factors and their downstream genes. Here, we built a transcription factor network for human monocytic THP-1 myeloid cells based on the experimentally curated FANTOM4 database where nodes are genes and the experimental interactions correspond to links. We present the topological parameters which define the network as well as some global structural features and introduce a relative inuence parameter to quantify the relevance of a transcription factor in the context of induction of a phenotype. Genes like ZHX2, ADNP, or SMAD6 seem to be highly regulated to avoid an avalanche transcription event. We compare these results with those of RegulonDB, a highly curated transcriptional network for the prokaryotic organism E. coli, finding similarities between general hallmarks on both transcriptional programs. We believe that an approach, such as the one shown here, could help to understand the one regulation of transcription in eukaryotic cells.
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8
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Valor LM, Rodríguez-Bayona B, Ramos-Amaya AB, Brieva JA, Campos-Caro A. The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies. PLoS One 2017; 12:e0183264. [PMID: 28817638 PMCID: PMC5560601 DOI: 10.1371/journal.pone.0183264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Plasma cells (PC) represent the heterogeneous final stage of the B cells (BC) differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i) tonsil PC, mainly consisting of early PC; ii) PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts); and, iii) bone marrow CD138+ PC that represent highly mature PC and include the long-lived PC compartment. This transcriptional transition involves subsets of genes related to key processes for PC maturation: the already known protein processing, apoptosis and homeostasis, and of new discovery including histones, macromolecule assembly, zinc-finger transcription factors and neuromodulation. This human PC signature is partially reproduced in vitro and is conserved in mouse. Moreover, the present study identifies genes that define PC subtypes (e.g., proliferation-associated genes for circulating PC and transcriptional-related genes for tonsil and bone marrow PC) and proposes some putative transcriptional regulators of the human PC signatures (e.g., OCT/POU, XBP1/CREB, E2F, among others). Finally, we also identified a restricted imbalance of the present PC transcriptional program in monoclonal gammopathies that correlated with PC malignancy.
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Affiliation(s)
- Luis M. Valor
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Beatriz Rodríguez-Bayona
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Ana B. Ramos-Amaya
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - José A. Brieva
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Antonio Campos-Caro
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
- * E-mail:
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9
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Kim SH, Jang YS. Yersinia enterocolitica Exploits Signal Crosstalk between Complement 5a Receptor and Toll-like Receptor 1/2 and 4 to Avoid the Bacterial Clearance in M cells. Immune Netw 2017; 17:228-236. [PMID: 28860952 PMCID: PMC5577300 DOI: 10.4110/in.2017.17.4.228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022] Open
Abstract
In the intestinal mucosal surface, microfold cells (M cells) are the representative gateway for the uptake of luminal antigens. At the same time, M cells are the primary infection site for pathogens invading mucosal surface for their infection. Although it is well recognized that many mucosal pathogens exploit the M cells for their infection, the mechanism to infect M cells utilized by pathogens is not clearly understood yet. In this study, we found that M cells expressing complement 5a (C5a) receptor (C5aR) also express Toll-like receptor (TLR) 1/2 and TLR4. Infection of Yersinia enterocolitica, an M cell-invading pathogen, synergistically regulated cyclic adenosine monophosphate-dependent protein kinase A (cAMP-PKA) signaling which are involved in signal crosstalk between C5aR and TLRs. In addition, Y. enterocolitica infection into M cells was enhanced by C5a treatment and this enhancement was abrogated by C5a antagonist treatment. Finally, Y. enterocolitica infection into M cells was unsuccessful in C5aR knock-out mice. Collectively, we suggest that exploit the crosstalk between C5aR and TLR signaling is one of infection mechanisms utilized by mucosal pathogens to infect M cells.
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Affiliation(s)
- Sae-Hae Kim
- Department of Molecular Biology and Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju 54896, Korea.,Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 54896, Korea
| | - Yong-Suk Jang
- Department of Molecular Biology and Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju 54896, Korea.,Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju 54896, Korea
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10
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Hunter ZR, Yang G, Xu L, Liu X, Castillo JJ, Treon SP. Genomics, Signaling, and Treatment of Waldenström Macroglobulinemia. J Clin Oncol 2017; 35:994-1001. [PMID: 28294689 DOI: 10.1200/jco.2016.71.0814] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing has revealed recurring somatic mutations in Waldenström macroglobulinemia (WM). Commonly recurring mutations include MYD88 (95% to 97%), CXCR4 (30% to 40%), ARID1A (17%), and CD79B (8% to 15%). Diagnostic discrimination of WM from overlapping B-cell malignancies is aided by MYD88 mutation status. Transcription is affected by MYD88 and CXCR4 mutations and includes overexpression of genes involved in VDJ recombination, CXCR4 pathway signaling, and BCL2 family members. Among patients with MYD88 mutations, those with CXCR4 mutations show transcriptional silencing of tumor suppressors associated with acquisition of mutated MYD88. Deletions involving chromosome 6q are common and include genes that modulate nuclear factor-κB, BCL2, BTK, apoptosis, differentiation, and ARID1B. Non-chromosome 6q genes are also frequently deleted and include LYN, a regulator of B-cell receptor signaling. MYD88 and CXCR4 mutations affect WM disease presentation and treatment outcome. Patients with wild-type MYD88 show lower bone marrow disease burden and serum immunoglobulin M levels but show an increased risk of death. Patients with CXCR4 mutations have higher bone marrow disease burden, and those with nonsense CXCR4 mutations have higher serum immunoglobulin M levels and incidence of symptomatic hyperviscosity. Mutated MYD88 triggers BTK, IRAK1/IRAK4, and HCK growth and survival signaling, whereas CXCR4 mutations promote AKT and extracellular regulated kinase-1/2 signaling and drug resistance in the presence of its ligand CXCL12. Ibrutinib is active in patients with WM and is affected by MYD88 and CXCR4 mutation status. Patients with mutated MYD88 and wild-type CXCR4 mutation status exhibit best responses to ibrutinib. Lower response rates and delayed responses to ibrutinib are associated with mutated CXCR4 in patients with WM. MYD88 and CXCR4 mutation status may be helpful in treatment selection for symptomatic patients. Novel therapeutic approaches under investigation include therapeutics targeting MYD88, CXCR4, and BCL2 signaling.
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Affiliation(s)
- Zachary R Hunter
- All authors: Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute; and Harvard Medical School, Boston, MA
| | - Guang Yang
- All authors: Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute; and Harvard Medical School, Boston, MA
| | - Lian Xu
- All authors: Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute; and Harvard Medical School, Boston, MA
| | - Xia Liu
- All authors: Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute; and Harvard Medical School, Boston, MA
| | - Jorge J Castillo
- All authors: Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute; and Harvard Medical School, Boston, MA
| | - Steven P Treon
- All authors: Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute; and Harvard Medical School, Boston, MA
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11
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Agarwal P, Alzrigat M, Párraga AA, Enroth S, Singh U, Ungerstedt J, Österborg A, Brown PJ, Ma A, Jin J, Nilsson K, Öberg F, Kalushkova A, Jernberg-Wiklund H. Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target. Oncotarget 2017; 7:6809-23. [PMID: 26755663 PMCID: PMC4872750 DOI: 10.18632/oncotarget.6843] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 12/29/2015] [Indexed: 02/02/2023] Open
Abstract
Multiple myeloma (MM) is a malignancy of the antibody-producing plasma cells. MM is a highly heterogeneous disease, which has hampered the identification of a common underlying mechanism for disease establishment as well as the development of targeted therapy. Here we present the first genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in MM patient samples, defining a common set of active H3K4me3-enriched genes and silent genes marked by H3K27me3 (H3K27me3 alone or bivalent) unique to primary MM cells, when compared to normal bone marrow plasma cells. Using this epigenome profile, we found increased silencing of H3K27me3 targets in MM patients at advanced stages of the disease, and the expression pattern of H3K27me3-marked genes correlated with poor patient survival. We also demonstrated that pharmacological inhibition of EZH2 had anti-myeloma effects in both MM cell lines and CD138+ MM patient cells. In addition, EZH2 inhibition decreased the global H3K27 methylation and induced apoptosis. Taken together, these data suggest an important role for the Polycomb repressive complex 2 (PRC2) in MM, and highlights the PRC2 component EZH2 as a potential therapeutic target in MM.
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Affiliation(s)
- Prasoon Agarwal
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mohammad Alzrigat
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Alba Atienza Párraga
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefan Enroth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Umashankar Singh
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, India
| | - Johanna Ungerstedt
- Department of Medicine, Center for Hematology and Regenerative Medicine (HERM), Karolinska Institute Huddinge, Stockholm, Sweden
| | - Anders Österborg
- Department of Oncology-Pathology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Anqi Ma
- Departments of Structural and Chemical Biology, Oncological Sciences, and Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Departments of Structural and Chemical Biology, Oncological Sciences, and Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kenneth Nilsson
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Öberg
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Antonia Kalushkova
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Helena Jernberg-Wiklund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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12
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Takagi Y, Shimada K, Shimada S, Sakamoto A, Naoe T, Nakamura S, Hayakawa F, Tomita A, Kiyoi H. SPIB is a novel prognostic factor in diffuse large B-cell lymphoma that mediates apoptosis via the PI3K-AKT pathway. Cancer Sci 2016; 107:1270-80. [PMID: 27348272 PMCID: PMC5021043 DOI: 10.1111/cas.13001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/14/2016] [Accepted: 06/26/2016] [Indexed: 12/28/2022] Open
Abstract
Although the clinical outcomes of diffuse large B-cell lymphoma (DLBCL) have improved in the immunochemotherapy era, approximately one-third of patients develop intractable disease. To improve clinical outcomes for these patients, it is important to identify those with poor prognosis prior to initial treatment in order to select optimal therapies. Here, we investigated the clinical and biological significance of SPIB, an Ets family transcription factor linked to lymphomagenesis, in DLBCL. We classified 134 DLBCL patients into SPIB negative (n = 108) or SPIB positive (n = 26) groups by immunohistochemical staining. SPIB positive patients had a significantly worse treatment response and poor prognosis compared with SPIB negative patients. Multivariate analysis for patient survival indicated that SPIB expression was an independent poor prognostic factor for both progression free survival (PFS) and overall survival (OS) (PFS, hazard ratio [HR] 2.65, 95% confidence interval [CI] 1.31-5.33, P = 0.006; OS, HR 3.56, 95% CI 1.43-8.91, P = 0.007). Subsequent analyses of the roles of SPIB expression in DLBCL pathogenesis revealed that SPIB expression in lymphoma cells resulted in resistance to the BH3-mimetic ABT-263 and contributed to apoptosis resistance via the PI3K-AKT pathway. The inhibition of AKT phosphorylation re-sensitized SPIB expressing lymphoma cells to ABT-263-induced cell death. Together, our data indicate that SPIB expression is a clinically novel poor prognostic factor in DLBCL that contributes to treatment resistance, at least in part, through an anti-apoptotic mechanism.
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Affiliation(s)
- Yusuke Takagi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuyuki Shimada
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan. .,Institute for Advanced Research, Nagoya University, Nagoya, Japan.
| | - Satoko Shimada
- Department of Pathology and Clinical Laboratories, Nagoya University Hospital, Nagoya, Japan
| | - Akihiko Sakamoto
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoki Naoe
- Department of Hematology, National Hospital Organization, Nagoya Medical Center, Nagoya, Japan
| | - Shigeo Nakamura
- Department of Pathology and Clinical Laboratories, Nagoya University Hospital, Nagoya, Japan
| | - Fumihiko Hayakawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akihiro Tomita
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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13
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Kiba T. Ventromedial hypothalamic lesions downregulate multiple immune signaling pathways in rat pancreatic islets. Neurosci Lett 2015; 610:177-81. [PMID: 26555798 DOI: 10.1016/j.neulet.2015.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 12/17/2022]
Abstract
It was recently reported that ventromedial hypothalamic lesions change the expression of cell proliferation-related genes and metabolism-related genes in rat pancreatic islets. This study has examined how gene families involved in immune responses are regulated in rat pancreatic islets after VMH lesions formation. Total pancreatic islets RNA was extracted, and differences in the gene expression profiles between rats at day 3 after VMH lesioning and sham-VMH-lesioned rats were investigated using DNA microarray and real-time polymerase chain reaction. VMH lesions downregulated multiple immune signaling pathways in rat pancreatic islets. Real-time polymerase chain reaction also confirmed that gene expressions of RT1 class II, locus Bb (RT1-Bb) was up-regulated and Spi-B transcription factor (Spib) was downregulated at day 3 after the VMH lesions. Ventromedial hypothalamic lesions may change the expression of multiple immune response genes in rat pancreatic islets.
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Affiliation(s)
- Takayoshi Kiba
- Division of Modern Medical Technology, Institute for Clinical Research, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Kure 737-0023, Japan.
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14
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The cellular origin and malignant transformation of Waldenström macroglobulinemia. Blood 2015; 125:2370-80. [DOI: 10.1182/blood-2014-09-602565] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/27/2015] [Indexed: 01/14/2023] Open
Abstract
Key Points
Benign (ie, IgM MGUS and smoldering WM) clonal B cells already harbor the phenotypic and molecular signatures of the malignant WM clone. Multistep transformation from benign (ie, IgM MGUS and smoldering WM) to malignant WM may require specific copy number abnormalities.
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