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Franco Acevedo A, Mack JJ, Valenzuela NM. The transcriptional repressor BCL6 regulates CXCR3 chemokine and HLA II expression in endothelial cells. Am J Transplant 2024:S1600-6135(24)00449-0. [PMID: 39074669 DOI: 10.1016/j.ajt.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/08/2024] [Accepted: 07/23/2024] [Indexed: 07/31/2024]
Abstract
IFNγ induces an endothelial pro-immunogenic phenotype through the JAK/STAT1 pathway, which can shape the activation of alloreactive leukocytes in transplant rejection. In immune cells, the DNA binding protein BCL6 controls transcription of inflammatory genes. This study tested if BCL6 modulates IFNγ-induced gene expression in endothelial cells (EC). In vitro, BCL6 was IFNγ-inducible in primary human endothelium, along with CXCR3 chemokines and HLA. BCL6 was also increased in human cardiac transplants during acute rejection, as were HLA II and CXCL9. Knockdown of BCL6 augmented, while overexpression and BTB domain inhibitors (BCL6-BTBi) suppressed, HLA II and CXCR3 chemokine expression but not HLA I. Further, BCL6 had a greater effect on HLA-DR and DP, but was less involved in regulating HLA-DQ expression. The effect correlated with BCL6 binding motifs in or near affected genes. The BCL6 DNA recognition sequence was highly similar to that of STAT1, and BTBi reduced STAT1's transcriptional activity in vitro. Our results show for the first time that BCL6 selectively controls IFNγ-induced endothelial gene expression, advancing our understanding of the endogenous mechanisms regulating donor immunogenicity.
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Affiliation(s)
- Adriana Franco Acevedo
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, USA
| | - Julia J Mack
- Department of Cardiology, University of California, Los Angeles, USA
| | - Nicole M Valenzuela
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, USA.
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2
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Benaglio P, Zhu H, Okino ML, Yan J, Elgamal R, Nariai N, Beebe E, Korgaonkar K, Qiu Y, Donovan MK, Chiou J, Wang G, Newsome J, Kaur J, Miller M, Preissl S, Corban S, Aylward A, Taipale J, Ren B, Frazer KA, Sander M, Gaulton KJ. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines. CELL GENOMICS 2022; 2:100214. [PMID: 36778047 PMCID: PMC9903835 DOI: 10.1016/j.xgen.2022.100214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/17/2022] [Accepted: 10/15/2022] [Indexed: 11/13/2022]
Abstract
We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta cell survival in response to proinflammatory cytokines. We mapped 38,931 cytokine-responsive candidate cis-regulatory elements (cCREs) in beta cells using ATAC-seq and snATAC-seq and linked them to target genes using co-accessibility and HiChIP. Using a genome-wide CRISPR screen in EndoC-βH1 cells, we identified 867 genes affecting cytokine-induced survival, and genes promoting survival and up-regulated in cytokines were enriched at T1D risk loci. Using SNP-SELEX, we identified 2,229 variants in cytokine-responsive cCREs altering transcription factor (TF) binding, and variants altering binding of TFs regulating stress, inflammation, and apoptosis were enriched for T1D risk. At the 16p13 locus, a fine-mapped T1D variant altering TF binding in a cytokine-induced cCRE interacted with SOCS1, which promoted survival in cytokine exposure. Our findings reveal processes and genes acting in beta cells during inflammation that modulate T1D risk.
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Affiliation(s)
- Paola Benaglio
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Han Zhu
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mei-Lin Okino
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jian Yan
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Ruth Elgamal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Naoki Nariai
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elisha Beebe
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Katha Korgaonkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Joshua Chiou
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Gaowei Wang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jacklyn Newsome
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jaspreet Kaur
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Sierra Corban
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Aylward
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Kelly A. Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Maike Sander
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats. Cells 2020; 9:cells9061435. [PMID: 32527043 PMCID: PMC7348746 DOI: 10.3390/cells9061435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Intrauterine growth retardation (IUGR), which induces epigenetic modifications and permanent changes in gene expression, has been associated with the development of type 2 diabetes. Using a rat model of IUGR, we performed ChIP-Seq to identify and map genome-wide histone modifications and gene dysregulation in islets from 2- and 10-week rats. IUGR induced significant changes in the enrichment of H3K4me3, H3K27me3, and H3K27Ac marks in both 2-wk and 10-wk islets, which were correlated with expression changes of multiple genes critical for islet function in IUGR islets. ChIP-Seq analysis showed that IUGR-induced histone mark changes were enriched at critical transcription factor binding motifs, such as C/EBPs, Ets1, Bcl6, Thrb, Ebf1, Sox9, and Mitf. These transcription factors were also identified as top upstream regulators in our previously published transcriptome study. In addition, our ChIP-seq data revealed more than 1000 potential bivalent genes as identified by enrichment of both H3K4me3 and H3K27me3. The poised state of many potential bivalent genes was altered by IUGR, particularly Acod1, Fgf21, Serpina11, Cdh16, Lrrc27, and Lrrc66, key islet genes. Collectively, our findings suggest alterations of histone modification in key transcription factors and genes that may contribute to long-term gene dysregulation and an abnormal islet phenotype in IUGR rats.
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Muraki M. Sensitization to cell death induced by soluble Fas ligand and agonistic antibodies with exogenous agents: A review. AIMS MEDICAL SCIENCE 2020. [DOI: 10.3934/medsci.2020011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Lin CT, Hsieh YT, Yang YJ, Chen SH, Wu CH, Hwang LH. B-Cell Lymphoma 6 (BCL6) Is a Host Restriction Factor That Can Suppress HBV Gene Expression and Modulate Immune Responses. Front Microbiol 2019; 9:3253. [PMID: 30687256 PMCID: PMC6335256 DOI: 10.3389/fmicb.2018.03253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/14/2018] [Indexed: 01/12/2023] Open
Abstract
Hepatitis B virus (HBV) infection causes acute and chronic liver inflammation. Recent studies have demonstrated that some viral antigens can suppress host innate and adaptive immunity, and thus lead to HBV liver persistency. However, the cellular factors that can help host cells to clear HBV during acute infection remain largely unknown. Here, we used HBV-cleared and HBV-persistent mouse models to seek for cellular factors that might participate in HBV clearance. HBV replicon DNA was delivered into the mouse liver by hydrodynamic injection. RNA-Seq analysis was conducted to identify immune-related genes that were differentially expressed in HBV-persistent and HBV-cleared mouse models. A cellular factor, B cell lymphoma 6 (BCL6), was found to be significantly upregulated in the liver of HBV-cleared mice upon HBV clearance. Co-expression of BCL6 and a persistent HBV clone rendered the clone largely cleared, implicating an important role of BCL6 in controlling HBV clearance. Mechanistic studies demonstrated that BCL6 functioned as a repressor, binding to and suppressing the activities of the four HBV promoters. Correspondingly, BCL6 expression significantly reduced the levels of HBV viral RNA, DNA, and proteins. BCL6 expression could be stimulated by inflammatory cytokines such as TNF-α; the BCL6 in turn synergized TNF-α signaling to produce large amounts of CXCL9 and CXCL10, leading to increased infiltrating immune cells and elevated cytokine levels in the liver. Thus, positive feedback loops on BCL6 expression and immune responses could be produced. Together, our results demonstrate that BCL6 is a novel host restriction factor that exerts both anti-HBV and immunomodulatory activities. Induction of BCL6 in the liver may ultimately assist host immune responses to clear HBV.
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Affiliation(s)
- Chun-Ta Lin
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.,Biomedical Industry Ph.D. Program, National Yang-Ming University, Taipei, Taiwan
| | - Yue-Ting Hsieh
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Yeng-Jey Yang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Hui Chen
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Cheng-Hsuan Wu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Lih-Hwa Hwang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
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High concentrations of glucose suppress etoposide-induced cell death of B-cell lymphoma through BCL-6. Biochem Biophys Res Commun 2014; 450:227-33. [DOI: 10.1016/j.bbrc.2014.05.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/21/2014] [Indexed: 11/18/2022]
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Kulkarni RM, Kutcher LW, Stuart WD, Carson DJ, Leonis MA, Waltz SE. Ron receptor-dependent gene regulation in a mouse model of endotoxin-induced acute liver failure. Hepatobiliary Pancreat Dis Int 2012; 11:383-92. [PMID: 22893465 PMCID: PMC4102423 DOI: 10.1016/s1499-3872(12)60196-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Prior experimentation has shown that loss of the tyrosine kinase (TK) signaling domain of the Ron receptor leads to marked hepatocyte protection in a model of lipopolysaccharide-induced acute liver failure (ALF) in D-galactosamine (GalN)-sensitized mice. The aim of this study was to identify the role of Ron in the regulation of hepatic gene expression. METHODS Microarray analyses were performed on liver RNA isolated sequentially from wild-type (WT) and TK-/- mice during the progression of ALF. Gene array data were validated using Western and immunohistochemistry analyses as well as with ex vivo culture systems. RESULTS At baseline, 101 genes were differentially expressed between WT and TK-/- livers, which regulate processes involved in hypoxia, proliferation, apoptosis and metabolism. One hour after ALF induction, WT livers exhibited increased cytokine expression compared to TK-/- livers, and after 4 hours, an induction of suppressor of cytokine signaling (SOCS) genes as well as JAK-STAT pathway activation were prominent in TK-/- livers compared to controls. CONCLUSION Our studies suggest a novel hepato-protective mechanism in Ron TK-/- mice wherein increased and sustained SOCS production and JAK-STAT activation in the hepatocyte may inhibit the destructive proinflammatory milieu and promote survival factors which blunt hepatic death and the ensuing development of ALF.
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Affiliation(s)
- Rishikesh M. Kulkarni
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, OH 45267-0521
| | - Louis W. Kutcher
- Department of Biology, University of Cincinnati, Cincinnati, OH 45267-0521
| | - William D. Stuart
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, OH 45267-0521
| | - Daniel J. Carson
- Department of Biology, University of Cincinnati, Cincinnati, OH 45267-0521
| | - Mike A. Leonis
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Susan E. Waltz
- Department of Cancer and Cell Biology, University of Cincinnati, Cincinnati, OH 45267-0521,Departments of Research, Shriner’s Hospital for Children, Cincinnati, OH 45267-0521,Cincinnati Veterans Affairs Medical Center, Cincinnati, OH 45267-0521,Corresponding Author: Susan E. Waltz, Ph.D., Department of Cancer and Cell Biology, 3125 Eden Ave., University of Cincinnati College of Medicine, Cincinnati, OH 45267-0521, Telephone: (513) 558-8675,
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Bonner SM, Pietropaolo SL, Fan Y, Chang Y, Sethupathy P, Morran MP, Beems M, Giannoukakis N, Trucco G, Palumbo MO, Solimena M, Pugliese A, Polychronakos C, Trucco M, Pietropaolo M. Sequence variation in promoter of Ica1 gene, which encodes protein implicated in type 1 diabetes, causes transcription factor autoimmune regulator (AIRE) to increase its binding and down-regulate expression. J Biol Chem 2012; 287:17882-17893. [PMID: 22447927 PMCID: PMC3366781 DOI: 10.1074/jbc.m111.319020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 03/15/2012] [Indexed: 12/22/2022] Open
Abstract
ICA69 (islet cell autoantigen 69 kDa) is a protein implicated in type 1 diabetes mellitus in both the non-obese diabetic (NOD) mouse model and humans. ICA69 is encoded by the Ica1 gene on mouse chromosome 6 A1-A2. We previously reported reduced ICA69 expression in the thymus of NOD mice compared with thymus of several non-diabetic mouse strains. We propose that reduced thymic ICA69 expression could result from variations in transcriptional regulation of the gene and that polymorphisms within the Ica1 core promoter may partially determine this transcriptional variability. We characterized the functional promoter of Ica1 in NOD mice and compared it with the corresponding portions of Ica1 in non-diabetic C57BL/6 mice. Luciferase reporter constructs demonstrated that the NOD Ica1 promoter region exhibited markedly reduced luciferase expression in transiently transfected medullary thymus epithelial (mTEC(+)) and B-cell (M12)-derived cell lines. However, in a non-diabetic strain, C57BL/6, the Ica1 promoter region was transcriptionally active when transiently transfected into the same cell lines. We concomitantly identified five single nucleotide polymorphisms within the NOD Ica1 promoter. One of these single nucleotide polymorphisms increases the binding affinity for the transcription factor AIRE (autoimmune regulator), which is highly expressed in thymic epithelial cells, where it is known to play a key role regulating self-antigen expression. We conclude that polymorphisms within the NOD Ica1 core promoter may determine AIRE-mediated down-regulation of ICA69 expression in medullary thymic epithelial cells, thus providing a novel mechanistic explanation for the loss of immunologic tolerance to this self-antigen in autoimmunity.
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Affiliation(s)
- Samantha M Bonner
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Susan L Pietropaolo
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Yong Fan
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Yigang Chang
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Michael P Morran
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Megan Beems
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Nick Giannoukakis
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224; Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - Giuliana Trucco
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - Michael O Palumbo
- Endocrine Genetics Laboratory, Montreal Children Hospital-Research Institute, McGill University Health Center, Montreal, Quebec H3H 1P3, Canada
| | - Michele Solimena
- Department of Molecular Diabetology, Paul Langerhans Institute Dresden, Carl Gustav Carus School of Medicine, Dresden University of Technology, 01307 Dresden, Germany
| | - Alberto Pugliese
- Immunogenetics Program, Diabetes Research Institute, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Constantin Polychronakos
- Endocrine Genetics Laboratory, Montreal Children Hospital-Research Institute, McGill University Health Center, Montreal, Quebec H3H 1P3, Canada
| | - Massimo Trucco
- Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224
| | - Massimo Pietropaolo
- Laboratory of Immunogenetics, Brehm Center for Diabetes Research, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48105.
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