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Sartoris S, Del Pozzo G. Exploring the HLA complex in autoimmunity: From the risk haplotypes to the modulation of expression. Clin Immunol 2024; 265:110266. [PMID: 38851519 DOI: 10.1016/j.clim.2024.110266] [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: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
The genes mapping at the HLA region show high density, strong linkage disequilibrium and high polymorphism, which affect the association of HLA class I and class II genes with autoimmunity. We focused on the HLA haplotypes, genomic structures consisting of an array of specific alleles showing some degrees of genetic association with different autoimmune disorders. GWASs in many pathologies have identified variants in either the coding loci or the flanking regulatory regions, both in linkage disequilibrium in haplotypes, that are frequently associated with increased risk and may influence gene expression. We discuss the relevance of the HLA gene expression because the level of surface heterodimers determines the number of complexes presenting self-antigen and, thus, the strength of pathogenic autoreactive T cells immune response.
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Affiliation(s)
- Silvia Sartoris
- Dept. of Medicine, Section of Immunology University of Verona School of Medicine, Verona, Italy
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso" National Research Council (CNR), Naples, Italy.
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2
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Li YR, Zhou Y, Yu J, Kim YJ, Li M, Lee D, Zhou K, Chen Y, Zhu Y, Wang YC, Li Z, Yu Y, Dunn ZS, Guo W, Cen X, Husman T, Bajpai A, Kramer A, Wilson M, Fang Y, Huang J, Li S, Zhou Y, Zhang Y, Hahn Z, Zhu E, Ma F, Pan C, Lusis AJ, Zhou JJ, Seet CS, Kohn DB, Wang P, Zhou XJ, Pellegrini M, Puliafito BR, Larson SM, Yang L. Generation of allogeneic CAR-NKT cells from hematopoietic stem and progenitor cells using a clinically guided culture method. Nat Biotechnol 2024:10.1038/s41587-024-02226-y. [PMID: 38744947 DOI: 10.1038/s41587-024-02226-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/28/2024] [Indexed: 05/16/2024]
Abstract
Cancer immunotherapy with autologous chimeric antigen receptor (CAR) T cells faces challenges in manufacturing and patient selection that could be avoided by using 'off-the-shelf' products, such as allogeneic CAR natural killer T (AlloCAR-NKT) cells. Previously, we reported a system for differentiating human hematopoietic stem and progenitor cells into AlloCAR-NKT cells, but the use of three-dimensional culture and xenogeneic feeders precluded its clinical application. Here we describe a clinically guided method to differentiate and expand IL-15-enhanced AlloCAR-NKT cells with high yield and purity. We generated AlloCAR-NKT cells targeting seven cancers and, in a multiple myeloma model, demonstrated their antitumor efficacy, expansion and persistence. The cells also selectively depleted immunosuppressive cells in the tumor microenviroment and antagonized tumor immune evasion via triple targeting of CAR, TCR and NK receptors. They exhibited a stable hypoimmunogenic phenotype associated with epigenetic and signaling regulation and did not induce detectable graft versus host disease or cytokine release syndrome. These properties of AlloCAR-NKT cells support their potential for clinical translation.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yang Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jiaji Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yu Jeong Kim
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Miao Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Derek Lee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kuangyi Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuning Chen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yichen Zhu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yu-Chen Wang
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhe Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yanqi Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zachary Spencer Dunn
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA
| | - Wenbin Guo
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xinjian Cen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tiffany Husman
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aarushi Bajpai
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam Kramer
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Matthew Wilson
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ying Fang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jie Huang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shuo Li
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yonggang Zhou
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuchong Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zoe Hahn
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Enbo Zhu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Feiyang Ma
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Calvin Pan
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aldons J Lusis
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, USA
- Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jin J Zhou
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher S Seet
- Eli and Edythe Broad Centre of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medicine, Division of Hematology/Oncology, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Donald B Kohn
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Centre of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pediatrics, Division of Hematology/Oncology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Pin Wang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA
| | - Xianghong Jasmine Zhou
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences-The Collaboratory, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin R Puliafito
- Department of Hematology and Oncology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah M Larson
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Internal Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lili Yang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Centre of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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3
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Skok Gibbs C, Mahmood O, Bonneau R, Cho K. PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization. Genome Biol 2024; 25:88. [PMID: 38589899 PMCID: PMC11003171 DOI: 10.1186/s13059-024-03226-6] [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: 03/30/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.
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Affiliation(s)
| | - Omar Mahmood
- Center for Data Science, New York University, New York, NY, 10011, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, 10011, USA
- Prescient Design, Genentech, New York, NY, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kyunghyun Cho
- Center for Data Science, New York University, New York, NY, 10011, USA.
- Prescient Design, Genentech, New York, NY, 10010, USA.
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4
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Jafari N, Khajenabi F, Masumi N, Abediankenari S, Ranjbaran H. Evaluation of HLA-DR and HLA-DQ expression in gastric cancer tissues. J Cancer Res Ther 2024; 20:204-210. [PMID: 38554322 DOI: 10.4103/jcrt.jcrt_144_22] [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: 01/19/2022] [Accepted: 09/15/2022] [Indexed: 04/01/2024]
Abstract
BACKGROUND AND OBJECTIVES Despite recent advances in understanding the gastric cancer (GC) biology, the precise molecular mechanism of gastric carcinogenesis and role of deregulated immune responses in GC progression are still not well understood. In this study, mRNA levels of human leukocyte antigen (HLA)-DRA and -DQA1 were assessed in GC patients to find a potential association between expression of these HLA-II molecules and gastric carcinogenesis. METHODS Using quantitative real-time (qRT)-PCR, mRNA levels of HLA-DRA and -DQA1 were assessed in 20 pairs of matched GC and normal tissues. RESULTS Our results showed that overall mRNA level of HLA-DRA was decreased in the tumor samples relative to control tissues (median fold change [FC] = 0.693; P = 0.445). Overall HLA-DQA1 level was increased in the tumor samples relative to control tissues (median FC = 1.659; P = 0.5117). However, the mentioned data were not statistically significant. Meanwhile, using a ≥ 2.5 FC as the cutoff to determine upregulation or downregulation, 35% of patients showed a downregulated expression of HLA-DRA, while 10% of those showed upregulation in HLA-DRA expression. Upregulation and downregulation of HLA-DQA1 expression were detected, respectively, in 35% and 25% of samples. A strong positive correlation was determined between HLA-DRA and HLA-DQA1 levels in tumor tissues (r = 0.7298; P = 0.0003). CONCLUSION The results reported here along with future studies can be useful to understand the interplay between immune system and GC, therefore, may be helpful to design an effective immune-based therapy.
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Affiliation(s)
- Narjes Jafari
- Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Khajenabi
- Department of Medical Laboratory Sciences, Khatam Al-Anbia Hospital, Behshahr, Iran
| | - Nastaran Masumi
- Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hossein Ranjbaran
- Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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5
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The Role of Dynamic DNA Methylation in Liver Transplant Rejection in Children. Transplant Direct 2022; 8:e1394. [PMID: 36259078 PMCID: PMC9575761 DOI: 10.1097/txd.0000000000001394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/14/2022] [Indexed: 11/04/2022] Open
Abstract
Transcriptional regulation of liver transplant (LT) rejection may reveal novel predictive and therapeutic targets. The purpose of this article is to test the role of differential DNA methylation in children with biopsy-proven acute cellular rejection after LT.
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Meyer S, Handke D, Mueller A, Biehl K, Kreuz M, Bukur J, Koehl U, Lazaridou MF, Berneburg M, Steven A, Massa C, Seliger B. Distinct Molecular Mechanisms of Altered HLA Class II Expression in Malignant Melanoma. Cancers (Basel) 2021; 13:cancers13153907. [PMID: 34359808 PMCID: PMC8345549 DOI: 10.3390/cancers13153907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/29/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The human leukocyte antigen (HLA) class II molecules are constitutively expressed in some melanoma, but the underlying molecular mechanisms have not yet been characterized. METHODS The expression of HLA class II antigen processing machinery (APM) components was determined in melanoma samples by qPCR, Western blot, flow cytometry and immunohistochemistry. Immunohistochemical and TCGA datasets were used for correlation of HLA class II expression to tumor grading, T-cell infiltration and patients' survival. RESULTS The heterogeneous HLA class II expression in melanoma samples allowed us to characterize four distinct phenotypes. Phenotype I totally lacks constitutive HLA class II surface expression, which is inducible by interferon-gamma (IFN-γ); phenotype II expresses low basal surface HLA class II that is further upregulated by IFN-γ; phenotype III lacks constitutive and IFN-γ controlled HLA class II expression, but could be induced by epigenetic drugs; and in phenotype IV, lack of HLA class II expression is not recovered by any drug tested. High levels of HLA class II APM component expression were associated with an increased intra-tumoral CD4+ T-cell density and increased patients' survival. CONCLUSIONS The heterogeneous basal expression of HLA class II antigens and/or APM components in melanoma cells is caused by distinct molecular mechanisms and has clinical relevance.
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Affiliation(s)
- Stefanie Meyer
- Department of Dermatology, University Hospital of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany; (S.M.); (M.B.)
| | - Diana Handke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
| | - Katharina Biehl
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
| | - Markus Kreuz
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany; (M.K.); (U.K.)
| | - Jürgen Bukur
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
| | - Ulrike Koehl
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany; (M.K.); (U.K.)
| | - Maria-Filothei Lazaridou
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
| | - Mark Berneburg
- Department of Dermatology, University Hospital of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany; (S.M.); (M.B.)
| | - André Steven
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle (Saale), Germany; (D.H.); (A.M.); (K.B.); (J.B.); (M.-F.L.); (A.S.); (C.M.)
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany; (M.K.); (U.K.)
- Correspondence: ; Tel.: +49-(0)-345-557-4054
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7
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Roerden M, Märklin M, Salih HR, Bethge WA, Klein R, Rammensee HG, Nelde A, Walz JS. Expression levels of HLA-DR in acute myeloid leukemia: implications for antigenicity and clinical outcome. Leuk Lymphoma 2021; 62:1907-1919. [PMID: 33648413 DOI: 10.1080/10428194.2021.1885659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Low human leukocyte antigen (HLA)-DR expression might compromise CD4+ T-cell-mediated anti-tumor immunity. Its immunological and clinical significance however remain undefined in non-promyelocytic acute myeloid leukemia (AML). Taking advantage of mass spectrometry-based immunopeptidome analysis of primary AML samples (n = 31), we studied the implications of low HLA-DR expression for antigen presentation and analyzed its association with disease characteristics and survival within a cohort of 399 AML patients. Remarkably, overall HLA-DR/DQ immunopeptidome diversity was preserved in AML with low HLA-DR expression (HLA-DRlow AML) and was associated with a shift in HLA-DR/DQ allotype abundances (HLA-DQ to HLA-DR/DQ ligand ratio 0.36 vs 0.19 in HLA-DRlow and HLA-DRhigh patients, respectively). Consistent with unimpaired antigenicity, survival was similar in HLA-DRlow and HLA-DRhigh patients. Demonstrating for the first time that overall HLA-DR/DQ antigen presentation is preserved in HLA-DRlow AML, our findings provide a rationale for the non-inferior outcome observed in HLA-DRlow AML patients.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Wolfgang A Bethge
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Annika Nelde
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
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8
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Epigenetic modification and therapeutic targets of diabetes mellitus. Biosci Rep 2020; 40:226148. [PMID: 32815547 PMCID: PMC7494983 DOI: 10.1042/bsr20202160] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022] Open
Abstract
The prevalence of diabetes and its related complications are increasing significantly globally. Collected evidence suggested that several genetic and environmental factors contribute to diabetes mellitus. Associated complications such as retinopathy, neuropathy, nephropathy and other cardiovascular complications are a direct result of diabetes. Epigenetic factors include deoxyribonucleic acid (DNA) methylation and histone post-translational modifications. These factors are directly related with pathological factors such as oxidative stress, generation of inflammatory mediators and hyperglycemia. These result in altered gene expression and targets cells in the pathology of diabetes mellitus without specific changes in a DNA sequence. Environmental factors and malnutrition are equally responsible for epigenetic states. Accumulated evidence suggested that environmental stimuli alter the gene expression that result in epigenetic changes in chromatin. Recent studies proposed that epigenetics may include the occurrence of ‘metabolic memory’ found in animal studies. Further study into epigenetic mechanism might give us new vision into the pathogenesis of diabetes mellitus and related complication thus leading to the discovery of new therapeutic targets. In this review, we discuss the possible epigenetic changes and mechanism that happen in diabetes mellitus type 1 and type 2 separately. We highlight the important epigenetic and non-epigenetic therapeutic targets involved in the management of diabetes and associated complications.
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Yamagata K, Nakayamada S, Tanaka Y. Critical roles of super-enhancers in the pathogenesis of autoimmune diseases. Inflamm Regen 2020; 40:16. [PMID: 32922569 PMCID: PMC7398324 DOI: 10.1186/s41232-020-00124-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
The super-enhancer (SE) is a cluster of enhancers involved in cell differentiation via enhanced gene expression that determines cell identity. Meanwhile, genome-wide association studies (GWASs) have reported the presence of gene clusters containing single nucleotide polymorphisms (SNPs) susceptible to various diseases. According to cell types, these disease-susceptible SNPs are frequently detected in activated SE domains. However, the roles of SEs in the pathogenesis of various diseases remain unclear. This review first presents various functions of enhancer RNAs (eRNAs) transcribed from SEs. Next, it describes how SNPs and eRNAs are involved in the pathology of each autoimmune disease, with a focus on typical diseases such as rheumatoid arthritis, systemic lupus erythematosus, and multiple sclerosis. This review aims to describe the roles of SEs in the pathogenesis of autoimmune diseases through multiple interactions of these factors, as well as a future outlook on this issue.
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Affiliation(s)
- Kaoru Yamagata
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahata-nishi-ku, Kitakyushu, 807-8555 Japan
| | - Shingo Nakayamada
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahata-nishi-ku, Kitakyushu, 807-8555 Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahata-nishi-ku, Kitakyushu, 807-8555 Japan
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10
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Cerna M. Epigenetic Regulation in Etiology of Type 1 Diabetes Mellitus. Int J Mol Sci 2019; 21:ijms21010036. [PMID: 31861649 PMCID: PMC6981658 DOI: 10.3390/ijms21010036] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
Type 1 diabetes mellitus (T1DM) is caused by an autoimmune destruction of the pancreatic β-cells, a process in which autoreactive T cells play a pivotal role, and it is characterized by islet autoantibodies. Consequent hyperglycemia is requiring lifelong insulin replacement therapy. T1DM is caused by the interaction of multiple environmental and genetic factors. The integrations of environments and genes occur via epigenetic regulations of the genome, which allow adaptation of organism to changing life conditions by alternation of gene expression. T1DM has increased several-fold over the past half century. Such a short time indicates involvement of environment factors and excludes genetic changes. This review summarizes the most current knowledge of epigenetic changes in that process leading to autoimmune diabetes mellitus.
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Affiliation(s)
- Marie Cerna
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 87, 100 00 Prague 10, Czech Republic
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11
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Zhou W, Triche TJ, Laird PW, Shen H. SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Res 2019; 46:e123. [PMID: 30085201 PMCID: PMC6237738 DOI: 10.1093/nar/gky691] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/20/2018] [Indexed: 12/18/2022] Open
Abstract
We report a new class of artifacts in DNA methylation measurements from Illumina HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed hybridization to target DNA, often due to germline or somatic deletions and manifest as incorrectly reported intermediate methylation. The artifacts often survive existing preprocessing pipelines, masquerade as epigenetic alterations and can confound discoveries in epigenome-wide association studies and studies of methylation-quantitative trait loci. We implement a solution, P-value with out-of-band (OOB) array hybridization (pOOBAH), in the R package SeSAMe. Our method effectively masks deleted and hyperpolymorphic regions, reducing or eliminating spurious reports of epigenetic silencing at oft-deleted tumor suppressor genes such as CDKN2A and RB1 in cases with somatic deletions. Furthermore, our method substantially decreases technical variation whilst retaining biological variation, both within and across HM450 and EPIC platform measurements. SeSAMe provides a light-weight, modular DNA methylation data analysis suite, with a performant implementation suitable for efficient analysis of thousands of samples.
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Affiliation(s)
- Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503 USA
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503 USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503 USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503 USA
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12
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Laugier L, Frade AF, Ferreira FM, Baron MA, Teixeira PC, Cabantous S, Ferreira LRP, Louis L, Rigaud VOC, Gaiotto FA, Bacal F, Pomerantzeff P, Bocchi E, Kalil J, Santos RHB, Cunha-Neto E, Chevillard C. Whole-Genome Cardiac DNA Methylation Fingerprint and Gene Expression Analysis Provide New Insights in the Pathogenesis of Chronic Chagas Disease Cardiomyopathy. Clin Infect Dis 2019; 65:1103-1111. [PMID: 28575239 PMCID: PMC5849099 DOI: 10.1093/cid/cix506] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/25/2017] [Indexed: 02/06/2023] Open
Abstract
Background Chagas disease, caused by the protozoan Trypanosoma cruzi, is endemic in Latin America and affects 10 million people worldwide. Approximately 12000 deaths attributable to Chagas disease occur annually due to chronic Chagas disease cardiomyopathy (CCC), an inflammatory cardiomyopathy presenting with heart failure and arrythmia; 30% of infected subjects develop CCC years after infection. Genetic mechanisms play a role in differential progression to CCC, but little is known about the role of epigenetic modifications in pathological gene expression patterns in CCC patients’ myocardium. DNA methylation is the most common modification in the mammalian genome. Methods We investigated the impact of genome-wide cardiac DNA methylation on global gene expression in myocardial samples from end-stage CCC patients, compared to control samples from organ donors. Results In total, 4720 genes were differentially methylated between CCC patients and controls, of which 399 were also differentially expressed. Several of them were related to heart function or to the immune response and had methylation sites in their promoter region. Reporter gene and in silico transcription factor binding analyses indicated promoter methylation modified expression of key genes. Among those, we found potassium channel genes KCNA4 and KCNIP4, involved in electrical conduction and arrythmia, SMOC2, involved in matrix remodeling, as well as enkephalin and RUNX3, potentially involved in the increased T-helper 1 cytokine-mediated inflammatory damage in heart. Conclusions Results support that DNA methylation plays a role in the regulation of expression of pathogenically relevant genes in CCC myocardium, and identify novel potential disease pathways and therapeutic targets in CCC.
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Affiliation(s)
- Laurie Laugier
- Aix Marseille Université, Génétique et Immunologie des Maladies Parasitaires, Unité Mixte de Recherche S906, INSERM U906, Marseille, France
| | - Amanda Farage Frade
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT.,Department of Bioengineering, Brazil University, and
| | - Frederico Moraes Ferreira
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT.,Health Sciences, University of Santo Amaro, São Paulo, Brazil
| | - Monique Andrade Baron
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT
| | - Priscila Camillo Teixeira
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT
| | - Sandrine Cabantous
- Aix Marseille Université, Génétique et Immunologie des Maladies Parasitaires, Unité Mixte de Recherche S906, INSERM U906, Marseille, France
| | - Ludmila Rodrigues Pinto Ferreira
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT.,Health Sciences, University of Santo Amaro, São Paulo, Brazil
| | - Laurence Louis
- Aix Marseille Université, Génétique médicale et génomique fonctionnelle (Plateforme Génomique et Transcriptomique), Unité Mixte de Recherche S910, INSERM U910, Marseille, France; Divisions of
| | - Vagner Oliveira Carvalho Rigaud
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT
| | | | | | | | - Edimar Bocchi
- Heart Failure Unit, Heart Institute, University of São Paulo School of Medicine, and
| | - Jorge Kalil
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT.,Division of Clinical Immunology and Allergy, University of São Paulo School of Medicine, Brazil
| | | | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute, University of São Paulo School of Medicine.,Institute for Investigation in Immunology (iii), INCT.,Division of Clinical Immunology and Allergy, University of São Paulo School of Medicine, Brazil
| | - Christophe Chevillard
- Aix Marseille Université, Génétique et Immunologie des Maladies Parasitaires, Unité Mixte de Recherche S906, INSERM U906, Marseille, France
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13
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DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis. Nat Commun 2018; 9:2397. [PMID: 29921915 PMCID: PMC6008330 DOI: 10.1038/s41467-018-04732-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
The human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-sensitive regulatory properties in vitro. Causal inference and Mendelian randomization provide evidence that HLA variants mediate risk for MS via changes in the HLA-DRB1 DMR that modify HLA-DRB1 expression. Meta-analysis of 14,259 cases and 171,347 controls confirms that these variants confer risk from DRB1*15:01 and also identifies a protective variant (rs9267649, p < 3.32 × 10-8, odds ratio = 0.86) after conditioning for all MS-associated variants in the region. rs9267649 is associated with increased DNA methylation at the HLA-DRB1 DMR and reduced expression of HLA-DRB1, suggesting a modulation of the DRB1*15:01 effect. Our integrative approach provides insights into the molecular mechanisms of MS susceptibility and suggests putative therapeutic strategies targeting a methylation-mediated regulation of the major risk gene.
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14
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Lee KH, Song Y, O'Sullivan M, Pereira G, Loh R, Zhang GB. The Implications of DNA Methylation on Food Allergy. Int Arch Allergy Immunol 2017; 173:183-192. [PMID: 28848217 DOI: 10.1159/000479513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Food allergy is a major clinical and public health concern worldwide. The risk factors are well defined, however, the mechanisms by which they affect immune development remain largely unknown, and unfortunately the effective treatment or prevention of food allergy is still being researched. Recent studies show that the genes that are critical for the development of food allergy are regulated through DNA methylation. Environmental factors can affect host DNA methylation status and subsequently predispose people to food allergy. DNA methylation is therefore an important mediator of gene-environment interactions in food allergy and key to understanding the mechanisms underlying the allergic development. Indeed, the modification and identification of the methylation levels of specific genetic loci have gained increasing attention for therapeutic and diagnostic application in combating food allergy. In this review, we summarize and discuss the recent developments of DNA methylation in food allergy, including the pathogenesis, therapy, and diagnosis. This review will also summarize and discuss the environmental factors that affect DNA methylation levels in food allergy.
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Affiliation(s)
- Khui Hung Lee
- School of Public Health, Curtin University of Technology, Bentley WA, Australia
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15
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Transancestral mapping and genetic load in systemic lupus erythematosus. Nat Commun 2017; 8:16021. [PMID: 28714469 PMCID: PMC5520018 DOI: 10.1038/ncomms16021] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (∼50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 × 10−8), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE. Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong ethnic and gender bias. In a transancestral genetic association study, Langefeld et al. identify 24 novel regions associated with risk to lupus and propose a cumulative hits hypothesis for loci conferring risk to SLE.
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16
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Cepek P, Zajacova M, Kotrbova-Kozak A, Silhova E, Cerna M. DNA methylation and mRNA expression of HLA-DQA1 alleles in type 1 diabetes mellitus. Immunology 2016; 148:150-9. [PMID: 26854762 DOI: 10.1111/imm.12593] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/29/2016] [Accepted: 02/04/2016] [Indexed: 11/29/2022] Open
Abstract
Type 1 diabetes (T1D) belongs among polygenic multifactorial autoimmune diseases. The highest risk is associated with human leucocyte antigen (HLA) class II genes, including HLA-DQA1 gene. Our aim was to investigate DNA methylation of HLA-DQA1 promoter alleles (QAP) and correlate methylation status with individual HLA-DQA1 allele expression of patients with T1D and healthy controls. DNA methylation is one of the epigenetic modifications that regulate gene expression and is known to be shaped by the environment.Sixty one patients with T1D and 39 healthy controls were involved in this study. Isolated DNA was treated with sodium bisulphite and HLA-DQA1 promoter sequence was amplified using nested PCR. After sequencing, DNA methylation of HLA-DQA1 promoter alleles was analysed. Individual mRNA HLA-DQA1 relative allele expression was assessed using two different endogenous controls (PPIA, DRA). We have found statistically significant differences in HLA-DQA1 allele 02:01 expression (PPIA normalization, Pcorr = 0·041; DRA normalization, Pcorr = 0·052) between healthy controls and patients with T1D. The complete methylation profile of the HLA-DQA1 promoter was gained with the most methylated allele DQA1*02:01 and the least methylated DQA1*05:01 in both studied groups. Methylation profile observed in patients with T1D and healthy controls was similar, and no correlation between HLA-DQA1 allele expression and DNA methylation was found. Although we have not proved significant methylation differences between the two groups, detailed DNA methylation status and its correlation with expression of each HLA-DQA1 allele in patients with T1D have been described for the first time.
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Affiliation(s)
- Pavel Cepek
- Department of General Biology and Genetics, Third Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Marta Zajacova
- Department of General Biology and Genetics, Third Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Kotrbova-Kozak
- Department of General Biology and Genetics, Third Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Elena Silhova
- University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Marie Cerna
- Department of General Biology and Genetics, Third Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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17
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Wu CC, Chen BS. Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. Int J Mol Sci 2016; 17:305. [PMID: 26927091 PMCID: PMC4813168 DOI: 10.3390/ijms17030305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 01/17/2023] Open
Abstract
While inflammation has generally been regarded as a negative factor in stroke recovery, this viewpoint has recently been challenged by demonstrating that inflammation is a necessary and sufficient factor for regeneration in the zebrafish brain injury model. This close relationship with inflammation suggests that a re-examination of the immune system’s role in strokes is necessary. We used a systems biology approach to investigate the role of immune-related functions via their interactions with other molecular functions in early cardioembolic stroke. Based on protein interaction models and on microarray data from the blood of stroke subjects and healthy controls, networks were constructed to delineate molecular interactions at four early stages (pre-stroke, 3 h, 5 h and 24 h after stroke onset) of cardioembolic stroke. A comparative analysis of functional networks identified interactions of immune-related functions with other molecular functions, including growth factors, neuro/hormone and housekeeping functions. These provide a potential pathomechanism for early stroke pathophysiology. In addition, several potential targets of miRNA and methylation regulations were derived based on basal level changes observed in the core networks and literature. The results provide a more comprehensive understanding of stroke progression mechanisms from an immune perspective and shed light on acute stroke treatments.
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Affiliation(s)
- Chia-Chou Wu
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
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18
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Ningappa M, Ashokkumar C, Higgs BW, Sun Q, Jaffe R, Mazariegos G, Li D, Weeks DE, Subramaniam S, Ferrell R, Hakonarson H, Sindhi R. Enhanced B Cell Alloantigen Presentation and Its Epigenetic Dysregulation in Liver Transplant Rejection. Am J Transplant 2016; 16:497-508. [PMID: 26663361 PMCID: PMC5082419 DOI: 10.1111/ajt.13509] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 07/30/2015] [Accepted: 08/20/2015] [Indexed: 01/25/2023]
Abstract
T cell suppression prevents acute cellular rejection but causes life-threatening infections and malignancies. Previously, liver transplant (LTx) rejection in children was associated with the single-nucleotide polymorphism (SNP) rs9296068 upstream of the HLA-DOA gene. HLA-DOA inhibits B cell presentation of antigen, a potentially novel antirejection drug target. Using archived samples from 122 white pediatric LTx patients (including 77 described previously), we confirmed the association between rs9296068 and LTx rejection (p = 0.001, odds ratio [OR] 2.55). Next-generation sequencing revealed that the putative transcription factor (CCCTC binding factor [CTCF]) binding SNP locus rs2395304, in linkage disequilibrium with rs9296068 (D' 0.578, r(2) = 0.4), is also associated with LTx rejection (p = 0.008, OR 2.34). Furthermore, LTx rejection is associated with enhanced B cell presentation of donor antigen relative to HLA-nonidentical antigen in a novel cell-based assay and with a downregulated HLA-DOA gene in a subset of these children. In lymphoblastoid B (Raji) cells, rs2395304 coimmunoprecipitates with CTCF, and CTCF knockdown with morpholino antisense oligonucleotides enhances alloantigen presentation and downregulates the HLA-DOA gene, reproducing observations made with HLA-DOA knockdown and clinical rejection. Alloantigen presentation is suppressed by inhibitors of methylation and histone deacetylation, reproducing observations made during resolution of rejection. Enhanced donor antigen presentation by B cells and its epigenetic dysregulation via the HLA-DOA gene represent novel opportunities for surveillance and treatment of transplant rejection.
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Affiliation(s)
- M Ningappa
- Hillman Center for Pediatric Transplantation, Thomas E Starzl Transplantation Institute, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), 4401 Penn Avenue, FP-6, Transplant, Room 6140, Mail Stop: CHL 03-06-02, Pittsburgh, PA 15224, USA
| | - C Ashokkumar
- Hillman Center for Pediatric Transplantation, Thomas E Starzl Transplantation Institute, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), 4401 Penn Avenue, FP-6, Transplant, Room 6140, Mail Stop: CHL 03-06-02, Pittsburgh, PA 15224, USA
| | - BW Higgs
- Hillman Center for Pediatric Transplantation, Thomas E Starzl Transplantation Institute, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), 4401 Penn Avenue, FP-6, Transplant, Room 6140, Mail Stop: CHL 03-06-02, Pittsburgh, PA 15224, USA
| | - Q Sun
- Hillman Center for Pediatric Transplantation, Thomas E Starzl Transplantation Institute, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), 4401 Penn Avenue, FP-6, Transplant, Room 6140, Mail Stop: CHL 03-06-02, Pittsburgh, PA 15224, USA
| | - R Jaffe
- Department of Pathology, University of Pittsburgh, Division of Pediatric Pathology, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), 4401 Penn Avenue, B255, Pittsburgh, PA 15224, USA
| | - G Mazariegos
- Hillman Center for Pediatric Transplantation, Thomas E Starzl Transplantation Institute, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), 4401 Penn Avenue, FP-6, Transplant, Room 6140, Mail Stop: CHL 03-06-02, Pittsburgh, PA 15224, USA
| | - D Li
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall, Room 431, 9500 Gilman Drive MC 0412, La Jolla, CA 92093-0412 USA
| | - DE Weeks
- Department of Human Genetics, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA 15261 USA
| | - S Subramaniam
- Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall, Room 431, 9500 Gilman Drive MC 0412, La Jolla, CA 92093-0412 USA
| | - R Ferrell
- Department of Human Genetics, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA 15261 USA
| | - H Hakonarson
- Center for Applied Genomics, 1216 E. Abramson’s Research Center, ARC 1216E, Children’s Hospital of Philadelphia, 34 and Civic Center Blvd., Philadelphia, PA 19104 USA
| | - R Sindhi
- Hillman Center for Pediatric Transplantation, Thomas E Starzl Transplantation Institute, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), 4401 Penn Avenue, FP-6, Transplant, Room 6140, Mail Stop: CHL 03-06-02, Pittsburgh, PA 15224, USA
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MHC class II super-enhancer increases surface expression of HLA-DR and HLA-DQ and affects cytokine production in autoimmune vitiligo. Proc Natl Acad Sci U S A 2016; 113:1363-8. [PMID: 26787888 DOI: 10.1073/pnas.1523482113] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic risk for autoimmunity in HLA genes is most often attributed to structural specificity resulting in presentation of self-antigens. Autoimmune vitiligo is strongly associated with the MHC class II region. Here, we fine-map vitiligo MHC class II genetic risk to three SNPs only 47 bp apart, located within a predicted super-enhancer in an intergenic region between HLA-DRB1 and HLA-DQA1, localized by a genome-wide association study of 2,853 Caucasian vitiligo patients. The super-enhancer corresponds to an expression quantitative trait locus for expression of HLA-DR and HLA-DQ RNA; we observed elevated surface expression of HLA-DR (P = 0.008) and HLA-DQ (P = 0.02) on monocytes from healthy subjects homozygous for the high-risk SNP haplotype. Unexpectedly, pathogen-stimulated peripheral blood mononuclear cells from subjects homozygous for the high-risk super-enhancer haplotype exhibited greater increase in production of IFN-γ and IL-1β than cells from subjects homozygous for the low-risk haplotype. Specifically, production of IFN-γ on stimulation of dectin-1, mannose, and Toll-like receptors with Candida albicans and Staphylococcus epidermidis was 2.5- and 2.9-fold higher in high-risk subjects than in low-risk subjects, respectively (P = 0.007 and P = 0.01). Similarly, production of IL-1β was fivefold higher in high-risk subjects than in low-risk subjects (P = 0.02). Increased production of immunostimulatory cytokines in subjects carrying the high-risk haplotype may act as an "adjuvant" during the presentation of autoantigens, tying together genetic variation in the MHC with the development of autoimmunity. This study demonstrates that for risk of autoimmune vitiligo, expression level of HLA class II molecules is as or more important than antigen specificity.
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Zajacova M, Kotrbova-Kozak A, Cepek P, Cerna M. Differences in promoter DNA methylation and mRNA expression of individual alleles of the HLA class II DQA1 gene. Immunol Lett 2015; 167:147-54. [DOI: 10.1016/j.imlet.2015.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/07/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
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21
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Majumder P, Scharer CD, Choi NM, Boss JM. B cell differentiation is associated with reprogramming the CCCTC binding factor-dependent chromatin architecture of the murine MHC class II locus. THE JOURNAL OF IMMUNOLOGY 2014; 192:3925-35. [PMID: 24634495 DOI: 10.4049/jimmunol.1303205] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The transcriptional insulator CCCTC binding factor (CTCF) was shown previously to be critical for human MHC class II (MHC-II) gene expression. Whether the mechanisms used by CTCF in humans were similar to that of the mouse and whether the three-dimensional chromatin architecture created was specific to B cells were not defined. Genome-wide CTCF occupancy was defined for murine B cells and LPS-derived plasmablasts by chromatin immunoprecipitation sequencing. Fifteen CTCF sites within the murine MHC-II locus were associated with high CTCF binding in B cells. Only one-third of these sites displayed significant CTCF occupancy in plasmablasts. CTCF was required for maximal MHC-II gene expression in mouse B cells. In B cells, a subset of the CTCF regions interacted with each other, creating a three-dimensional architecture for the locus. Additional interactions occurred between MHC-II promoters and the CTCF sites. In contrast, a novel configuration occurred in plasma cells, which do not express MHC-II genes. Ectopic CIITA expression in plasma cells to induce MHC-II expression resulted in high levels of MHC-II proteins, but did not alter the plasma cell architecture completely. These data suggest that reorganizing the three-dimensional chromatin architecture is an epigenetic mechanism that accompanies the silencing of MHC-II genes as part of the cell fate commitment of plasma cells.
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Affiliation(s)
- Parimal Majumder
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
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22
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Mégarbané A, Noguier F, Stora S, Manchon L, Mircher C, Bruno R, Dorison N, Pierrat F, Rethoré MO, Trentin B, Ravel A, Morent M, Lefranc G, Piquemal D. The intellectual disability of trisomy 21: differences in gene expression in a case series of patients with lower and higher IQ. Eur J Hum Genet 2013; 21:1253-9. [PMID: 23422941 PMCID: PMC3798834 DOI: 10.1038/ejhg.2013.24] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 12/27/2012] [Accepted: 01/22/2013] [Indexed: 12/25/2022] Open
Abstract
Trisomy 21 (T21), or Down syndrome (DS), is the most frequent and recognizable cause of intellectual disabilities. The level of disability, as evaluated by the intelligence quotient (IQ) test, varies considerably between patients independent of other factors. To determine the genetic or molecular basis of this difference, a high throughput transcriptomic analysis was performed on twenty T21 patients with high and low IQ, and 10 healthy controls using Digital Gene Expression. More than 90 millions of tags were sequenced in the three libraries. A total of 80 genes of potential interest were selected for the qPCR experiment validation, and three housekeeping genes were used for normalizing purposes. HLA DQA1 and HLA DRB1 were significantly downregulated among the patients with a low IQ, the values found in the healthy controls being intermediate between those noted in the IQ+ and IQ- T21 patients. Interestingly, the intergenic region between these genes contains a binding sequence for the CCCTC-binding factor, or CTCF, and cohesin (a multisubunit complex), both of which are essential for expression of HLA DQA1 and HLA DRB1 and numerous other genes. Our results might lead to the discovery of genes, or genetic markers, that are directly involved in several phenotypes of DS and, eventually, to the identification of potential targets for therapeutic interventions.
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Affiliation(s)
- André Mégarbané
- Institut Jérôme Lejeune, Paris, France
- Unité de Génétique Médicale et Laboratoire Associé INSERM UMR_S910, Beirut, Lebanon
| | | | | | | | | | | | | | | | | | | | | | | | - Gerard Lefranc
- Université Montpellier 2 et CNRS UPR 1142, Institut de Génétique Humaine, Montpellier, France
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Leung A, Schones DE, Natarajan R. Using epigenetic mechanisms to understand the impact of common disease causing alleles. Curr Opin Immunol 2012; 24:558-63. [PMID: 22857822 DOI: 10.1016/j.coi.2012.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 06/29/2012] [Accepted: 07/09/2012] [Indexed: 02/05/2023]
Abstract
Many common genetic variants have been identified to be associated with autoimmune diseases such as Type I diabetes. Methods to identify these genetic loci have become powerful, but deciphering the functional effects of these variants in disease progression remains a major challenge. Recent studies have shown that single nucleotide polymorphisms are associated with altered DNA methylation and chromatin accessibility, suggesting that genetic variants can alter epigenetic features and epigenetic variations can mediate genetic variability. In this review, we highlight recent studies that have examined the relationship between genetics and epigenetics, and how epigenetic studies may complement genetic studies in understanding the impact of common disease causing alleles.
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Affiliation(s)
- Amy Leung
- Department of Diabetes, Beckman Research Institute of the City of Hope, Duarte, CA 91010, United States
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Suarez-Alvarez B, Rodriguez RM, Fraga MF, López-Larrea C. DNA methylation: a promising landscape for immune system-related diseases. Trends Genet 2012; 28:506-14. [PMID: 22824525 DOI: 10.1016/j.tig.2012.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/13/2012] [Accepted: 06/20/2012] [Indexed: 01/31/2023]
Abstract
During hematopoiesis, a unique hematopoietic stem cell (HSC) from the bone marrow gives rise to a subset of mature blood cells that directs all the immune responses. Recent studies have shown that this well-defined, hierarchical process is regulated in part by epigenetic mechanisms. Changes in the DNA methylation profile have a critical role in the division of these stem cells into the myeloid and lymphoid lineages and in the establishment of a specific phenotype and functionality in each terminally differentiated cell type. In this review, we describe how the DNA methylation patterns are modified during hematopoietic differentiation and what their role is in cell plasticity and immune function. An in-depth knowledge of these epigenetic mechanisms will help clarify how cell type-specific gene programs are established, and how they can be leveraged in the development of novel strategies for treating immune system-related pathologies.
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de Necochea-Campion R, Ghochikyan A, Josephs SF, Zacharias S, Woods E, Karimi-Busheri F, Alexandrescu DT, Chen CS, Agadjanyan MG, Carrier E. Expression of the epigenetic factor BORIS (CTCFL) in the human genome. J Transl Med 2011; 9:213. [PMID: 22168535 PMCID: PMC3264669 DOI: 10.1186/1479-5876-9-213] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 12/14/2011] [Indexed: 11/10/2022] Open
Abstract
BORIS, or CTCFL, the so called Brother of the Regulator of Imprinted Sites because of the extensive homology in the central DNA binding region of the protein to the related regulator, CTCF, is expressed in early gametogenesis and in multiple cancers but not in differentiated somatic cells. Thus it is a member of the cancer testes antigen group (CTAs). Since BORIS and CTCF target common DNA binding sites, these proteins function on two levels, the first level is their regulation via the methylation context of the DNA target site and the second level is their distinct and different epigenetic associations due to differences in the non-homologous termini of the proteins. The regulation on both of these levels is extensive and complex and the sphere of influence of each of these proteins is associated with vastly different cellular signaling processes. On the level of gene expression, BORIS has three known promoters and multiple spliced mRNAs which adds another level of complexity to this intriguing regulator. BORIS expression is observed in the majority of cancer tissues and cell lines analyzed up to today. The expression profile and essential role of BORIS in cancer make this molecule very attractive target for cancer immunotherapy. This review summarizes what is known about BORIS regarding its expression, structure, and function and then presents some theoretical considerations with respect to its genome wide influence and its potential for use as a vaccine for cancer immunotherapy.
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Meldi L, Brickner JH. Compartmentalization of the nucleus. Trends Cell Biol 2011; 21:701-8. [PMID: 21900010 PMCID: PMC3970429 DOI: 10.1016/j.tcb.2011.08.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 12/14/2022]
Abstract
The nucleus is a spatially organized compartment. The most obvious way in which this is achieved is at the level of chromosomes. The positioning of chromosomes with respect to nuclear landmarks and with respect to each other is both non-random and cell-type specific. This suggests that cells possess molecular mechanisms to influence the folding and disposition of chromosomes within the nucleus. The localization of many proteins is also heterogeneous within the nucleus. Therefore, chromosome folding and the localization of proteins leads to a model in which individual genes are positioned in distinct protein environments that can affect their transcriptional state. We focus here on the spatial organization of the nucleus and how it impacts upon gene expression.
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Affiliation(s)
- Lauren Meldi
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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