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Zhang S, Meng Y, Zhou L, Qiu L, Wang H, Su D, Zhang B, Chan K, Han J. Targeting epigenetic regulators for inflammation: Mechanisms and intervention therapy. MedComm (Beijing) 2022; 3:e173. [PMID: 36176733 PMCID: PMC9477794 DOI: 10.1002/mco2.173] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 11/11/2022] Open
Abstract
Emerging evidence indicates that resolution of inflammation is a critical and dynamic endogenous process for host tissues defending against external invasive pathogens or internal tissue injury. It has long been known that autoimmune diseases and chronic inflammatory disorders are characterized by dysregulated immune responses, leading to excessive and uncontrol tissue inflammation. The dysregulation of epigenetic alterations including DNA methylation, posttranslational modifications to histone proteins, and noncoding RNA expression has been implicated in a host of inflammatory disorders and the immune system. The inflammatory response is considered as a critical trigger of epigenetic alterations that in turn intercede inflammatory actions. Thus, understanding the molecular mechanism that dictates the outcome of targeting epigenetic regulators for inflammatory disease is required for inflammation resolution. In this article, we elucidate the critical role of the nuclear factor‐κB signaling pathway, JAK/STAT signaling pathway, and the NLRP3 inflammasome in chronic inflammatory diseases. And we formulate the relationship between inflammation, coronavirus disease 2019, and human cancers. Additionally, we review the mechanism of epigenetic modifications involved in inflammation and innate immune cells. All that matters is that we propose and discuss the rejuvenation potential of interventions that target epigenetic regulators and regulatory mechanisms for chronic inflammation‐associated diseases to improve therapeutic outcomes.
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Affiliation(s)
- Su Zhang
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Yang Meng
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Lian Zhou
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Lei Qiu
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Heping Wang
- Department of Neurosurgery Tongji Hospital of Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Dan Su
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
| | - Bo Zhang
- Laboratory of Cancer Epigenetics and Genomics Department of Gastrointestinal Surgery Frontiers Science Center for Disease‐Related Molecular Network West China Hospital Sichuan University Chengdu China
| | - Kui‐Ming Chan
- Department of Biomedical Sciences City University of Hong Kong Hong Kong China
| | - Junhong Han
- Laboratory of Cancer Epigenetics and Genomics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu China
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Xu J, Xu HM, Yang MF, Liang YJ, Peng QZ, Zhang Y, Tian CM, Wang LS, Yao J, Nie YQ, Li DF. New Insights Into the Epigenetic Regulation of Inflammatory Bowel Disease. Front Pharmacol 2022; 13:813659. [PMID: 35173618 PMCID: PMC8841592 DOI: 10.3389/fphar.2022.813659] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the colonic mucosa. Environmental factors, genetics, intestinal microbiota, and the immune system are all involved in the pathophysiology of IBD. Lately, accumulating evidence has shown that abnormal epigenetic changes in DNA methylation, histone markers, and non-coding RNA expression greatly contribute to the development of the entire disease. Epigenetics regulates many functions, such as maintaining the homeostasis of the intestinal epithelium and regulating the immune system of the immune cells. In the present study, we systematically summarized the latest advances in epigenetic modification of IBD and how epigenetics reveals new mechanisms of IBD. Our present review provided new insights into the pathophysiology of IBD. Moreover, exploring the patterns of DNA methylation and histone modification through epigenetics can not only be used as biomarkers of IBD but also as a new target for therapeutic intervention in IBD patients.
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Affiliation(s)
- Jing Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Hao-ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Mei-feng Yang
- Department of Hematology, Yantian District People’s Hospital, Shenzhen, China
| | | | - Quan-zhou Peng
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, China
| | - Cheng-mei Tian
- Department of Emergency, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Li-sheng Wang
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - Yu-qiang Nie
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - De-feng Li
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
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Ai R, Boyle DL, Wang W, Firestein GS. Distinct DNA Methylation Patterns of Rheumatoid Arthritis Peripheral Blood and Synovial Tissue T Cells. ACR Open Rheumatol 2021; 3:127-132. [PMID: 33544432 PMCID: PMC7966880 DOI: 10.1002/acr2.11231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/28/2020] [Indexed: 01/08/2023] Open
Abstract
Objective To study epigenetic patterns in T lymphocytes that accumulate in the rheumatoid arthritis (RA) synovium, we characterized DNA methylation of CD3+ T cells in peripheral blood and synovial tissue in patients with RA and osteoarthritis (OA). Methods Genomic DNA of CD3+ T cells was isolated from patients with RA (n = 8) and OA (n = 5) from blood or the synovium at the time of an arthroplasty using antibodies and magnetic beads. Methylation was measured by using the Illumina Infinium MethylationEPIC Kit. Differentially methylated loci (DML) and differentially methylated genes (DMGs) were identified by using Welch’s t‐test. Principal component analysis, hierarchical clustering, and pathway analysis were used to determine relationships among groups. Results When we compared DNA methylation of CD3+ T cells between peripheral blood and synovial tissue within each disease, 4615 and 164 DML were identified in RA and OA samples, respectively, resulting in 832 and 36 DMGs. A principal component analysis showed that methylation differences in T cells were greater on the basis of on location (blood vs synovium) rather than disease (RA vs OA). Differentially modified pathways were significantly enriched between RA blood and synovial T cells, especially in genes related to complement, integrin cell surface interactions, and the P53 pathway. The limited number of DMGs identified between OA blood and synovial T cells did not conform to biologic pathways. Conclusion The patterns of DNA methylation in RA show location‐specific differences related to immune pathways, whereas methylation differences in OA are limited. The RA joint‐specific signatures could be due to selective accumulation of T‐cell populations or expansion of differentially marked adaptive immune cells. Understanding epigenetic patterns could provide clues to the types of T cells that accumulate in the RA joint and identify potential therapeutic targets.
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Affiliation(s)
- Rizi Ai
- University of CaliforniaSan Diego
| | | | - Wei Wang
- University of CaliforniaSan Diego
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Petzl-Erler ML. Beyond the HLA polymorphism: A complex pattern of genetic susceptibility to pemphigus. Genet Mol Biol 2020; 43:e20190369. [PMID: 32639508 PMCID: PMC7341728 DOI: 10.1590/1678-4685-gmb-2019-0369] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Pemphigus is a group of autoimmune bullous skin diseases that result in
significant morbidity. As for other multifactorial autoimmune disorders,
environmental factors may trigger the disease in genetically susceptible
individuals. The goals of this review are to summarize the state of knowledge
about the genetic variation that may affect the susceptibility and pathogenesis
of pemphigus vulgaris and pemphigus foliaceus – both the endemic and the
sporadic forms –, to compare and discuss the possible meaning of the
associations reported, and to propose recommendations for new research
initiatives. Understanding how genetic variants translate into pathogenic
mechanisms and phenotypes remains a mystery for most of the polymorphisms that
contribute to disease susceptibility. However, genetic studies provide a strong
foundation for further developments in this field by generating testable
hypotheses. Currently, results still have limited influence on disease
prevention and prognosis, drug development, and clinical practice, although the
perspectives for future applications for the benefit of patients are
encouraging. Recommendations for the continued advancement of our understanding
as to the impact of genetic variation on pemphigus include these partially
overlapping goals: (1) Querying the functional effect of genetic variants on the
regulation of gene expression through their impact on the nucleotide sequence of
cis regulatory DNA elements such as promoters and enhancers, the splicing of
RNA, the structure of regulatory RNAs and proteins, binding of these regulatory
molecules to regulatory DNA elements, and alteration of epigenetic marks; (2)
identifying key cell types and cell states that are implicated in pemphigus
pathogenesis and explore their functional genomes; (3) integrating structural
and functional genomics data; (4) performing disease-progression longitudinal
studies to disclose the causal relationships between genetic and epigenetic
variation and intermediate disease phenotypes; (5) understanding the influence
of genetic and epigenetic variation in the response to treatment and the
severity of the disease; (6) exploring gene-gene and genotype-environment
interactions; (7) developing improved pemphigus-prone and non-prone animal
models that are appropriate for research about the mechanisms that link
genotypes to pemphigus. Achieving these goals will demand larger samples of
patients and controls and multisite collaborations.
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Affiliation(s)
- Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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6
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Ai R, Laragione T, Hammaker D, Boyle DL, Wildberg A, Maeshima K, Palescandolo E, Krishna V, Pocalyko D, Whitaker JW, Bai Y, Nagpal S, Bachman KE, Ainsworth RI, Wang M, Ding B, Gulko PS, Wang W, Firestein GS. Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes. Nat Commun 2018; 9:1921. [PMID: 29765031 PMCID: PMC5953939 DOI: 10.1038/s41467-018-04310-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/23/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetics contributes to the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first comprehensive epigenomic characterization of RA fibroblast-like synoviocytes (FLS), including histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3), open chromatin, RNA expression and whole-genome DNA methylation. To address complex multidimensional relationship and reveal epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells and are associated with active enhancers and promoters and specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with “Huntington’s Disease Signaling” identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets. Fibroblast-like synoviocytes (FLS) in the intimal layer of the synovium can become invasive and destroy cartilage in patients with rheumatoid arthritis (RA). Here the authors integrate a variety of epigenomic data to map the epigenome of FLS in RA and identify potential therapeutic targets.
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Affiliation(s)
- Rizi Ai
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Teresina Laragione
- Division of Rheumatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Deepa Hammaker
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA
| | - Andre Wildberg
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Keisuke Maeshima
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA
| | | | - Vinod Krishna
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - David Pocalyko
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - John W Whitaker
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Yuchen Bai
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Sunil Nagpal
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Kurtis E Bachman
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Richard I Ainsworth
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Mengchi Wang
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Bo Ding
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Percio S Gulko
- Division of Rheumatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Wei Wang
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA. .,Department of Cellular and Molecular Medicine, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA.
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA.
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7
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Kernaleguen M, Daviaud C, Shen Y, Bonnet E, Renault V, Deleuze JF, Mauger F, Tost J. Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution. Methods Mol Biol 2018. [PMID: 29524144 DOI: 10.1007/978-1-4939-7774-1_18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines. Here we provide two detailed protocols based on commercial kits for the preparation of sequencing libraries for the comprehensive whole-genome analysis of DNA methylation and/or hydroxymethylation. If only DNA methylation is of interest, sequencing libraries can be constructed from limited amounts of input DNA by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. For samples with significant levels of hydroxymethylation such as stem cells or brain tissue, we describe the protocol of oxidative bisulfite sequencing (OxBs-seq), which in its current version uses a post-bisulfite adaptor tagging (PBAT) approach. Two methylomes need to be generated: a classic methylome following bisulfite conversion and analyzing both methylated and hydroxymethylated cytosines and a methylome analyzing only methylated cytosines, respectively. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocols have been successfully applied to different human samples and yield robust and reproducible results.
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Affiliation(s)
- Magali Kernaleguen
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Yimin Shen
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Eric Bonnet
- Laboratory for Bio-analysis, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Victor Renault
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, France
| | - Jean-François Deleuze
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France.,Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, France
| | - Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France.
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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9
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Daviaud C, Renault V, Mauger F, Deleuze JF, Tost J. Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol. Methods Mol Biol 2018; 1708:83-104. [PMID: 29224140 DOI: 10.1007/978-1-4939-7481-8_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can be considered the gold standard for a comprehensive and quantitative analysis of cytosine methylation throughout the genome. Several approaches including tagmentation- and post bisulfite adaptor tagging (PBAT)-based WGBS have been devised. Here, we provide a detailed protocol based on a commercial kit for the preparation of libraries for WGBS from limited amounts of input DNA (50-100 ng) using the classical approach of WGBS by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. The converted library is then amplified with an optimal number of PCR cycles to ensure high sequence diversity and low duplicate rates. Spike-in of unmethylated DNA allows for the precise estimation of bisulfite conversion rates. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocol has been successfully applied to different human samples as well as DNA extracted from plant tissues and yields robust and reproducible results.
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Affiliation(s)
- Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Victor Renault
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu, Paris, 75010, France
| | - Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jean-François Deleuze
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu, Paris, 75010, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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Strong upregulation of inflammatory genes accompanies photoreceptor demise in canine models of retinal degeneration. PLoS One 2017; 12:e0177224. [PMID: 28486508 PMCID: PMC5423635 DOI: 10.1371/journal.pone.0177224] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/24/2017] [Indexed: 01/18/2023] Open
Abstract
We have analyzed the complex pattern of the inflammatory response in early-onset canine models of human retinitis pigmentosa, rcd1, xlpra2 and erd, as well as late-onset xlpra1, in comparative manner. The time course of immune response genes and proteins expression was examined along the timeline of photoreceptors degeneration. Gene expression analysis of the early-onset models prior to and after the peak of photoreceptors death identified the involvement of multiple immune response genes including those encoding constituents of the NLRP3 inflammasome, its substrates, pro-IL1B, pro-IL18, and common components of IL1B, IL18 and TLR4 pathways. Out of two activated caspase-1 cleavage products, IL1B and IL18, only IL1B was detected in rcd1 and xlpra2 while precursor IL18 remained unprocessed in the same protein extract highlighting prominence of IL1B pathway. An overall immune response was most prominent in rcd1 followed by xlpra2 and least prominent in erd. Noticeably, in rcd1 and xlpra2, but not in erd, early induction of the immune response was accompanied by sustained intraretinal migration and activation of retinal microglia. Lastly, delayed activation of the anti-inflammatory factors in all early-onset models was insufficient to counterbalance rapidly progressing inflammation. In contrast to early-onset models, in late-onset xlpra1 retinas a subset of the pro-inflammatory genes was highly upregulated long before any disease-related structural changes occurred, but was counterbalanced by an adequate anti-inflammatory response. Results point out to upregulated immune response accompanying disease progression in animal models of retinal degeneration, and to potential benefits of early anti-inflammatory therapy.
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Potaczek DP, Harb H, Michel S, Alhamwe BA, Renz H, Tost J. Epigenetics and allergy: from basic mechanisms to clinical applications. Epigenomics 2017; 9:539-571. [PMID: 28322581 DOI: 10.2217/epi-2016-0162] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Allergic diseases are on the rise in the Western world and well-known allergy-protecting and -driving factors such as microbial and dietary exposure, pollution and smoking mediate their influence through alterations of the epigenetic landscape. Here, we review key facts on the involvement of epigenetic modifications in allergic diseases and summarize and critically evaluate the lessons learned from epigenome-wide association studies. We show the potential of epigenetic changes for various clinical applications: as diagnostic tools, to assess tolerance following immunotherapy or possibly predict the success of therapy at an early time point. Furthermore, new technological advances such as epigenome editing and DNAzymes will allow targeted alterations of the epigenome in the future and provide novel therapeutic tools.
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Affiliation(s)
- Daniel P Potaczek
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL).,John Paul II Hospital, Krakow, Poland
| | - Hani Harb
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL)
| | - Sven Michel
- Secarna Pharmaceuticals GmbH & Co KG, Planegg, Germany
| | - Bilal Alashkar Alhamwe
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL)
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
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12
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Pullamsetti SS, Perros F, Chelladurai P, Yuan J, Stenmark K. Transcription factors, transcriptional coregulators, and epigenetic modulation in the control of pulmonary vascular cell phenotype: therapeutic implications for pulmonary hypertension (2015 Grover Conference series). Pulm Circ 2017; 6:448-464. [PMID: 28090287 DOI: 10.1086/688908] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pulmonary hypertension (PH) is a complex and multifactorial disease involving genetic, epigenetic, and environmental factors. Numerous stimuli and pathological conditions facilitate severe vascular remodeling in PH by activation of a complex cascade of signaling pathways involving vascular cell proliferation, differentiation, and inflammation. Multiple signaling cascades modulate the activity of certain sequence-specific DNA-binding transcription factors (TFs) and coregulators that are critical for the transcriptional regulation of gene expression that facilitates PH-associated vascular cell phenotypes, as demonstrated by several studies summarized in this review. Past studies have largely focused on the role of the genetic component in the development of PH, while the presence of epigenetic alterations such as microRNAs, DNA methylation, histone levels, and histone deacetylases in PH is now also receiving increasing attention. Epigenetic regulation of chromatin structure is also recognized to influence gene expression in development or disease states. Therefore, a complete understanding of the mechanisms involved in altered gene expression in diseased cells is vital for the design of novel therapeutic strategies. Recent technological advances in DNA sequencing will provide a comprehensive improvement in our understanding of mechanisms involved in the development of PH. This review summarizes current concepts in TF and epigenetic control of cell phenotype in pulmonary vascular disease and discusses the current issues and possibilities in employing potential epigenetic or TF-based therapies for achieving complete reversal of PH.
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Affiliation(s)
- Soni S Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, member of the German Center for Lung Research (DZL), Bad Nauheim, Germany; Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), member of the DZL, Justus-Liebig University, Giessen, Germany
| | - Frédéric Perros
- Université Paris-Sud; and Institut national de la santé et de la recherche médicale (Inserm) Unité Mixte de Recherche (UMR_S) 999, Hôpital Marie Lannelongue, Le Plessis-Robinson, France
| | - Prakash Chelladurai
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Jason Yuan
- University of Arizona, Tucson, Arizona, USA
| | - Kurt Stenmark
- Cardiovascular Pulmonary Research Laboratories, Department of Medicine and Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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The Histone Modification Code in the Pathogenesis of Autoimmune Diseases. Mediators Inflamm 2017; 2017:2608605. [PMID: 28127155 PMCID: PMC5239974 DOI: 10.1155/2017/2608605] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/08/2016] [Indexed: 12/19/2022] Open
Abstract
Autoimmune diseases are chronic inflammatory disorders caused by a loss of self-tolerance, which is characterized by the appearance of autoantibodies and/or autoreactive lymphocytes and the impaired suppressive function of regulatory T cells. The pathogenesis of autoimmune diseases is extremely complex and remains largely unknown. Recent advances indicate that environmental factors trigger autoimmune diseases in genetically predisposed individuals. In addition, accumulating results have indicated a potential role of epigenetic mechanisms, such as histone modifications, in the development of autoimmune diseases. Histone modifications regulate the chromatin states and gene transcription without any change in the DNA sequence, possibly resulting in phenotype alteration in several different cell types. In this paper, we discuss the significant roles of histone modifications involved in the pathogenesis of autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, primary biliary cirrhosis, and type 1 diabetes.
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Epigenetic Changes in Chronic Inflammatory Diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:139-189. [DOI: 10.1016/bs.apcsb.2016.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. Nat Commun 2016; 7:11849. [PMID: 27282753 PMCID: PMC4906396 DOI: 10.1038/ncomms11849] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/05/2016] [Indexed: 01/03/2023] Open
Abstract
Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. Using genome-wide methods, we show differences between RA knee and hip FLS in the methylation of genes encoding biological pathways, such as IL-6 signalling via JAK-STAT pathway. Furthermore, differentially expressed genes are identified between knee and hip FLS using RNA-sequencing. Double-evidenced genes that are both differentially methylated and expressed include multiple HOX genes. Joint-specific DNA signatures suggest that RA disease mechanisms might vary from joint to joint, thus potentially explaining some of the diversity of drug responses in RA patients. Rheumatoid arthritis is an inflammatory disease that selectively affects different joints. Here the authors show that gene expression and DNA methylation patterns of fibroblast-like synoviocytes differ between hip and knee joints in patients with RA, thus providing epigenetic and transcriptomic evidence for this anatomic selectivity of inflammation.
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Miceli-Richard C, Wang-Renault SF, Boudaoud S, Busato F, Lallemand C, Bethune K, Belkhir R, Nocturne G, Mariette X, Tost J. Overlap between differentially methylated DNA regions in blood B lymphocytes and genetic at-risk loci in primary Sjögren's syndrome. Ann Rheum Dis 2015; 75:933-40. [PMID: 26183421 PMCID: PMC4853580 DOI: 10.1136/annrheumdis-2014-206998] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/26/2015] [Indexed: 01/20/2023]
Abstract
BACKGROUND Beyond genetics, epigenetics alterations and especially those related to DNA methylation, play key roles in the pathogenesis of autoimmune diseases such as primary Sjögren's syndrome (pSS) and systemic lupus erythematosus. This study aimed to assess the role of methylation deregulation in pSS pathogeny through a genome-wide methylation approach. PATIENTS AND METHODS 26 female patients with pSS and 22 age-matched controls were included in this study. CD4+ T cells and CD19+ B cells were isolated from peripheral blood mononuclear cells by magnetic microbeads and their genome-wide DNA methylation profiles were analysed using Infinium Human Methylation 450 K BeadChips. Probes with a median DNA methylation difference of at least 7% and p<0.01 between patients and controls were considered significantly differentially methylated. RESULTS Methylation alterations were mainly present in B cells compared with T cells. In B cells, an enrichment of genes with differentially methylated probes in genetic at-risk loci was observed, suggesting involvement of both genetic and epigenetic abnormalities in the same genes. Methylation alterations in B cells were more frequent in some specific pathways including Interferon Regulated Genes, mainly among patients who were autoantibody positive. Moreover, genes with differentially methylated probes were over-represented in B cells from patients with active disease. CONCLUSIONS This study demonstrated more important deregulation of DNA methylation patterns in B cells compared with T cells, emphasising the importance of B cells in the pathogenesis of the disease. Overlap between genes with differentially methylated probes in B lymphocytes and genetic at-risk loci is a new finding highlighting their importance in pSS.
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Affiliation(s)
- Corinne Miceli-Richard
- Université Paris-Sud, Hôpitaux Universitaires Paris-Sud, AP-HP, Institut National de la Santé et de la Recherche Médicale (INSERM) U1184, Center for immunology of viral infections and autoimmune diseases, Le Kremlin Bicêtre, France
| | - Shu-Fang Wang-Renault
- Laboratory for Epigenetics and Environment, Centre National de Génotypage-CEA/Institut de Génomique, Evry, France CEA, IDMIT Center, DSV/iMETI, INSERM U1184, Fontenay-aux-Roses, France
| | - Saida Boudaoud
- Université Paris-Sud, Hôpitaux Universitaires Paris-Sud, AP-HP, Institut National de la Santé et de la Recherche Médicale (INSERM) U1184, Center for immunology of viral infections and autoimmune diseases, Le Kremlin Bicêtre, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Génotypage-CEA/Institut de Génomique, Evry, France
| | - Céline Lallemand
- Laboratory for Epigenetics and Environment, Centre National de Génotypage-CEA/Institut de Génomique, Evry, France
| | - Kevin Bethune
- Laboratory for Epigenetics and Environment, Centre National de Génotypage-CEA/Institut de Génomique, Evry, France
| | - Rakiba Belkhir
- Université Paris-Sud, Hôpitaux Universitaires Paris-Sud, AP-HP, Institut National de la Santé et de la Recherche Médicale (INSERM) U1184, Center for immunology of viral infections and autoimmune diseases, Le Kremlin Bicêtre, France
| | - Gaétane Nocturne
- Université Paris-Sud, Hôpitaux Universitaires Paris-Sud, AP-HP, Institut National de la Santé et de la Recherche Médicale (INSERM) U1184, Center for immunology of viral infections and autoimmune diseases, Le Kremlin Bicêtre, France
| | - Xavier Mariette
- Université Paris-Sud, Hôpitaux Universitaires Paris-Sud, AP-HP, Institut National de la Santé et de la Recherche Médicale (INSERM) U1184, Center for immunology of viral infections and autoimmune diseases, Le Kremlin Bicêtre, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage-CEA/Institut de Génomique, Evry, France
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Bos SD, Page CM, Andreassen BK, Elboudwarej E, Gustavsen MW, Briggs F, Quach H, Leikfoss IS, Bjølgerud A, Berge T, Harbo HF, Barcellos LF. Genome-wide DNA methylation profiles indicate CD8+ T cell hypermethylation in multiple sclerosis. PLoS One 2015; 10:e0117403. [PMID: 25734800 PMCID: PMC4348521 DOI: 10.1371/journal.pone.0117403] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/21/2014] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Determine whether MS-specific DNA methylation profiles can be identified in whole blood or purified immune cells from untreated MS patients. METHODS Whole blood, CD4+ and CD8+ T cell DNA from 16 female, treatment naïve MS patients and 14 matched controls was profiled using the HumanMethylation450K BeadChip. Genotype data were used to assess genetic homogeneity of our sample and to exclude potential SNP-induced DNA methylation measurement errors. RESULTS As expected, significant differences between CD4+ T cells, CD8+ T cells and whole blood DNA methylation profiles were observed, regardless of disease status. Strong evidence for hypermethylation of CD8+ T cell, but not CD4+ T cell or whole blood DNA in MS patients compared to controls was observed. Genome-wide significant individual CpG-site DNA methylation differences were not identified. Furthermore, significant differences in gene DNA methylation of 148 established MS-associated risk genes were not observed. CONCLUSION While genome-wide significant DNA methylation differences were not detected for individual CpG-sites, strong evidence for DNA hypermethylation of CD8+ T cells for MS patients was observed, indicating a role for DNA methylation in MS. Further, our results suggest that large DNA methylation differences for CpG-sites tested here do not contribute to MS susceptibility. In particular, large DNA methylation differences for CpG-sites within 148 established MS candidate genes tested in our study cannot explain missing heritability. Larger studies of homogenous MS patients and matched controls are warranted to further elucidate the impact of CD8+ T cell and more subtle DNA methylation changes in MS development and pathogenesis.
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Affiliation(s)
- Steffan D. Bos
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- * E-mail:
| | - Christian M. Page
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bettina K. Andreassen
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo, Oslo, Norway
- Epi-Gen, Institute of Clinical Medicine, Akershus University Hospital, University of Oslo, Oslo, Norway
| | - Emon Elboudwarej
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, United States of America
| | - Marte W. Gustavsen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Farren Briggs
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, United States of America
| | - Hong Quach
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, United States of America
| | - Ingvild S. Leikfoss
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anja Bjølgerud
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tone Berge
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Hanne F. Harbo
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lisa F. Barcellos
- Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, United States of America
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Epigenetic control of autoimmune diseases: From bench to bedside. Clin Immunol 2015; 157:1-15. [DOI: 10.1016/j.clim.2014.12.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/17/2014] [Accepted: 12/18/2014] [Indexed: 01/10/2023]
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Effects of microRNA-21 on the interleukin 12/signal transducer and activator of transcription 4 signaling pathway in asthmatic mice. Cent Eur J Immunol 2014; 39:40-5. [PMID: 26155098 PMCID: PMC4439986 DOI: 10.5114/ceji.2014.42121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/10/2014] [Indexed: 01/04/2023] Open
Abstract
Objective To study the effect of microRNA-21 (miRNA-21) on the regulation of the interleukin 12 (IL-12)/signal transducer and activator of transcription 4 (STAT4) pathway in the lung tissue of asthmatic mice. Material and methods Forty five male C57BL/6 mice were randomly divided into three groups of 15 mice each: normal control, asthmatic model, and dexamethasone. Our mouse model of allergic asathma was established using OVA sensitization and challenge. Hematoxylin and eosin staining was performed to observe the pathological changes in lung tissue morphology. Both the total cell number and the amount of eosinophils (EOS) in the bronchoalveolar lavage fluid (BALF) were manually counted. The expression of miRNA-21 was detected by real time quantitative PCR. The expression levels of IL-12 and STAT4 in lung tissue were assayed via western blot, and immunohistochemistry was used to observe the distribution of their expression. Results The expression levels of miRNA-21 as well as the total number of BALF cells and EOS were significantly higher in the asthmatic model group than in the control or dexamethasone groups, with significantly higher amounts found in the dexamethasone group than in the control group. The expression levels of IL-12 and STAT4 proteins were lower in the asthmatic model group than in the control and dexamethasone groups, with a significantly lower expression of IL-12 and STAT4 in the dexamethasone group than in the control group. Conclusions The expression level of miRNA-21 was significantly increased and the expression level of IL-12 and STAT4 proteins was significantly decreased in allergic asthmatic mice compared with normal control mice. These findings suggest a role for miRNA-21 and the IL-12/STAT4 pathway in the development of allergic asthma.
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Lindroth AM, Park YJ. Epigenetic biomarkers: a step forward for understanding periodontitis. J Periodontal Implant Sci 2013; 43:111-20. [PMID: 23837125 PMCID: PMC3701832 DOI: 10.5051/jpis.2013.43.3.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/10/2013] [Indexed: 12/30/2022] Open
Abstract
Periodontitis is a common oral disease that is characterized by infection and inflammation of the tooth supporting tissues. While its incidence is highly associated with outgrowth of the pathogenic microbiome, some patients show signs of predisposition and quickly fall into recurrence after treatment. Recent research using genetic associations of candidates as well as genome-wide analysis highlights that variations in genes related to the inflammatory response are associated with an increased risk of periodontitis. Intriguingly, some of the genes are regulated by epigenetic modifications, supposedly established and reprogrammed in response to environmental stimuli. In addition, the treatment with epigenetic drugs improves treatment of periodontitis in a mouse model. In this review, we highlight some of the recent progress identifying genetic factors associated with periodontitis and point to promising approaches in epigenetic research that may contribute to the understanding of molecular mechanisms involving different responses in individuals and the early detection of predispositions that may guide in future oral treatment and disease prevention.
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Affiliation(s)
- Anders M Lindroth
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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