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Mamabolo K, Wadee R, Perner Y, Magangane P, Duze ST, Marimani M. Differential Epigenetic Regulation in Uninfected and Tuberculosis-Human Immunodeficiency Virus Co-Infected Patients. Microorganisms 2024; 12:1001. [PMID: 38792830 PMCID: PMC11123988 DOI: 10.3390/microorganisms12051001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
This study aimed to compare the degree of epigenetic modifications between a TB-HIV co-infected cohort and uninfected subjects. Formalin-fixed paraffin-embedded (FFPE) tissues were retrieved from 45 TB-HIV co-infected and 45 control individuals. Real-time PCR was applied to compare the level of expression of genes involved in epigenetic regulation. The protein multiplex assay was used to assess the degree of protein modification. DNA sequencing was used to determine the evolutionary relationships between the infecting HIV and Mtb strains. Our results indicated a significant increase in the expression of the five candidate genes in the patients with TB-HIV relative to the control cohort. A sharp increase in the degree of histone methylation, acetylation and phosphorylation was observed in TB-HIV co-infected patients. The phylogenetic analysis classified the strains into three distinct HIV clusters and five Mtb clusters. The disparities in the expression profiles of our candidate genes between the TB-HIV cohort and non-TB-HIV group highlights the important role played by various TB and HIV strains in regulating the host gene expression landscape.
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Affiliation(s)
- Katlego Mamabolo
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Reubina Wadee
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Yvonne Perner
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Pumza Magangane
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Sanelisiwe Thinasonke Duze
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Musa Marimani
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
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Mijač S, Banić I, Genc AM, Lipej M, Turkalj M. The Effects of Environmental Exposure on Epigenetic Modifications in Allergic Diseases. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:110. [PMID: 38256371 PMCID: PMC10820670 DOI: 10.3390/medicina60010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Allergic diseases are one of the most common chronic conditions and their prevalence is on the rise. Environmental exposure, primarily prenatal and early life influences, affect the risk for the development and specific phenotypes of allergic diseases via epigenetic mechanisms. Exposure to pollutants, microorganisms and parasites, tobacco smoke and certain aspects of diet are known to drive epigenetic changes that are essential for immune regulation (e.g., the shift toward T helper 2-Th2 cell polarization and decrease in regulatory T-cell (Treg) differentiation). DNA methylation and histone modifications can modify immune programming related to either pro-allergic interleukin 4 (IL-4), interleukin 13 (IL-13) or counter-regulatory interferon γ (IFN-γ) production. Differential expression of small non-coding RNAs has also been linked to the risk for allergic diseases and associated with air pollution. Certain exposures and associated epigenetic mechanisms play a role in the susceptibility to allergic conditions and specific clinical manifestations of the disease, while others are thought to have a protective role against the development of allergic diseases, such as maternal and early postnatal microbial diversity, maternal helminth infections and dietary supplementation with polyunsaturated fatty acids and vitamin D. Epigenetic mechanisms are also known to be involved in mediating the response to common treatment in allergic diseases, for example, changes in histone acetylation of proinflammatory genes and in the expression of certain microRNAs are associated with the response to inhaled corticosteroids in asthma. Gaining better insight into the epigenetic regulation of allergic diseases may ultimately lead to significant improvements in the management of these conditions, earlier and more precise diagnostics, optimization of current treatment regimes, and the implementation of novel therapeutic options and prevention strategies in the near future.
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Affiliation(s)
- Sandra Mijač
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
| | - Ivana Banić
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
- Department of Innovative Diagnostics, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia
| | - Ana-Marija Genc
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
| | - Marcel Lipej
- IT Department, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia;
| | - Mirjana Turkalj
- Department of Pediatric Allergy and Pulmonology, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia;
- Faculty of Medicine, J.J. Strossmayer University of Osijek, J. Huttlera 4, HR-31000 Osijek, Croatia
- Faculty of Medicine, Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
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Locatelli M, Faure-Dupuy S. Virus hijacking of host epigenetic machinery to impair immune response. J Virol 2023; 97:e0065823. [PMID: 37656959 PMCID: PMC10537592 DOI: 10.1128/jvi.00658-23] [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] [Indexed: 09/03/2023] Open
Abstract
Epigenetic modifications, such as DNA hypermethylation, histone acetylation/methylation, or nucleosome positioning, result in differential gene expression. These modifications can have an impact on various pathways, including host antiviral immune responses. In this review, we summarize the current understanding of epigenetic modifications induced by viruses to counteract host antiviral immune responses, which are crucial for establishing and maintaining infection of viruses. Finally, we provide insights into the potential use of epigenetic modulators in combating viral infections and virus-induced diseases.
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Affiliation(s)
- Maëlle Locatelli
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Suzanne Faure-Dupuy
- Université de Paris Cité, Institut Cochin, Inserm U1016-CNRS UMR8104, Paris, France
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Manríquez RA, Sandoval M, Loncoman C, Tafalla C, Avendaño-Herrera R, Cárcamo JG. Epigenetic reprogramming around IFN1 and IFNy2 promoters in rainbow trout cells inoculated with infectious pancreatic necrosis virus (IPNV). FISH & SHELLFISH IMMUNOLOGY 2023; 140:108947. [PMID: 37454879 DOI: 10.1016/j.fsi.2023.108947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Infectious pancreatic necrosis virus (IPNV) has proven to effectively evade the host antiviral responses. This study clarifies whether the modulation of the antiviral immune response exerted by IPNV involves epigenetic mechanisms. An in-silico characterization of the rainbow trout IFN1 and IFNγ2 promoters was performed, identifying the islands or sequences rich in CpG dinucleotides and the putative transcription factor binding sites (TBS) for both gene promoters. RTS11 cells (rainbow trout monocyte/macrophage) were infected with IPNV, and the course of viral infection was followed up to 48 h post infection (hpi). Infected cells showed increased IFN1 and IFNγ2 transcriptional expression at 6 and 24 hpi, respectively. IPNV infection caused increases and decreases in global IFNγ2 promoter methylation at 6 and 24 hpi, respectively. The CpG dinucleotides at positions -392 and + 38 of this promoter were the most sensitive to methylation changes. The IFN1 promoter remained fully unmethylated during the course of the infection, similar to the control. The changes in the methylation pattern observed for the IFNγ2 promoter were coincident with the changes in DNA methyltransferase (DNMT) expression levels, increasing at 6 hpi and decreasing below basal level at 24 hpi. Similarly, the H4 histones associated with the IFN1 and IFNγ2 promoters were hyperacetylated at 6 hpi, subsequently decreasing their acetylation below basal levels at 24 hpi, in both promoters. Coincidentally with the above, overexpression of histone acetyltransferase (HAT) was observed at 6 hpi and of histone deacetylase (HDAC) at 24 hpi, with return to baseline of HAT. These results suggest that IPNV would epigenetically modulate the expression of IFN1 by changing acetylation levels of the histones H4 associated with its promoter. Also, the modulation of the expression of IFNy2 would be by switching methylation/demethylation levels of its promoter, in addition to changes in acetylation levels of histones H4 associated with this promoter. This study is the first to demonstrate the effect of epigenetic reprogramming after IPNV infection in salmonid cells, demonstrating that promoter methylation/demethylation level and changes in the histone code associated with promoters may play a role in the modulation of the immune response induced by the virus.
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Affiliation(s)
- René A Manríquez
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Valdivia, Chile
| | - Moisés Sandoval
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Valdivia, Chile
| | - Carlos Loncoman
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Carolina Tafalla
- Animal Health Research Center (CISA), INIA-CSIC, Valdeolmos-Alalpardo, 28130, Madrid, Spain
| | - R Avendaño-Herrera
- Interdisciplinary Center for Aquaculture Research (INCAR), Valdivia, Chile; Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Universidad Andrés Bello, Viña del Mar, Chile; Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Juan G Cárcamo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Valdivia, Chile.
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Yadav RK, Kambham MR, Parepally SK, Vyas M, Manem KR, Kamala Jayanthi PD. Encounter With a Selfish Virus Sabotages Its Vector to Orient Toward Requisite Host Plant: A Case Study With Chili Leaf Curl Virus-Whitefly. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.819023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interactions of a virus with its vector and host plant have challenged entomologists, pathologists and biologists alike. Phytophagous insects depend on specific host volatile cues to locate suitable host plants for feeding and oviposition. Several studies have revealed that plant viruses modify their insect vector’s orientation toward specific host plants to facilitate their spread and survival. The ecological and molecular basis of this vector behavior modification remains largely unknown and was therefore explored in this study. Interestingly, host volatile preference for non-viruliferous female whiteflies [Bemisia tabaci (Genn.)] was found to be preferentially oriented toward infected chili plant [with chili leaf curl (ChLCV)] volatiles, while viruliferous whiteflies preferred healthy chili plant (Capsicum annum L.) volatiles in olfactometer. The electrophysiological studies involving electroantennogram (EAG) assays exhibited similar trend in EAG response amplitudes. Gas Chromatography linked electroantennodetection (GC EAD) revealed specific plant volatile cues responsible for altered host orientation behavior of the vector. Transcriptome profiling of the viruliferous and non-viruliferous whiteflies and Realtime qPCR validation showed differential expression of certain odorant binding proteins (OBPs) in viruliferous whiteflies. Our results suggest that there is a plant virus mediated altered chemoecological behavior in the vector with respect to orientation toward its host plant. Based on the findings we speculate that the virus mediates such change in the vector for a continued transmission success to the host.
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Bobak CA, Abhimanyu, Natarajan H, Gandhi T, Grimm SL, Nishiguchi T, Koster K, Longlax SC, Dlamini Q, Kahari J, Mtetwa G, Cirillo JD, O’Malley J, Hill JE, Coarfa C, DiNardo AR. Increased DNA methylation, cellular senescence and premature epigenetic aging in guinea pigs and humans with tuberculosis. Aging (Albany NY) 2022; 14:2174-2193. [PMID: 35256539 PMCID: PMC8954968 DOI: 10.18632/aging.203936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/22/2022] [Indexed: 12/02/2022]
Abstract
Background: Tuberculosis (TB) is the archetypical chronic infection, with patients having months of symptoms before diagnosis. In the two years after successful therapy, survivors of TB have a three-fold increased risk of death. Methods: Guinea pigs were infected with Mycobacterium tuberculosis (Mtb) for 45 days, followed by RRBS DNA methylation analysis. In humans, network analysis of differentially expressed genes across three TB cohorts were visualized at the pathway-level. Serum levels of inflammation were measured by ELISA. Horvath (DNA methylation) and RNA-seq biological clocks were used to investigate shifts in chronological age among humans with TB. Results: Guinea pigs with TB demonstrated DNA hypermethylation and showed system-level similarity to humans with TB (p-value = 0.002). The transcriptome in TB in multiple cohorts was enriched for DNA methylation and cellular senescence. Senescence associated proteins CXCL9, CXCL10, and TNF were elevated in TB patients compared to healthy controls. Humans with TB demonstrate 12.7 years (95% CI: 7.5, 21.9) and 14.38 years (95% CI: 10.23–18.53) of cellular aging as measured by epigenetic and gene expression based cellular clocks, respectively. Conclusions: In both guinea pigs and humans, TB perturbs epigenetic processes, promoting premature cellular aging and inflammation, a plausible means to explain the long-term detrimental health outcomes after TB.
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Affiliation(s)
- Carly A. Bobak
- Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Abhimanyu
- The Global Tuberculosis Program, Baylor College of Medicine, Houston, TX 77030, USA
- William Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
- Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harini Natarajan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Tanmay Gandhi
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L. Grimm
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Baylor College of Medicine, Houston, TX 77030, USA
- William Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
- Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kent Koster
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health, Bryan, TX 77807, USA
| | - Santiago Carrero Longlax
- The Global Tuberculosis Program, Baylor College of Medicine, Houston, TX 77030, USA
- William Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
- Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiniso Dlamini
- Baylor-Swaziland Children’s Foundation, Mbabane, Swaziland
| | | | - Godwin Mtetwa
- Baylor-Swaziland Children’s Foundation, Mbabane, Swaziland
| | - Jeffrey D. Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health, Bryan, TX 77807, USA
| | - James O’Malley
- Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
- The Dartmouth Institute, Dartmouth College, Hanover, NH 03755, USA
| | - Jane E. Hill
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew R. DiNardo
- The Global Tuberculosis Program, Baylor College of Medicine, Houston, TX 77030, USA
- William Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
- Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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Inhibitors of DNA Methylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:471-513. [DOI: 10.1007/978-3-031-11454-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Arumugam T, Ramphal U, Adimulam T, Chinniah R, Ramsuran V. Deciphering DNA Methylation in HIV Infection. Front Immunol 2021; 12:795121. [PMID: 34925380 PMCID: PMC8674454 DOI: 10.3389/fimmu.2021.795121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
With approximately 38 million people living with HIV/AIDS globally, and a further 1.5 million new global infections per year, it is imperative that we advance our understanding of all factors contributing to HIV infection. While most studies have focused on the influence of host genetic factors on HIV pathogenesis, epigenetic factors are gaining attention. Epigenetics involves alterations in gene expression without altering the DNA sequence. DNA methylation is a critical epigenetic mechanism that influences both viral and host factors. This review has five focal points, which examines (i) fluctuations in the expression of methylation modifying factors upon HIV infection (ii) the effect of DNA methylation on HIV viral genes and (iii) host genome (iv) inferences from other infectious and non-communicable diseases, we provide a list of HIV-associated host genes that are regulated by methylation in other disease models (v) the potential of DNA methylation as an epi-therapeutic strategy and biomarker. DNA methylation has also been shown to serve as a robust therapeutic strategy and precision medicine biomarker against diseases such as cancer and autoimmune conditions. Despite new drugs being discovered for HIV, drug resistance is a problem in high disease burden settings such as Sub-Saharan Africa. Furthermore, genetic therapies that are under investigation are irreversible and may have off target effects. Alternative therapies that are nongenetic are essential. In this review, we discuss the potential role of DNA methylation as a novel therapeutic intervention against HIV.
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Affiliation(s)
- Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Romona Chinniah
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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Mantovani N, Defelicibus A, da Silva IT, Cicero MF, Santana LC, Arnold R, de Castro DF, Duro RLS, Nishiyama-Jr MY, Junqueira-de-Azevedo ILM, da Silva BCM, da Silva Duarte AJ, Casseb J, de Barros Tenore S, Hunter J, Diaz RS, Komninakis SCV. Latency-associated DNA methylation patterns among HIV-1 infected individuals with distinct disease progression courses or antiretroviral virologic response. Sci Rep 2021; 11:22993. [PMID: 34837007 PMCID: PMC8626465 DOI: 10.1038/s41598-021-02463-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022] Open
Abstract
DNA methylation is one of the epigenetic modifications that configures gene transcription programs. This study describes the DNA methylation profile of HIV-infected individuals with distinct characteristics related to natural and artificial viremia control. Sheared DNA from circulating mononuclear cells was subjected to target enrichment bisulfite sequencing designed to cover CpG-rich genomic regions. Gene expression was assessed through RNA-seq. Hypermethylation in virologic responders was highly distributed closer to Transcription Start Sites (p-value = 0.03). Hyper and hypomethylation levels within TSS adjacencies varied according to disease progression status (Kruskal-Wallis, p < 0.001), and specific differentially methylated regions associated genes were identified for each group. The lower the promoter methylation, the higher the gene expression in subjects undergoing virologic failure (R = - 0.82, p = 0.00068). Among the inversely correlated genes, those supporting glycolysis and its related pathways were hypomethylated and up-regulated in virologic failures. Disease progression heterogeneity was associated with distinct DNA methylation patterns in terms of rates and distribution. Methylation was associated with the expression of genes sustaining intracellular glucose metabolism in subjects undergoing antiretroviral virologic failure. Our findings highlight that DNA methylation is associated with latency, disease progression, and fundamental cellular processes.
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Affiliation(s)
- Nathalia Mantovani
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil.
| | - Alexandre Defelicibus
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, Rua Taguá, 440, São Paulo, SP, 01508-010, Brazil
| | - Israel Tojal da Silva
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, Rua Taguá, 440, São Paulo, SP, 01508-010, Brazil
| | - Maira Ferreira Cicero
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Luiz Claudio Santana
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Rafael Arnold
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Daniela Funayama de Castro
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Rodrigo Lopes Sanz Duro
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Milton Yutaka Nishiyama-Jr
- Laboratório de Toxinologia Aplicada, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo, SP, 05503-900, Brazil
| | | | - Bosco Christiano Maciel da Silva
- Laboratório de Investigação Médica 56 (LIM/56), Faculdade de Medicina FMUSP, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Alberto José da Silva Duarte
- Laboratório de Investigação Médica 56 (LIM/56), Faculdade de Medicina FMUSP, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Jorge Casseb
- Laboratório de Investigação Médica 56 (LIM/56), Faculdade de Medicina FMUSP, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Simone de Barros Tenore
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - James Hunter
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Ricardo Sobhie Diaz
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Shirley Cavalcante Vasconcelos Komninakis
- Retrovirology Laboratory, Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Rua Pedro de Toledo 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
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Tawe L, Grover S, Zetola N, Robertson ES, Gaseitsiwe S, Moyo S, Kasvosve I, Paganotti GM, Narasimhamurthy M. Promoter Hypermethylation Analysis of Host Genes in Cervical Cancer Patients With and Without Human Immunodeficiency Virus in Botswana. Front Oncol 2021; 11:560296. [PMID: 33718129 PMCID: PMC7952881 DOI: 10.3389/fonc.2021.560296] [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: 05/11/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Epidemics of human immunodeficiency virus (HIV) and cervical cancer are interconnected. DNA hypermethylation of host genes' promoter in cervical lesions has also been recognized as a contributor to cervical cancer progression. Methods: For this purpose we analyzed promoter methylation of four tumor suppressor genes (RARB, CADM1, DAPK1 and PAX1) and explored their possible association with cervical cancer in Botswana among women of known HIV status. Overall, 228 cervical specimens (128 cervical cancers and 100 non-cancer subjects) were used. Yates-corrected chi-square test and Fisher's exact test were used to explore the association of promoter methylation for each host gene and cancer status. Subsequently, a logistic regression analysis was performed to find which factors, HIV status, high risk-HPV genotypes, patient's age and promoter methylation, were associated with the following dependent variables: cancer status, cervical cancer stage and promoter methylation rate. Results: In patients with cervical cancer the rate of promoter methylation observed was greater than 64% in all the genes studied. Analysis also showed a higher risk of cervical cancer according to the increased number of methylated promoter genes (OR = 6.20; 95% CI: 3.66–10.51; P < 0.001). RARB methylation showed the strongest association with cervical cancer compared to other genes (OR = 15.25; 95% CI: 6.06–40.0; P < 0.001). Cervical cancer and promoter methylation of RARB and DAPK1 genes were associated with increasing age (OR = 1.12; 95% CI: 1.01-1.26; P = 0.037 and OR = 1.05; 95% CI: 1.00-1.10; P = 0.040). The presence of epigenetic changes at those genes appeared to be independent of HIV status among subjects with cervical cancer. Moreover, we found that cervical cancer stage was influenced by RARB (χ2= 7.32; P = 0.002) and CADM1 (χ2=12.68; P = 0.013) hypermethylation, and HIV status (χ2= 19.93; P = 0.001). Conclusion: This study confirms the association between invasive cervical cancer and promoter gene methylation of tumor suppressing genes at the site of cancer. HIV infection did not show any association to methylation changes in this group of cervical cancer patients from Botswana. Further studies are needed to better understand the role of HIV in methylation of host genes among cancer subjects leading to cervical cancer progression.
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Affiliation(s)
- Leabaneng Tawe
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana.,Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Surbhi Grover
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nicola Zetola
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Erle S Robertson
- Department of Otorhinolaryngology-Head and Neck Surgery, and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, United States
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, United States
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Giacomo M Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Mohan Narasimhamurthy
- Department of Pathology, Faculty of Medicine, University of Botswana, Gaborone, Botswana
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11
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Jochems SP, Jacquelin B, Tchitchek N, Busato F, Pichon F, Huot N, Liu Y, Ploquin MJ, Roché E, Cheynier R, Dereuddre-Bosquet N, Stahl-Henning C, Le Grand R, Tost J, Müller-Trutwin M. DNA methylation changes in metabolic and immune-regulatory pathways in blood and lymph node CD4 + T cells in response to SIV infections. Clin Epigenetics 2020; 12:188. [PMID: 33298174 PMCID: PMC7724887 DOI: 10.1186/s13148-020-00971-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The molecular mechanisms underlying HIV-induced inflammation, which persists even during effective long-term treatment, remain incompletely defined. Here, we studied pathogenic and nonpathogenic simian immunodeficiency virus (SIV) infections in macaques and African green monkeys, respectively. We longitudinally analyzed genome-wide DNA methylation changes in CD4 + T cells from lymph node and blood, using arrays. DNA methylation changes after SIV infection were more pronounced in lymph nodes than blood and already detected in primary infection. Differentially methylated genes in pathogenic SIV infection were enriched for Th1-signaling (e.g., RUNX3, STAT4, NFKB1) and metabolic pathways (e.g., PRKCZ). In contrast, nonpathogenic SIVagm infection induced DNA methylation in genes coding for regulatory proteins such as LAG-3, arginase-2, interleukin-21 and interleukin-31. Between 15 and 18% of genes with DNA methylation changes were differentially expressed in CD4 + T cells in vivo. Selected identified sites were validated using bisulfite pyrosequencing in an independent cohort of uninfected, viremic and SIV controller macaques. Altered DNA methylation was confirmed in blood and lymph node CD4 + T cells in viremic macaques but was notably absent from SIV controller macaques. Our study identified key genes differentially methylated already in primary infection and in tissues that could contribute to the persisting metabolic disorders and inflammation in HIV-infected individuals despite effective treatment.
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Affiliation(s)
- Simon P Jochems
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
- Sorbonne Paris Cité, Université Paris Diderot, Paris, France
- Leiden University Medical Center, Leiden, The Netherlands
| | - Beatrice Jacquelin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Nicolas Tchitchek
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Fabien Pichon
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Nicolas Huot
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Yi Liu
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Mickaël J Ploquin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Elodie Roché
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Rémi Cheynier
- UMR8104, CNRS, U1016, INSERM, Institut Cochin, Université de Paris, 75014, Paris, France
| | - Nathalie Dereuddre-Bosquet
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | | | - Roger Le Grand
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Michaela Müller-Trutwin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France.
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12
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Marimani M, Ahmad A, Stacey S, Duse A. Examining the levels of acetylation, DNA methylation and phosphorylation in HIV-1 positive and multidrug-resistant TB-HIV patients. J Glob Antimicrob Resist 2020; 23:232-242. [PMID: 33045438 DOI: 10.1016/j.jgar.2020.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/30/2020] [Accepted: 09/27/2020] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES In this study, we examined the impact of epigenetic modifications on host gene functioning by assessing the expression of seven candidate genes in three separate groups including healthy, multidrug-resistant (MDR) TB-HIV co-infected and HIV-1 positive individuals. METHODS Ten patients with MDR TB and HIV-1 co-infection on TB and HIV therapy and a cohort comprised of 10 newly diagnosed individuals with HIV-1 infection were recruited from the TB and HIV clinics at the Charlotte Maxeke Johannesburg Academic Hospital. Notably, the HIV-1 positive individuals were not placed on antiretroviral therapy (ART) at the time of recruitment and blood collection. A third group consisting of 10 healthy participants without MDR TB or HIV infection was recruited from the University of the Witwatersrand. Blood samples collected from all three cohorts were employed for extraction of plasma, total RNA and genomic DNA. RESULTS Our data indicated that the expression of DNA methyltransferase 1 (DNMT1) and Ten-eleven translocation methylcytosine dioxygenase 1 (TET1) genes was significantly increased in HIV-1 positive patients and was lowest in MDR TB-HIV co-infected patients. By contrast, histone acetyltransferase (HAT), histone deacetylase (HDAC), protein tyrosine kinase (PtkA) and protein tyrosine phosphatase (PtpA) mRNA expression levels were substantially enhanced in HIV-1 infected and were lowest in healthy individuals. Conversely, Dicer expression levels were comparable among all three study groups. CONCLUSION Promising preliminary data emanating from this investigation may potentially be used for generation of novel vaccines and therapeutic compounds capable of neutralising MDR TB-HIV and HIV-1 infection.
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Affiliation(s)
- Musa Marimani
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa.
| | - Sarah Stacey
- Division of Pulmonology, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Adriano Duse
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa
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13
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Bannister S, Messina NL, Novakovic B, Curtis N. The emerging role of epigenetics in the immune response to vaccination and infection: a systematic review. Epigenetics 2020; 15:555-593. [PMID: 31914857 PMCID: PMC7574386 DOI: 10.1080/15592294.2020.1712814] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 12/14/2022] Open
Abstract
Extensive research has highlighted the role of infection-induced epigenetic events in the development of cancer. More recently, attention has focused on the ability of non-carcinogenic infections, as well as vaccines, to modify the human epigenome and modulate the immune response. This review explores this rapidly evolving area of investigation and outlines the many and varied ways in which vaccination and natural infection can influence the human epigenome from modulation of the innate and adaptive immune response, to biological ageing and modification of disease risk. The implications of these epigenetic changes on immune regulation and their potential application to the diagnosis and treatment of chronic infection and vaccine development are also discussed.
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Affiliation(s)
- Samantha Bannister
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia
- Infectious Diseases Unit, Royal Children’s Hospital Melbourne, Parkville, Australia
| | - Nicole L. Messina
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia
| | - Boris Novakovic
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Epigenetics Research Group, Murdoch Children’s Research Institute, Parkville, Australia
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia
- Infectious Diseases Unit, Royal Children’s Hospital Melbourne, Parkville, Australia
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14
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Abstract
Human immunodeficiency virus 1 (HIV-1) replicates through the integration of its viral DNA into the genome of human immune target cells. Chronically infected individuals thus carry a genomic burden of virus-derived sequences that persists through antiretroviral therapy. This burden consists of a small fraction of intact, but transcriptionally silenced, i.e. latent, viral genomes and a dominant fraction of defective sequences. Remarkably, all viral-derived sequences are subject to interaction with host cellular physiology at various levels. In this review, we focus on epigenetic aspects of this interaction. We provide a comprehensive overview of how epigenetic mechanisms contribute to establishment and maintenance of HIV-1 gene repression during latency. We furthermore summarize findings indicating that HIV-1 infection leads to changes in the epigenome of target and bystander immune cells. Finally, we discuss how an improved understanding of epigenetic features and mechanisms involved in HIV-1 infection could be exploited for clinical use.
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15
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Liu S, Liu L, Xu G, Cao Z, Wang Q, Li S, Peng N, Yin J, Yu H, Li M, Xia Z, Zhou L, Lin Y, Wang X, Li Q, Zhu C, Yang X, Wang J, She Y, Lu M, Zhu Y. Epigenetic Modification Is Regulated by the Interaction of Influenza A Virus Nonstructural Protein 1 with the De Novo DNA Methyltransferase DNMT3B and Subsequent Transport to the Cytoplasm for K48-Linked Polyubiquitination. J Virol 2019; 93:e01587-18. [PMID: 30651365 PMCID: PMC6430541 DOI: 10.1128/jvi.01587-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
The influenza virus nonstructural protein 1 (NS1) is a nonstructural protein that plays a major role in antagonizing host interferon responses during infection. However, a clear role for the NS1 protein in epigenetic modification has not been established. In this study, NS1 was found to regulate the expression of some key regulators of JAK-STAT signaling by inhibiting the DNA methylation of their promoters. Furthermore, DNA methyltransferase 3B (DNMT3B) is responsible for this process. Upon investigating the mechanisms underlying this event, NS1 was found to interact with DNMT3B but not DNMT3A, leading to the dissociation of DNMT3B from the promoters of the corresponding genes. In addition, the interaction between NS1 and DNMT3B changed the localization of DNMT3B from the nucleus to the cytosol, resulting in K48-linked ubiquitination and degradation of DNMT3B in the cytosol. We conclude that NS1 interacts with DNMT3B and changes its localization to mediate K48-linked polyubiquitination, subsequently contributing to the modulation of the expression of JAK-STAT signaling suppressors.IMPORTANCE The nonstructural protein 1 (NS1) of the influenza A virus (IAV) is a multifunctional protein that counters cellular antiviral activities and is a virulence factor. However, the involvement of NS1 in DNA methylation during IAV infection has not been established. Here, we reveal that the NS1 protein binds the cellular DNMT3B DNA methyltransferase, thereby inhibiting the methylation of the promoters of genes encoding suppressors of JAK-STAT signaling. As a result, these suppressor genes are induced, and JAK-STAT signaling is inhibited. Furthermore, we demonstrate that the NS1 protein transports DNMT3B to the cytoplasm for ubiquitination and degradation. Thus, we identify the NS1 protein as a potential trigger of the epigenetic deregulation of JAK-STAT signaling suppressors and illustrate a novel mechanism underlying the regulation of host immunity during IAV infection.
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Affiliation(s)
- Shi Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Gang Xu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhongying Cao
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qing Wang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shun Li
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Nanfang Peng
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jingchuan Yin
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Haisheng Yu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengqi Li
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhangchuan Xia
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Zhou
- Animal Biosafety Level III Laboratory, Center for Animal Experiment, School of Medicine, Wuhan University, Wuhan, China
| | - Yong Lin
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Xueyu Wang
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Qian Li
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Chengliang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xuecheng Yang
- Department of Infectious Diseases, Union Hospital, Wuhan, China
| | - Jun Wang
- Center of Clinical Laboratory, The Fifth People's Hospital of Wuxi, Affiliated with Jiangnan University, Wuxi, Jiangsu, China
| | - Yinglong She
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengji Lu
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ying Zhu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
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16
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Abstract
DNA methylation is an epigenetic mechanism most commonly associated with transcriptional repression. While it is clear that DNA methylation can silence HIV proviral expression in in vitro latency models, its correlation with HIV persistence and expression in vivo is ambiguous, particularly in persons living with HIV (PLWH) receiving antiretroviral therapy (ART). DNA methylation is an epigenetic mechanism most commonly associated with transcriptional repression. While it is clear that DNA methylation can silence HIV proviral expression in in vitro latency models, its correlation with HIV persistence and expression in vivo is ambiguous, particularly in persons living with HIV (PLWH) receiving antiretroviral therapy (ART). Several factors potentially contribute to discrepancies between results in the literature, including differences in integration sites, functional proviral load, sampling bias, and stochastic PCR amplification. Recent studies into genomic features of cytosine methylation sites in mammalian genes offer potentially significant insights into this mechanism. Here, we discuss the importance of these factors in the context of the HIV.
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17
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Nunes JM, Furtado MN, de Morais Nunes ER, Sucupira MCA, Diaz RS, Janini LMR. Modulation of epigenetic factors during the early stages of HIV-1 infection in CD4 + T cells in vitro. Virology 2018; 523:41-51. [PMID: 30077875 DOI: 10.1016/j.virol.2018.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 11/15/2022]
Abstract
Several studies have related epigenetic mechanisms to HIV-1 latency. However, the epigenetic modifications of the host cell genome involved in the early stages of HIV-1 infection remain unclear. This study aimed to investigate epigenetic factors that are regulated at the beginning of HIV-1 infection in activated and resting CD4+ T cells. We analyzed the gene expression of 84 epigenetic targets, global DNA methylation, and HIV-1 replication kinetics for 36 h after infecting CD4+ T cells obtained from the blood of twelve healthy donors. The epigenetic targets aurora kinase B (AURKB), aurora kinase C (AURKC) and DNA methyltransferase 3B (DNMT3B), and the global DNA methylation profile are regulated during HIV-1 replication in CD4+ T cells, and this regulation can be influenced by the activation state of the cell at the time of infection. Approaches that affect the expression of these epigenetic targets could help current strategies to suppress HIV-1 replication.
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Affiliation(s)
- Jorge Meneses Nunes
- Laboratory of Retrovirology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Sao Paulo, SP, Brazil.
| | - Maria Nadiege Furtado
- Laboratory of Retrovirology, Discipline of Infectious Diseases, Universidade Federal de São Paulo, Sao Paulo, SP, Brazil.
| | - Edsel Renata de Morais Nunes
- Laboratory of Retrovirology, Discipline of Infectious Diseases, Universidade Federal de São Paulo, Sao Paulo, SP, Brazil.
| | - Maria Cecilia Araripe Sucupira
- Laboratory of Retrovirology, Discipline of Infectious Diseases, Universidade Federal de São Paulo, Sao Paulo, SP, Brazil.
| | - Ricardo Sobhie Diaz
- Laboratory of Retrovirology, Discipline of Infectious Diseases, Universidade Federal de São Paulo, Sao Paulo, SP, Brazil.
| | - Luiz Mário Ramos Janini
- Laboratory of Retrovirology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Sao Paulo, SP, Brazil; Laboratory of Retrovirology, Discipline of Infectious Diseases, Universidade Federal de São Paulo, Sao Paulo, SP, Brazil.
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18
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Kremer WW, Van Zummeren M, Novianti PW, Richter KL, Verlaat W, Snijders PJF, Heideman DAM, Steenbergen RDM, Dreyer G, Meijer CJLM. Detection of hypermethylated genes as markers for cervical screening in women living with HIV. J Int AIDS Soc 2018; 21:e25165. [PMID: 30101434 PMCID: PMC6088247 DOI: 10.1002/jia2.25165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/02/2018] [Indexed: 01/01/2023] Open
Abstract
INTRODUCTION To evaluate the performance of hypermethylation analysis of ASCL1, LHX8 and ST6GALNAC5 in physician-taken cervical scrapes for detection of cervical cancer and cervical intraepithelial neoplasia (CIN) grade 3 in women living with HIV (WLHIV) in South Africa. METHODS Samples from a prospective observational cohort study were used for these analyses. Two cohorts were included: a cohort of WLHIV who were invited for cervical screening (n = 321) and a gynaecologic outpatient cohort of women referred for evaluation of abnormal cytology or biopsy proven cervical cancer (n = 108, 60% HIV seropositive). Cervical scrapes collected from all subjects were analysed for hypermethylation of ASCL1, LHX8 and ST6GALNAC5 by multiplex quantitative methylation specific PCR (qMSP). Histology endpoints were available for all study subjects. RESULTS Hypermethylation levels of ASCL1, LHX8 and ST6GALNAC5 increased with severity of cervical disease. The performance for detection of CIN3 or worse (CIN3+ ) as assessed by the area under the receiver operating characteristic (ROC) curves (AUC) was good for ASCL1 and LHX8 (AUC 0.79 and 0.81 respectively), and moderate for ST6GALNAC5 (AUC 0.71). At a threshold corresponding to 75% specificity, CIN3+ sensitivity was 72.1% for ASCL1 and 73.8% for LHX8 and all samples from women with cervical cancer scored positive for these two markers. CONCLUSIONS Hypermethylation analysis of ASCL1 or LHX8 in cervical scrape material of WLHIV detects all cervical carcinomas with an acceptable sensitivity and good specificity for CIN3+ , warranting further exploration of these methylation markers as a stand-alone test for cervical screening in low-resource settings.
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Affiliation(s)
- Wieke W Kremer
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Marjolein Van Zummeren
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Putri W Novianti
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
- Department of Epidemiology and BiostatisticsVU University Medical CenterAmsterdamThe Netherlands
| | - Karin L Richter
- Department of Medical VirologyUniversity of Pretoria and National Health Laboratory ServicesPretoriaSouth Africa
| | - Wina Verlaat
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Peter JF Snijders
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Daniëlle AM Heideman
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Renske DM Steenbergen
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Greta Dreyer
- Department of Obstetrics and GynaecologyUniversity of PretoriaPretoriaSouth Africa
| | - Chris JLM Meijer
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
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19
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DiNardo AR, Nishiguchi T, Mace EM, Rajapakshe K, Mtetwa G, Kay A, Maphalala G, Secor WE, Mejia R, Orange JS, Coarfa C, Bhalla KN, Graviss EA, Mandalakas AM, Makedonas G. Schistosomiasis Induces Persistent DNA Methylation and Tuberculosis-Specific Immune Changes. THE JOURNAL OF IMMUNOLOGY 2018; 201:124-133. [PMID: 29752313 DOI: 10.4049/jimmunol.1800101] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Abstract
Epigenetic mechanisms, such as DNA methylation, determine immune cell phenotype. To understand the epigenetic alterations induced by helminth coinfections, we evaluated the longitudinal effect of ascariasis and schistosomiasis infection on CD4+ T cell DNA methylation and the downstream tuberculosis (TB)-specific and bacillus Calmette-Guérin-induced immune phenotype. All experiments were performed on human primary immune cells from a longitudinal cohort of recently TB-exposed children. Compared with age-matched uninfected controls, children with active Schistosoma haematobium and Ascaris lumbricoides infection had 751 differentially DNA-methylated genes, with 72% hypermethylated. Gene ontology pathway analysis identified inhibition of IFN-γ signaling, cellular proliferation, and the Th1 pathway. Targeted real-time quantitative PCR after methyl-specific endonuclease digestion confirmed DNA hypermethylation of the transcription factors BATF3, ID2, STAT5A, IRF5, PPARg, RUNX2, IRF4, and NFATC1 and cytokines or cytokine receptors IFNGR1, TNFS11, RELT (TNF receptor), IL12RB2, and IL12B (p < 0.001; Sidak-Bonferroni). Functional blockage of the IFN-γ signaling pathway was confirmed, with helminth-infected individuals having decreased upregulation of IFN-γ-inducible genes (Mann-Whitney p < 0.05). Hypomethylation of the IL-4 pathway and DNA hypermethylation of the Th1 pathway was confirmed by Ag-specific multidimensional flow cytometry demonstrating decreased TB-specific IFN-γ and TNF and increased IL-4 production by CD4+ T cells (Wilcoxon signed-rank p < 0.05). In S. haematobium-infected individuals, these DNA methylation and immune phenotypic changes persisted at least 6 mo after successful deworming. This work demonstrates that helminth infection induces DNA methylation and immune perturbations that inhibit TB-specific immune control and that the duration of these changes are helminth specific.
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Affiliation(s)
- Andrew R DiNardo
- The Global Tuberculosis Program, Immigrant and Global Health, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030;
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Immigrant and Global Health, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Emily M Mace
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Hospital Center for Human Immunobiology, Department of Pediatrics, Texas Children's Hospital Center for Human Immunobiology, Baylor College of Medicine, Houston, TX 77030
| | - Kimal Rajapakshe
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Godwin Mtetwa
- Baylor-Swaziland Children's Foundation, Mbabane H100, Swaziland
| | - Alexander Kay
- Baylor-Swaziland Children's Foundation, Mbabane H100, Swaziland
| | | | - W Evan Secor
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA 30333
| | - Rojelio Mejia
- Department of Pediatrics, National School of Tropical Medicine, Texas Children's Hospital Center for Human Immunobiology, Houston, TX 77030
| | - Jordan S Orange
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Hospital Center for Human Immunobiology, Department of Pediatrics, Texas Children's Hospital Center for Human Immunobiology, Baylor College of Medicine, Houston, TX 77030
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Kapil N Bhalla
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX 77030; and
| | - Edward A Graviss
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX 77030
| | - Anna M Mandalakas
- The Global Tuberculosis Program, Immigrant and Global Health, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - George Makedonas
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030.,Texas Children's Hospital Center for Human Immunobiology, Department of Pediatrics, Texas Children's Hospital Center for Human Immunobiology, Baylor College of Medicine, Houston, TX 77030
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20
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Nag M, De Paris K, E Fogle J. Epigenetic Modulation of CD8⁺ T Cell Function in Lentivirus Infections: A Review. Viruses 2018; 10:v10050227. [PMID: 29710792 PMCID: PMC5977220 DOI: 10.3390/v10050227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/16/2023] Open
Abstract
CD8+ T cells are critical for controlling viremia during human immunodeficiency virus (HIV) infection. These cells produce cytolytic factors and antiviral cytokines that eliminate virally- infected cells. During the chronic phase of HIV infection, CD8+ T cells progressively lose their proliferative capacity and antiviral functions. These dysfunctional cells are unable to clear the productively infected and reactivated cells, representing a roadblock in HIV cure. Therefore, mechanisms to understand CD8+ T cell dysfunction and strategies to boost CD8+ T cell function need to be investigated. Using the feline immunodeficiency virus (FIV) model for lentiviral persistence, we have demonstrated that CD8+ T cells exhibit epigenetic changes such as DNA demethylation during the course of infection as compared to uninfected cats. We have also demonstrated that lentivirus-activated CD4+CD25+ T regulatory cells induce forkhead box P3 (Foxp3) expression in virus-specific CD8+ T cell targets, which binds the interleukin (IL)-2, tumor necrosis factor (TNF)-α, and interferon (IFN)-γ promoters in these CD8+ T cells. Finally, we have reported that epigenetic modulation reduces Foxp3 binding to these promoter regions. This review compares and contrasts our current understanding of CD8+ T cell epigenetics and mechanisms of lymphocyte suppression during the course of lentiviral infection for two animal models, FIV and simian immunodeficiency virus (SIV).
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Affiliation(s)
- Mukta Nag
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
| | - Kristina De Paris
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jonathan E Fogle
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
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21
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Epigenetic alterations are associated with monocyte immune dysfunctions in HIV-1 infection. Sci Rep 2018; 8:5505. [PMID: 29615725 PMCID: PMC5882962 DOI: 10.1038/s41598-018-23841-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/20/2018] [Indexed: 01/28/2023] Open
Abstract
Monocytes are key cells in the immune dysregulation observed during human immunodeficiency virus (HIV) infection. The events that take place specifically in monocytes may contribute to the systemic immune dysfunction characterized by excessive immune activation in infected individuals, which directly correlates with pathogenesis and progression of the disease. Here, we investigated the immune dysfunction in monocytes from untreated and treated HIV + patients and associated these findings with epigenetic changes. Monocytes from HIV patients showed dysfunctional ability of phagocytosis and killing, and exhibited dysregulated cytokines and reactive oxygen species production after M. tuberculosis challenge in vitro. In addition, we showed that the expression of enzymes responsible for epigenetic changes was altered during HIV infection and was more prominent in patients that had high levels of soluble CD163 (sCD163), a newly identified plasmatic HIV progression biomarker. Among the enzymes, histone acetyltransferase 1 (HAT1) was the best epigenetic biomarker correlated with HIV - sCD163 high patients. In conclusion, we confirmed that HIV impairs effector functions of monocytes and these alterations are associated with epigenetic changes that once identified could be used as targets in therapies aiming the reduction of the systemic activation state found in HIV patients.
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DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis. Viruses 2018; 10:v10020082. [PMID: 29438328 PMCID: PMC5850389 DOI: 10.3390/v10020082] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses have evolved various mechanisms to evade host immunity and ensure efficient viral replication and persistence. Several DNA tumor viruses modulate host DNA methyltransferases for epigenetic dysregulation of immune-related gene expression in host cells. The host immune responses suppressed by virus-induced aberrant DNA methylation are also frequently involved in antitumor immune responses. Here, we describe viral mechanisms and virus–host interactions by which DNA tumor viruses regulate host DNA methylation to evade antiviral immunity, which may contribute to the generation of an immunosuppressive microenvironment during cancer development. Recent trials of immunotherapies have shown promising results to treat multiple cancers; however, a significant number of non-responders necessitate identifying additional targets for cancer immunotherapies. Thus, understanding immune evasion mechanisms of cancer-causing viruses may provide great insights for reversing immune suppression to prevent and treat associated cancers.
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Expression profiling of chromatin-modifying enzymes and global DNA methylation in CD4+ T cells from patients with chronic HIV infection at different HIV control and progression states. Clin Epigenetics 2018; 10:20. [PMID: 29449904 PMCID: PMC5812196 DOI: 10.1186/s13148-018-0448-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/24/2018] [Indexed: 12/19/2022] Open
Abstract
Background Integration of human immunodeficiency virus type 1 (HIV-1) into the host genome causes global disruption of the chromatin environment. The abundance level of various chromatin-modifying enzymes produces these alterations and affects both the provirus and cellular gene expression. Here, we investigated potential changes in enzyme expression and global DNA methylation in chronically infected individuals with HIV-1 and compared these changes with non-HIV infected individuals. We also evaluated the effect of viral replication and degree of disease progression over these changes. Results Individuals with HIV-1 had a significant surge in the expression of DNA and histone methyltransferases (DNMT3A and DNMT3B, SETDB1, SUV39H1) compared with non-infected individuals, with the exception of PRMT6, which was downregulated. Some histone deacetylases (HDAC2 and HDAC3) were also upregulated in patients with HIV. Among individuals with HIV-1 with various degrees of progression and HIV control, the group of treated patients with undetectable viremia showed greater differences with the other two groups (untreated HIV-1 controllers and non-controllers). These latter two groups exhibited a similar behavior between them. Of interest, the overexpression of genes that associate with viral protein Tat (such as SETDB1 along with DNMT3A and HDAC1, and SIRT-1) was more prevalent in treated patients. We also observed elevated levels of global DNA methylation in individuals with HIV-1 in an inverse correlation with the CD4/CD8 ratio. Conclusions The current study shows an increase in chromatin-modifying enzymes and remodelers and in global DNA methylation in patients with chronic HIV-1 infection, modulated by various levels of viral control and progression.
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24
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Boehm D, Ott M. Host Methyltransferases and Demethylases: Potential New Epigenetic Targets for HIV Cure Strategies and Beyond. AIDS Res Hum Retroviruses 2017; 33:S8-S22. [PMID: 29140109 DOI: 10.1089/aid.2017.0180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A successful HIV cure strategy may require reversing HIV latency to purge hidden viral reservoirs or enhancing HIV latency to permanently silence HIV transcription. Epigenetic modifying agents show promise as antilatency therapeutics in vitro and ex vivo, but also affect other steps in the viral life cycle. In this review, we summarize what we know about cellular DNA and protein methyltransferases (PMTs) as well as demethylases involved in HIV infection. We describe the biology and function of DNA methyltransferases, and their controversial role in HIV infection. We further explain the biology of PMTs and their effects on lysine and arginine methylation of histone and nonhistone proteins. We end with a focus on protein demethylases, their unique modes of action and their emerging influence on HIV infection. An outlook on the use of methylation-modifying agents in investigational HIV cure strategies is provided.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
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25
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Abstract
OBJECTIVE Cervical cancer is the leading cause of cancer-related death in women in South Africa. This study evaluates DNA methylation levels in cervical (pre)cancer and aims to assess the value of high-risk human papillomavirus (hrHPV) testing and methylation analysis, alone or in combination, on physician-taken cervical scrapes to detect cervical cancer, and cervical intraepithelial neoplasia grade 3 (CIN3) in an HIV-infected South African population. DESIGN Prospective observational multicentre cohort study. METHODS Women from a cohort of women living with HIV (n = 355) and a referral cohort (n = 109, 60% HIV seropositive) were included. Cervical scrapes were collected for hrHPV testing and methylation analysis of cell adhesion molecule 1, T-lymphocyte maturation-associated protein, and microRNA124-2 genes. Histologic endpoints were available for all participants. Performance for detection of CIN3 or worse (CIN3+) was determined in the cohort of women living with HIV and different testing strategies were compared. RESULTS HrHPV and methylation positivity rates increased with severity of cervical disease in the two study cohorts, each reaching 100% in samples of women with carcinoma. HrHPV testing showed a sensitivity for CIN3+ of 83.6%, at a specificity of 67.7%. Methylation analysis showed a comparable CIN3+ sensitivity of 85.2%, but a significantly lower specificity of 49.6%. HrHPV testing with reflex methylation analysis showed a CIN3+ sensitivity of 73.8%, at a specificity of 81.5%. CONCLUSION In this HIV-infected South African population, stratifying hrHPV-positive women with reflex methylation analysis detects all cervical carcinomas and yields an acceptable sensitivity and specificity for CIN3+.
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26
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Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K. Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics 2016; 11:750-760. [PMID: 27672717 PMCID: PMC5094631 DOI: 10.1080/15592294.2016.1221569] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic control of human immunodeficiency virus-1 (HIV-1) genes is critical for viral integration and latency. However, epigenetic changes in the HIV-1-infected host genome have not been well characterized. Here, we report the first large-scale epigenome-wide association study of DNA methylation for HIV-1 infection. We recruited HIV-infected (n = 261) and uninfected (n = 117) patients from the Veteran Aging Cohort Study (VACS) and all samples were profiled for 485,521 CpG sites in DNA extracted from the blood. After adjusting for cell type and clinical confounders, we identified 20 epigenome-wide significant CpGs for HIV-1 infection. Importantly, 2 CpGs in the promoter of the NLR family, CARD domain containing gene 5 (NLRC5), a key regulator of major histocompatibility complex class I gene expression, showed significantly lower methylation in HIV-infected subjects than in uninfected subjects (cg07839457: t = −6.03, Pnominal = 4.96 × 10−9; cg16411857: t = −7.63, Pnominal = 3.07 × 10−13). Hypomethylation of these 2 CpGs was replicated in an independent sample (GSE67705: cg07839457: t = −4.44, Pnominal = 1.61 × 10−5; cg16411857: t = −5.90; P = 1.99 × 10−8). Methylation of these 2 CpGs in NLRC5 was negatively correlated with viral load in the 2 HIV-infected samples (cg07839457: P = 1.8 × 10−4; cg16411857: P = 0.03 in the VACS; and cg07839457: P = 0.04; cg164111857: P = 0.01 in GSE53840). Our findings demonstrate that differential DNA methylation is associated with HIV infection and suggest the involvement of a novel host gene, NLRC5, in HIV pathogenesis.
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Affiliation(s)
- Xinyu Zhang
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Amy C Justice
- c Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System , West Haven , CT , USA
| | - Ying Hu
- d Center for Biomedical Informatics & Information Technology, National Cancer Institute , Bethesda , MD , USA
| | - Zuoheng Wang
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Hongyu Zhao
- f Department of Biostatistics , Yale School of Public Health , New Haven , CT , USA
| | - Guilin Wang
- g Yale Center of Genomic Analysis, West Campus , Orange , CT , USA
| | - Eric O Johnson
- h Fellow Program and Behavioral Health and Criminal Justice Division, RTI International , Research Triangle Park, NC , USA
| | - Brinda Emu
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - Richard E Sutton
- e Department of Internal Medicine , Division of Infectious Disease, Yale University School of Medicine , New Haven , CT , USA
| | - John H Krystal
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
| | - Ke Xu
- a Department of Psychiatry , Yale School of Medicine , New Haven , CT , USA.,b Connecticut Veteran Health System , West Haven , CT , USA
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HIV-Induced Epigenetic Alterations in Host Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 879:27-38. [PMID: 26659262 DOI: 10.1007/978-3-319-24738-0_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human immunodeficiency virus (HIV), a member of the Retroviridae family, is a positive-sense, enveloped RNA virus. HIV, the causative agent of acquired immunodeficiency syndrome (AIDS) has two major types, HIV-1 and HIV-2 In HIV-infected cells the single stranded viral RNA genome is reverse transcribed and the double-stranded viral DNA integrates into the cellular DNA, forming a provirus. The proviral HIV genome is controlled by the host epigenetic regulatory machinery. Cellular epigenetic regulators control HIV latency and reactivation by affecting the chromatin state in the vicinity of the viral promoter located to the 5' long terminal repeat (LTR) sequence. In turn, distinct HIV proteins affect the epigenotype and gene expression pattern of the host cells. HIV-1 infection of CD4(+) T cells in vitro upregulated DNMT activity and induced hypermethylation of distinct cellular promoters. In contrast, in the colon mucosa and peripheral blood mononuclear cells from HIV-infected patients demethylation of the FOXP3 promoter was observed, possibly due to the downregulation of DNA methyltransferase 1. For a curative therapy of HIV infected individuals and AIDS patients, a combination of antiretroviral drugs with epigenetic modifying compounds have been suggested for the reactivation of latent HIV-1 genomes. These epigenetic drugs include histone deacetylase inhibitors (HDACI), histone methyltransferase inhibitors (HMTI), histone demethylase inhibitors, and DNA methyltransferase inhibitors (DNMTI).
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28
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HIV mono-infection is associated with an impaired anti-hepatitis C virus activity of natural killer cells. AIDS 2016; 30:355-63. [PMID: 26558728 DOI: 10.1097/qad.0000000000000963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Hepatitis C virus (HCV) infection in HIV(+) patients is associated with faster liver disease progression compared with HCV mono-infection. HIV-associated immune defects are considered to play an important role in this context. Here, we analyzed the effects of HIV infection on natural killer (NK)-cell-mediated anti-HCV activity. DESIGN NK cell phenotype and interferon gamma (IFN-γ) production, NK cell-mediated inhibition of HCV replication and CD4 T-cell/NK cell interactions were studied in treatment naive HIV (n = 22), and HIV patients under combined antiretroviral therapy (n = 29), compared with healthy controls (n = 20). METHODS NK cell-mediated inhibition of HCV replication was analyzed using the HuH7A2HCVreplicon model. IFN-γ production of NK cells as well as interleukin-2 secretion of CD4 T lymphocytes were studied by flow cytometry. RESULTS Peripheral blood mononuclear cells from HIV(+) patients displayed a significantly impaired anti-HCV activity, irrespective of combined antiretroviral therapy. This could in part be explained by HIV-associated decline in NK cell numbers. In addition, NK cell IFN-γ production was significantly impaired in HIV infection. Accordingly, we found low frequency of IFN-γ(+) NK cells in HIV(+) patients to be associated with ineffective inhibition of HCV replication. Finally, we show that CD4 T-cell-mediated stimulation of NK cell IFN-γ production was dysregulated in HIV infection with an impaired interleukin-2 response of NK cells. CONCLUSION HIV infection has a strong suppressive effect on anti-HCV activity of NK cells. This may contribute to low spontaneous clearance rate and accelerated progression of HCV-associated liver disease observed in HIV(+) patients.
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Dahlen HG, Downe S, Wright ML, Kennedy HP, Taylor JY. Childbirth and consequent atopic disease: emerging evidence on epigenetic effects based on the hygiene and EPIIC hypotheses. BMC Pregnancy Childbirth 2016; 16:4. [PMID: 26762406 PMCID: PMC4712556 DOI: 10.1186/s12884-015-0768-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/02/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In most high and middle income countries across the world, at least 1:4 women give birth by cesarean section. Rates of labour induction and augmentation are rising steeply; and in some countries up to 50% of laboring women and newborns are given antibiotics. Governments and international agencies are increasingly concerned about the clinical, economic and psychosocial effects of these interventions. DISCUSSION There is emerging evidence that certain intrapartum and early neonatal interventions might affect the neonatal immune response in the longer term, and perhaps trans-generationally. Two theories lead the debate in this area. Those aligned with the hygiene (or 'Old Friends') hypothesis have examined the effect of gut microbiome colonization secondary to mode of birth and intrapartum/neonatal pharmacological interventions on immune response and epigenetic phenomena. Those working with the EPIIC (Epigenetic Impact of Childbirth) hypothesis are concerned with the effects of eustress and dys-stress on the epigenome, secondary to mode of birth and labour interventions. This paper examines the current and emerging findings relating to childbirth and atopic/autoimmune disease from the perspective of both theories, and proposes an alliance of research effort. This is likely to accelerate the discovery of important findings arising from both approaches, and to maximize the timely understanding of the longer-term consequences of childbirth practices.
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Affiliation(s)
- H G Dahlen
- School of Nursing and Midwifery, Western Sydney University, Locked Bag 1797, Penrith, 2751, NSW, Australia.
| | - S Downe
- University of Central Lancashire, Preston, PR3 2LE, Lancashire, UK.
| | - M L Wright
- Yale School of Nursing, 400 West Campus Drive, West Haven, CT, 06516, USA.
| | - H P Kennedy
- Yale School of Nursing, 400 West Campus Drive, West Haven, CT, 06516, USA.
| | - J Y Taylor
- Yale School of Nursing, 400 West Campus Drive, West Haven, CT, 06516, USA.
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30
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Lopez M, Halby L, Arimondo PB. DNA Methyltransferase Inhibitors: Development and Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:431-473. [DOI: 10.1007/978-3-319-43624-1_16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Yang T, Li S, Zhang X, Pang X, Lin Q, Cao J. Resveratrol, sirtuins, and viruses. Rev Med Virol 2015; 25:431-45. [DOI: 10.1002/rmv.1858] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/19/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Tao Yang
- College of Food Science and Technology; Central South University of Forestry and Technology; Changsha Hunan Province China
| | - Shugang Li
- Construction Corps Key Laboratory of Deep Processing on Featured Agricultural Products in South Xinjiang; Tarim University; Alar Xinjiang China
| | - Xuming Zhang
- Department of Microbiology and Immunology; University of Arkansas for Medical Sciences; Little Rock AR USA
| | - Xiaowu Pang
- Departments of Oral Pathology, College of Dentistry; Howard University; Washington DC USA
| | - Qinlu Lin
- College of Food Science and Technology; Central South University of Forestry and Technology; Changsha Hunan Province China
| | - Jianzhong Cao
- College of Food Science and Technology; Central South University of Forestry and Technology; Changsha Hunan Province China
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32
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Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1. Sci Rep 2015; 5:10806. [PMID: 26039376 PMCID: PMC4454074 DOI: 10.1038/srep10806] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/29/2015] [Indexed: 12/18/2022] Open
Abstract
Nowadays, the knowledge in DNA methylation-mediated gene regulation has shed light on the understanding of virus-host interplay in the context of genome alteration. It has also been shown that HIV is able to change the DNA methylation pattern by DNA methyltransferases and such changes can be correlated with the progression of AIDS. In this study, we have investigated the relationship between genome-wide DNA methylation pattern and HIV infection using the methylated DNA immunoprecipitation - microarray method. A pair of monozygotic twins was recruited: one of the twins was infected with HIV while the other was not. Based on data from the microarray experiment, 4679 differentially methylated regions in the HIV positive subject with the significant peak values were identified. Selected genes were then validated in human T lymphocyte CEM*174 cell line and HIV/AIDS patients by comparing with normal subjects. We found that IGFBP6 and SATB2 were significantly down-regulated in HIV-infected CEM*174 cells and 3 different cohorts of HIV/AIDS patients while their promoters were predominantly hyper-methylated compared with normal controls. This study also provides a resource for the identification of HIV-induced methylation and contributes to better understanding of the development of HIV/AIDS.
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Miller MM, Akaronu N, Thompson EM, Hood SF, Fogle JE. Modulating DNA methylation in activated CD8+ T cells inhibits regulatory T cell-induced binding of Foxp3 to the CD8+ T Cell IL-2 promoter. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 194:990-8. [PMID: 25548225 PMCID: PMC4297683 DOI: 10.4049/jimmunol.1401762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have previously demonstrated that CD4(+)CD25(+) regulatory T cells (Tregs) activated during the course of feline immunodeficiency virus (FIV) infection suppress CD8(+) CTL function in a TGF-β-dependent fashion, inhibiting IFN-γ and IL-2 production and inducing G1 cell-cycle arrest. In this article, we describe the molecular events occurring at the IL-2 promoter leading to suppression of IL-2 production. These experiments demonstrate that Foxp3 induced by lentivirus-activated Tregs in the CD8(+) target cells binds to the IL-2 promoter, actively repressing IL-2 transcription. We further demonstrate that the chronic activation of CD8(+) T cells during FIV infection results in chromatin remodeling at the IL-2 promoter, specifically, demethylation of CpG residues. These DNA modifications occur during active transcription and translation of IL-2; however, these changes render the IL-2 promoter permissive to Foxp3-induced transcriptional repression. These data help explain, in part, the seemingly paradoxical observations that CD8(+) T cells displaying an activation phenotype exhibit altered antiviral function. Further, we demonstrate that blocking demethylation of CpG residues at the IL-2 promoter inhibits Foxp3 binding, suggesting a potential mechanism for rescue and/or reactivation of CD8(+) T cells. Using the FIV model for lentiviral persistence, these studies provide a framework for understanding how immune activation combined with Treg-mediated suppression may affect CD8(+) T cell IL-2 transcription, maturation, and antiviral function.
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Affiliation(s)
- Michelle M Miller
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Nnenna Akaronu
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Elizabeth M Thompson
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Sylvia F Hood
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
| | - Jonathan E Fogle
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607
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34
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Smith NLD, Denning DW. Clinical implications of interferon-γ genetic and epigenetic variants. Immunology 2015; 143:499-511. [PMID: 25052001 DOI: 10.1111/imm.12362] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 12/25/2022] Open
Abstract
Interferon-γ (IFN-γ) is an integral and critical molecule of the immune system, with multiple functions, mostly related to the T helper type 1 (Th1) response to infection. It is critical for defence against mycobacterial infection and is of increasing interest in defence against fungi. In this article, we review the genetic and epigenetic variants affecting IFN-γ expression and investigate its role in disease, with an emphasis on fungal diseases such as invasive and chronic pulmonary aspergillosis. Over 347 IFN-γ gene variants have been described, in multiple ethnic populations. Many appear to confer a susceptibility to disease, especially tuberculosis (TB) and hepatitis, but also some non-infectious conditions such as aplastic anaemia, cervical cancer and psoriasis. Several epigenetic modifications are also described, increasing IFN-γ expression in Th1 lymphocytes and reducing IFN-γ expression in Th2 lymphocytes. Recombinant IFN-γ administration is licensed for the prophylaxis of infection (bacterial and fungal) in patients with the phagocyte functional deficiency syndrome chronic granulomatous disease, although the benefits appear limited. Interferon-γ therapy is given to patients with profound defects in IFN-γ and interleukin-12 production and appears to be beneficial for patients with invasive aspergillosis and cryptococcal meningitis, but the studies are not definitive. A high proportion of patients with chronic pulmonary aspergillosis are poor producers of IFN-γ in response to multiple stimuli and could also benefit from IFN-γ administration. The investigation and management of patients with possible or demonstrated IFN-γ deficiency in adulthood is poorly studied and could be greatly enhanced with the integration of genetic data.
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Affiliation(s)
- Nicola L D Smith
- Manchester Fungal Infection Group, Faculty of Medical and Human Science, The University of Manchester, Manchester, UK; Manchester Academic Health Science Centre, University Hospital South Manchester NHS Foundation Trust, Manchester, UK; NIHR South Manchester Respiratory and Allergy Clinical Research Facility, Manchester, UK
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Küçükali Cİ, Kürtüncü M, Çoban A, Çebi M, Tüzün E. Epigenetics of multiple sclerosis: an updated review. Neuromolecular Med 2014; 17:83-96. [PMID: 24652042 DOI: 10.1007/s12017-014-8298-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/13/2014] [Indexed: 01/24/2023]
Abstract
Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease characterized with autoimmune response against myelin proteins and progressive axonal loss. The heterogeneity of the clinical course and low concordance rates in monozygotic twins have indicated the involvement of complex heritable and environmental factors in MS pathogenesis. MS is more often transmitted to the next generation by mothers than fathers suggesting an epigenetic influence. One of the possible reasons of this parent-of-origin effect might be the human leukocyte antigen-DRB1*15 allele, which is the major risk factor for MS and regulated by epigenetic mechanisms such as DNA methylation and histone deacetylation. Moreover, major environmental risk factors for MS, vitamin D deficiency, smoking and Ebstein-Barr virus are all known to exert epigenetic changes. In the last few decades, compelling evidence implicating the role of epigenetics in MS has accumulated. Increased or decreased acetylation, methylation and citrullination of genes regulating the expression of inflammation and myelination factors appear to be particularly involved in the epigenetics of MS. Although much less is known about epigenetic factors causing neurodegeneration, epigenetic mechanisms regulating axonal loss, apoptosis and mitochondrial dysfunction in MS are in the process of identification. Additionally, expression levels of several microRNAs (miRNAs) (e.g., miR-155 and miR-326) are increased in MS brains and potential mechanisms by which these factors might influence MS pathogenesis have been described. Certain miRNAs may also be potentially used as diagnostic biomarkers in MS. Several reagents, especially histone deacetylase inhibitors have been shown to ameliorate the symptoms of experimental allergic encephalomyelitis. Ongoing efforts in this field are expected to result in characterization of epigenetic factors that can be used in prediction of treatment responsive MS patients, diagnostic screening panels and treatment methods with specific mechanism of action.
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Affiliation(s)
- Cem İsmail Küçükali
- Department of Neuroscience, Institute for Experimental Medicine (DETAE), Istanbul University, Istanbul, Turkey
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Takahashi K. Influence of bacteria on epigenetic gene control. Cell Mol Life Sci 2014; 71:1045-54. [PMID: 24132510 PMCID: PMC11113846 DOI: 10.1007/s00018-013-1487-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 01/26/2023]
Abstract
Cellular information is inherited by daughter cells through epigenetic routes in addition to genetic routes. Epigenetics, which is primarily mediated by inheritable DNA methylation and histone post-translational modifications, involves changes in the chromatin structure important for regulating gene expression. It is widely known that epigenetic control of gene expression plays an essential role in cell differentiation processes in vertebrates. Furthermore, because epigenetic changes can occur reversibly depending on environmental factors in differentiated cells, they have recently attracted considerable attention as targets for disease prevention and treatment. These environmental factors include diet, exposure to bacteria or viruses, and air pollution, of which this review focuses on the influence of bacteria on epigenetic gene control in a host. Host-bacterial interactions not only occur upon pathogenic bacterial infection but also continuously exist between commensal bacteria and the host. These bacterial stimuli play an essential role in various biological responses involving external stimuli and in maintaining physiological homeostasis by altering epigenetic markers and machinery.
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Affiliation(s)
- Kyoko Takahashi
- Food and Physiological Functions Laboratory, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa-shi, Kanagawa, 252-0880, Japan,
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Zhang JC, Gao B, Yu ZT, Liu XB, Lu J, Xie F, Luo HJ, Li HP. Promoter hypermethylation of p14 (ARF) , RB, and INK4 gene family in hepatocellular carcinoma with hepatitis B virus infection. Tumour Biol 2013; 35:2795-802. [PMID: 24254306 DOI: 10.1007/s13277-013-1372-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/28/2013] [Indexed: 01/14/2023] Open
Abstract
Both hepatitis B virus (HBV) and gene methylation play important roles in hepatocarcinogenesis. However, their association between HBV infection and gene methylation is not fully understood. Cell cycle control involving RB1 gene-related cell inhibitors is one of the main regulatory pathways were reported to be altered in hepatocellular carcinoma (HCC). The purpose of this research is to assess the methylation status of p14 (ARF) and INK4 gene family (p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and p18 (INK4C) ) in HCC with HBV infection and HCC without it, and discuss possible role of HBV-induced hypermethylation in the mechanism of hepatocarcinogenesis. Methylation status of RB, p14 (ARF) , and INK4 gene family in 64 case of HCC with HBV infection and 24 cases without it were detected by methylation-specific polymerase chain reaction, and HBV-DNA of the plasma were detected by quantitative real-time polymerase chain reaction. p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB hypermethylation were observed in 30 (34.1%), 50 (56.8%), 62 (70.5%), and 24(27.3%) of 88 hepatocellular carcinomas, respectively. Methylation frequencies of them between HCC with HBV infection and HCC without it were 43.8% versus 8.3 % (p14 (ARF) ), 68.9% versus 25% (p15 (INK4B) ), 90.6% versus 16.7% ( p16 (INK4A) ), and 28.1 % versus 25% (RB), respectively. In HBV-associated HCC, the numbers of methylated genes were also more than HCC without virus infection, more than two methylated genes were seen in 48 of 64 (75 %) cases; more than three methylated genes were found in 32 of 64 (50%); correspondently, no one case has more than two genes methylated. p18 (INK4C) methylation product was not found in cancerous or non-cancerous tissues of 88 HCC. HBV infection is associated with p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB gene methylation (P = 0.048, 0.035, 0.02); HBV-DNA replication is associated with p14 (ARF) , p15 (INK4B) , p16 (INK4A) , and RB gene methylation (P = 0.048, 0.035, 0.02); high rate of p14 (ARF) , p15 (INK4B) , and p16 (INK4A) in HCC with HBV infection suggests that HBV-induced hypermethylation may be one of the mechanisms of HBV involved in hepatocellular carcinogenesis.
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Affiliation(s)
- Ji-Cai Zhang
- Department of Laboratory Medicine, Taihe Hospital Affiliated to Hubei University of Medicine, Shiyan, 442000, People's Republic of China
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Niller HH, Banati F, Nagy K, Buzas K, Minarovits J. Update on microbe-induced epigenetic changes: bacterial effectors and viral oncoproteins as epigenetic dysregulators. Future Virol 2013. [DOI: 10.2217/fvl.13.97] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Pathoepigenetics is a new discipline describing how disturbances in epigenetic regulation alter the epigenotype and gene-expression pattern of human, animal or plant cells. Such ‘epigenetic reprogramming’ may play an important role in the initiation and progression of a wide variety of diseases. Infectious diseases also belong to this category: recent data demonstrated that microbial pathogens, including bacteria and viruses, are capable of dysregulating the epigenetic machinery of their host cell. The resulting heritable changes in host cell gene expression may favor the colonization, growth or spread of infectious pathogens. It may also facilitate the establishment of latency and malignant cell transformation. In this article, we review how bacterial epigenetic effectors and inflammatory processes elicited by bacteria alter the host cell epigenotype, and describe how oncoproteins encoded by human tumor viruses act as epigenetic dysregulators to alter the phenotype and behavior of host cells.
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Affiliation(s)
- Hans Helmut Niller
- Institute for Medical Microbiology & Hygiene, University of Regensburg, Franz-Josef-Strauss Allee 11, Regensburg D93053, Germany
| | - Ferenc Banati
- RT-Europe Nonprofit Research Center, H-9200 Mosonmagyarovar, Pozsonyi út 88, Hungary
| | - Katalin Nagy
- University of Szeged, Faculty of Dentistry, Department of Oral Surgery, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
| | - Krisztina Buzas
- University of Szeged, Faculty of Dentistry, Department of Oral Biology & Experimental Dental Research, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
| | - Janos Minarovits
- University of Szeged, Faculty of Dentistry, Department of Oral Biology & Experimental Dental Research, H-6720 Szeged, Tisza Lajos Krt. 64, Hungary
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Pion M, Jaramillo-Ruiz D, Martínez A, Muñoz-Fernández MA, Correa-Rocha R. HIV infection of human regulatory T cells downregulates Foxp3 expression by increasing DNMT3b levels and DNA methylation in the FOXP3 gene. AIDS 2013; 27:2019-29. [PMID: 24201117 DOI: 10.1097/qad.0b013e32836253fd] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Regulatory T cells (Tregs) play an important role in infections modulating host immune responses and avoiding overreactive immunity. The mechanisms underlying their action in HIV-infected patients have not been well established. HIV can infect Treg, but little is known about the effects of the infection on Treg phenotype and function. The objective of this study was to investigate whether in-vitro HIV infection modifies the phenotype and suppressive capacity of Treg cells. DESIGN Because Treg cells are a subset of CD4 T cells, HIV infection could produce alterations in the phenotype and methylation pattern of Treg disturbing the functionality of these cells. METHODS Isolated Treg cells from healthy volunteers were cultured in the presence of HIV-1, and phenotype, methylation pattern of FOXP3 locus, cytokine secretion profile and suppressive function of infected Treg were analysed in comparison with noninfected Treg. RESULTS We demonstrate that HIV-1 directly infects Treg and deregulates the function and the phenotype that define these cells. HIV infection downregulates the Foxp3 expression in Treg, which is followed by the loss of suppressive capacity and alterations in cytokine secretion pattern, with decreased production of transforming growth factor-beta (TGF-β) and an increased production of interleukin (IL)-4. Foxp3 downregulation in HIV-infected Treg was related to an increase in the expression of DNA methyltransferase3b (DNMT3b) associated with higher methylation of CpG sites in the FOXP3 locus. CONCLUSION These findings are pivotal to our understanding of the role of Treg in HIV infection and indicate that regulatory function could be seriously impaired in HIV-infected patients contributing to the immune hyperactivation.
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Affiliation(s)
- Marjorie Pion
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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40
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Wang XX, Ying P, Diao F, Wang Q, Ye D, Jiang C, Shen N, Xu N, Chen WB, Lai SS, Jiang S, Miao XL, Feng J, Tao WW, Zhao NW, Yao B, Xu ZP, Sun HX, Li JM, Sha JH, Huang XX, Shi QH, Tang H, Gao X, Li CJ. Altered protein prenylation in Sertoli cells is associated with adult infertility resulting from childhood mumps infection. ACTA ACUST UNITED AC 2013; 210:1559-74. [PMID: 23825187 PMCID: PMC3727317 DOI: 10.1084/jem.20121806] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Loss of GGPPS from childhood mumps infection or deletion in mice results in constitutively activated MAPK and NF-kB signaling that induces spermatogonium apoptosis, macrophage invasion into seminiferous tubules, and sterility. Mumps commonly affects children 5–9 yr of age, and can lead to permanent adult sterility in certain cases. However, the etiology of this long-term effect remains unclear. Mumps infection results in progressive degeneration of the seminiferous epithelium and, occasionally, Sertoli cell–only syndrome. Thus, the remaining Sertoli cells may be critical to spermatogenesis recovery after orchitis healing. Here, we report that the protein farnesylation/geranylgeranylation balance is critical for patients’ fertility. The expression of geranylgeranyl diphosphate synthase 1 (GGPPS) was decreased due to elevated promoter methylation in the testes of infertile patients with mumps infection history. When we deleted GGPPS in mouse Sertoli cells, these cells remained intact, whereas the adjacent spermatogonia significantly decreased after the fifth postnatal day. The proinflammatory MAPK and NF-κB signaling pathways were constitutively activated in GGPPS−/− Sertoli cells due to the enhanced farnesylation of H-Ras. GGPPS−/− Sertoli cells secreted an array of cytokines to stimulate spermatogonia apoptosis, and chemokines to induce macrophage invasion into the seminiferous tubules. Invaded macrophages further blocked spermatogonia development, resulting in a long-term effect through to adulthood. Notably, this defect could be rescued by GGPP administration in EMCV-challenged mice. Our results suggest a novel mechanism by which mumps infection during childhood results in adult sterility.
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Affiliation(s)
- Xiu-Xing Wang
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center and Jiangsu Key Laboratory of Molecular Medicine of the School of Medicine, Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
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Martinez-Colom A, Lasarte S, Fernández-Pineda A, Relloso M, Muñoz-Fernández MA. A new chimeric protein represses HIV-1 LTR-mediated expression by DNA methylase. Antiviral Res 2013; 98:394-400. [PMID: 23588231 DOI: 10.1016/j.antiviral.2013.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 04/03/2013] [Accepted: 04/04/2013] [Indexed: 12/19/2022]
Abstract
Once the human immunodeficiency virus (HIV) genome is inserted into the host genome, the virus cannot be removed, which results in latency periods and makes it difficult to eradicate. The majority of strategies to eradicate HIV have been based on preventing virus latency, thereby enabling antiretroviral drugs to act against HIV replication. Another innovative strategy is permanently silencing the integrated virus to prevent the spread of infection. Epigenetic processes are natural mechanisms that can silence viral replication. We describe a new chimeric protein (IN3b) that consists of a HIV-1 integrase domain, which recognises the HIV long terminal repeat (LTR) and the catalytic domain of DNA methyltransferase DNMT3b. Our objective was to silence HIV replication by the specific delivery of the catalytic methyltransferase domain to the LTR promoter to induce its methylation. We found that our IN3b chimeric protein was expressed in the nucleus and decreased LTR-associated HIV genome expression and HIV replication. Therefore, the IN3b chimeric protein may be an effective tool against HIV replication and maybe used in a new line of research to induce or maintain HIV latency.
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Affiliation(s)
- Alberto Martinez-Colom
- Laboratorio InmunoBiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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42
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Dong J, Chang HD, Ivascu C, Qian Y, Rezai S, Okhrimenko A, Cosmi L, Maggi L, Eckhardt F, Wu P, Sieper J, Alexander T, Annunziato F, Gossen M, Li J, Radbruch A, Thiel A. Loss of methylation at the IFNG promoter and CNS-1 is associated with the development of functional IFN-γ memory in human CD4(+) T lymphocytes. Eur J Immunol 2013; 43:793-804. [PMID: 23255246 DOI: 10.1002/eji.201242858] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/19/2012] [Accepted: 12/12/2012] [Indexed: 12/17/2022]
Abstract
Cytokine memory for IFN-γ production by effector/memory Th1 cells plays a key role in both protective and pathological immune responses. To understand the epigenetic mechanism determining the ontogeny of effector/memory Th1 cells characterized by stable effector functions, we identified a T-cell-specific methylation pattern at the IFNG promoter and CNS-1 in ex vivo effector/memory Th1 cells, and investigated methylation dynamics of these regions during the development of effector/memory Th1 cells. During Th1 differentiation, demethylation occurred at both the promoter and CNS-1 regions of IFNG as early as 16 h, and this process was independent of cell proliferation and DNA synthesis. Using an IFN-γ capture assay, we found early IFN-γ-producing cells from 2-day differentiating cultures acquired "permissive" levels of demethylation and developed into effector/memory Th1 cells undergoing progressive demethylation at the IFNG promoter and CNS-1 when induced by IL-12. Methylation levels of these regions in effector/memory Th1 cells of peripheral blood from rheumatoid arthritis patients correlated inversely with reduced frequencies of IFN-γ-producers, coincident with recruitment of effector/memory Th1 cells to the site of inflammation. Thus, after termination of TCR stimulation, IL-12 signaling potentiates the stable functional IFN-γ memory in effector/memory Th1 cells characterized by hypomethylation at the IFNG promoter and CNS-1.
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Affiliation(s)
- Jun Dong
- Regenerative Immunology and Aging, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany.
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Jacoby M, Gohrbandt S, Clausse V, Brons NH, Muller CP. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 2012; 7:1421-34. [PMID: 23151460 DOI: 10.4161/epi.22845] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA methylation regulates gene expression in a cell-type specific way. Although peripheral blood mononuclear cells (PBMCs) comprise a heterogeneous cell population, most studies of DNA methylation in blood are performed on total mononuclear cells. In this study, we investigated high resolution methylation profiles of 58 CpG sites dispersed over eight immune response genes in multiple purified blood cells from healthy adults and newborns. Adjacent CpG sites showed methylation levels that were increasingly correlated in adult blood vs. cord blood. Thus, while interindividual variability increases from newborn to adult blood, the underlying methylation changes may not be merely stochastic, but seem to be orchestrated as clusters of adjacent CpG sites. Multiple linear regression analysis showed that interindividual methylation variability was influenced by distance of average methylation levels to the closest border (0 or 100%), presence of transcription factor binding sites, CpG conservation across species and age. Furthermore, CD4+ and CD14+ cell types were negative predictors of methylation variability. Concerns that PBMC methylation differences may be confounded by variations in blood cell composition were justified for CpG sites with large methylation differences across cell types, such as in the IFN-γ gene promoter. Taken together, our data suggest that unsorted mononuclear cells are reasonable surrogates of CD8+ and, to a lesser extent, CD4+ T cell methylation in adult peripheral, but not in neonatal, cord blood.
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Affiliation(s)
- Monique Jacoby
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
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Mohamed Ariff I, Mitra A, Basu A. Epigenetic regulation of self-renewal and fate determination in neural stem cells. J Neurosci Res 2011; 90:529-39. [DOI: 10.1002/jnr.22804] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/18/2011] [Accepted: 09/02/2011] [Indexed: 01/30/2023]
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45
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Fan XP, Zou ZQ, Long B, Guo YM, Wang SK, Jia DX, Xu AL, Li FC, Fan YC, Wang K. Enhanced demethylation of interferon-γ gene promoter in peripheral blood mononuclear cells is associated with acute-on-chronic hepatitis B liver failure. TOHOKU J EXP MED 2011; 224:13-9. [PMID: 21505270 DOI: 10.1620/tjem.224.13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Acute-on-chronic hepatitis B liver failure (ACHBLF) refers to liver failure occurring in patients with chronic hepatitis B (CHB) related liver diseases. Interferon-γ (IFN-γ) plays an important role in the exacerbation of liver function. However, the exact mechanism, by which IFN-γ mediates ACHBLF, is not fully understood. Forty patients with ACHBLF, fifteen patients with CHB and ten healthy controls were included in this present study. ELISA was performed to measure the level of serum IFN-γ. The methylation status of IFN-γ promoter in peripheral blood mononuclear cells (PBMCs) was determined using methylation-specific PCR. Model for End-stage Liver Disease (MELD) scoring was performed for evaluating the severity of liver failure. The serum level of IFN-γ in patients with ACHBLF or CHB was significantly lower than that in healthy controls, while the serum IFN-γ level in ACHBLF patients was significantly higher than that in CHB patients. In ACHBLF patients, the level of IFN-γ was positively correlated with total bilirubin and MELD score, but negatively correlated with prothrombin time activity. These results suggest the involvement of IFN-γ in the pathogenesis of ACHBLF. Importantly, the degree of methylation of the IFN-γ gene promoter in ACHBLF patients (60%, 24/40) was significantly lower than that in CHB patients (93%, 14/15), but was higher than that in the control group (20%, 2/10). Furthermore, in ACHBLF patients, the serum IFN-γ level was significantly higher in unmethylation group than that in methylation group. In conclusion, enhanced demethylation of IFN-γ gene promoter in PBMCs may be associated with the onset of ACHBLF.
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Affiliation(s)
- Xiao-Peng Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, PR China
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Marsh LM, Pfefferle PI, Pinkenburg O, Renz H. Maternal signals for progeny prevention against allergy and asthma. Cell Mol Life Sci 2011; 68:1851-62. [PMID: 21369709 PMCID: PMC11115134 DOI: 10.1007/s00018-011-0644-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 02/08/2011] [Accepted: 02/15/2011] [Indexed: 01/04/2023]
Abstract
Allergy and asthma are chronic inflammatory diseases which result from complex gene-environment interactions. Recent evidence indicates the importance of prenatal and postnatal developmental processes in terms of maturation of balanced immune responses. According to the current view, gene-environment interactions during a restricted time frame are responsible for programming of the immune system in favor of allergic immune mechanisms later in life. The interaction between genes and environment is complex and only partially understood; however, heritable epigenetic modifications including chemical additions in and alternative packaging of the DNA have been shown to play a crucial role in this context. Novel data indicate that epigenetic mechanisms contribute to the development of T-helper cell function. Environmental factors, including diesel exhaust particles (DEP), vitamins and tobacco smoke, operate through such mechanisms. Furthermore, the role of environmental microbes provides another and maybe even more important group of exogenous exposures which operates in this critical time frame.
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Affiliation(s)
- Leigh Matthew Marsh
- Department of Clinical Chemistry and Molecular Diagnostics, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Petra Ina Pfefferle
- Department of Clinical Chemistry and Molecular Diagnostics, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Olaf Pinkenburg
- Department of Clinical Chemistry and Molecular Diagnostics, Philipps-University of Marburg, 35043 Marburg, Germany
| | - Harald Renz
- Institute for Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Medical Faculty, Philipps University of Marburg, Baldingerstraße 1, 35043 Marburg, Germany
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47
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Martino D, Prescott S. Epigenetics and prenatal influences on asthma and allergic airways disease. Chest 2011; 139:640-647. [PMID: 21362650 DOI: 10.1378/chest.10-1800] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Uterine life is arguably the most critical time in developmental programming, when environmental exposures may have the greatest potential to influence evolving fetal structure and function. There has been substantial progress in understanding the epigenetic mechanisms through which environmental exposures can permanently alter the expression of fetal genes and contribute to the increasing propensity for many complex diseases. These concepts of "developmental origins" of disease are being applied across virtually all fields of medicine, and emerging epigenetic paradigms are the likely mechanism behind the environment-driven epidemic of asthma and allergic disease. Here, we examine the epigenetic regulation of immune development and the early immune profiles that contribute to allergic risk. In particular we review new evidence that key environmental exposures, such as microbial exposure, dietary changes, tobacco smoke, and pollutants, can induce epigenetic changes in gene expression and alter disease risk. Although most of these factors have already been clearly implicated in epidemiologic studies of asthma and allergic disease, new studies investigating the mechanisms of these effects may provide new avenues for using these pathways for disease prevention.
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Affiliation(s)
- David Martino
- School of Paediatrics and Child Health Research, University of Western Australia, Perth, WA, Australia
| | - Susan Prescott
- School of Paediatrics and Child Health Research, University of Western Australia, Perth, WA, Australia.
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48
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Cumulative Epigenetic Abnormalities in Host Genes with Viral and Microbial Infection during Initiation and Progression of Malignant Lymphoma/Leukemia. Cancers (Basel) 2011; 3:568-81. [PMID: 24212629 PMCID: PMC3756377 DOI: 10.3390/cancers3010568] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 01/25/2011] [Accepted: 01/25/2011] [Indexed: 01/08/2023] Open
Abstract
Although cancers have been thought to be predominantly driven by acquired genetic changes, it is becoming clear that microenvironment-mediated epigenetic alterations play important roles. Aberrant promoter hypermethylation is a prevalent phenomenon in human cancers as well as malignant lymphoma/leukemia. Tumor suppressor genes become frequent targets of aberrant hypermethylation in the course of gene-silencing due to the increased and deregulated DNA methyltransferases (DNMTs). The purpose of this article is to review the current status of knowledge about the contribution of cumulative epigenetic abnormalities of the host genes after microbial and virus infection to the crisis and progression of malignant lymphoma/leukemia. In addition, the relevance of this knowledge to malignant lymphoma/leukemia assessment, prevention and early detection will be discussed.
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49
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50
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Li Y, Tollefsbol TO. Combined chromatin immunoprecipitation and bisulfite methylation sequencing analysis. Methods Mol Biol 2011; 791:239-51. [PMID: 21913084 DOI: 10.1007/978-1-61779-316-5_18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic mechanisms control gene transcription primarily through regulating chromatin structures and DNA methylation. Transcription factors can also affect gene transcription through binding of the key transcriptional machinery to the gene promoter. These factors normally jointly influence the transcriptional processes, leading to silencing or activation of gene expression. A novel technique has been recently explored in our laboratory, which is a combination of conventional chromatin immunoprecipitation (ChIP) with bisulfite methylation sequencing assays, so-called ChIP and bisulfite methylation sequencing (ChIP-BMS). This technique provides precise information of DNA methylation status at the selected DNA fragments precipitated by the antibodies to histone molecules or transcription factors of interest. This method also helps to investigate the interactions between histone modification and DNA methylation, and how this crosstalking can affect gene expression. More importantly, it is easy to determine potential methylation-sensitive transcription factors that influence transcription mainly depending on methylation status of the binding sites. In this chapter, we discuss the detailed procedures of this novel technique and its broad application in epigenetic and genetic fields.
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Affiliation(s)
- Yuanyuan Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
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