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Advani J, Mehta PA, Hamel AR, Mehrotra S, Kiel C, Strunz T, Corso-Díaz X, Kwicklis M, van Asten F, Ratnapriya R, Chew EY, Hernandez DG, Montezuma SR, Ferrington DA, Weber BHF, Segrè AV, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. Nat Commun 2024; 15:1972. [PMID: 38438351 PMCID: PMC10912779 DOI: 10.1038/s41467-024-46063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.
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Affiliation(s)
- Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Kiel
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Tobias Strunz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Kwicklis
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Freekje van Asten
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, Clinical Trials Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
- Doheny Eye Institute, Pasadena, CA, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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Advani J, Corso-Diaz X, Kwicklis M, van Asten F, Ratnapriya R, Mehta P, Hamel A, Mahrotra S, Segrè A, Kiel C, Strunz T, Weber B, Chew E, Hernandez D, Montezuma S, Ferrington D, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. RESEARCH SQUARE 2023:rs.3.rs-3011096. [PMID: 37398472 PMCID: PMC10312909 DOI: 10.21203/rs.3.rs-3011096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 mQTLs and 12,505 eQTLs) and 13,747 eQTMs (DNAm loci affecting gene expression), with over one-third specific to the retina. mQTLs and eQTMs show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration (AMD). Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of AMD pathology by genotype-environment interaction in retina.
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Affiliation(s)
| | | | | | | | | | - Puja Mehta
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Andrew Hamel
- Department of Ophthalmology, Massachusetts Eye and Ear
| | | | | | | | | | | | - Emily Chew
- National Eye Institute/National Institutes of Health
| | | | | | | | - Anand Swaroop
- National Eye Institute, National Institutes of Health
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Santillán-Sidón P, Pérez-Morales R, Anguiano G, Ruiz-Baca E, Osten JRV, Olivas-Calderón E, Vazquez-Boucard C. Glutathione S-transferase activity and genetic polymorphisms associated with exposure to organochloride pesticides in Todos Santos, BCS, Mexico: a preliminary study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:43223-43232. [PMID: 32734539 DOI: 10.1007/s11356-020-10206-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The objective of this study was to identify and evaluate the impact of exposure to mixtures of organochloride pesticides (OCPs) in agricultural workers by detecting their effects on the activity of the enzyme glutathione S-transferase (GST) and the presence of polymorphisms of the GSTT1 and GSTM1 genes. The presence of OCPs was identified and quantified by gas chromatography, while spectrophotometry was used to measure enzymatic GST activity. The frequencies of the GSTM1 genotypes were analyzed by multiplex PCR. A total of 18 metabolites of OCPs were identified in the workers' blood, most of which are either prohibited (DDT and its metabolites p, p'DDD and p, p'DDE, dieldrin, endrin, aldrin) and/or restricted (δ hexachlorocyclohexane, cis chlordane, methoxychlor, and endosulfan). The results obtained indicate lower levels of GST activity at higher OCPs concentrations detected in blood from exposed workers, together with an increase in OCP levels in individuals who presented the GSTT1*0 and GSTM1*0 genotypes. These conditions place the detoxification process in agricultural workers with null polymorphisms in the GST genes and high concentrations of OCPs in the blood (especially DDT and its metabolites, DDD and DDE) at risk, and increase their susceptibility to develop serious diseases.
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Affiliation(s)
- Patricia Santillán-Sidón
- Molecular Biomedicine Laboratory, Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Veterinarias s/n, Circuito Universitario, 34120, Durango, Mexico
| | - Rebeca Pérez-Morales
- Molecular Cell Biology Laboratory, Universidad Juárez del Estado de Durango, Av. Articulo #123 Filadelfia, CP 35010, Gómez Palacio, Durango, Mexico
| | - Gerardo Anguiano
- Molecular Biomedicine Laboratory, Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Veterinarias s/n, Circuito Universitario, 34120, Durango, Mexico
| | - Estela Ruiz-Baca
- Genoproteomic Laboratory, Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Veterinarias s/n, Circuito Universitario, 34120, Durango, Mexico
| | - Jaime Rendón-Von Osten
- Laboratory of Identification of Persistent Organic Pollutants. EPOMEX, Universidad Autónoma de Campeche, Agustín de Melgar y Juan de la Barrera s/n, 24039, Campeche, Mexico
| | - Edgar Olivas-Calderón
- Molecular Cell Biology Laboratory, Universidad Juárez del Estado de Durango, Av. Articulo #123 Filadelfia, CP 35010, Gómez Palacio, Durango, Mexico
| | - Celia Vazquez-Boucard
- Proteomic and Genetic Toxicology Laboratory, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional, Calle IPN, #195 Playa Palo de Santa Rita Sur, 23096, La Paz, Baja California Sur, Mexico.
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Bjørklund G, Peana M, Maes M, Dadar M, Severin B. The glutathione system in Parkinson's disease and its progression. Neurosci Biobehav Rev 2020; 120:470-478. [PMID: 33068556 DOI: 10.1016/j.neubiorev.2020.10.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023]
Abstract
Redox dysfunctions and neuro-oxidative stress play a major role in the pathophysiology and progression of Parkinson's disease (PD). Glutathione (GSH) and the reduced/oxidized glutathione (GSH/GSSG) ratio are lowered in oxidative stress conditions and may lead to increased oxidative toxicity. GSH is involved not only in neuro-immune and neuro-oxidative processes, including thiol redox signaling, but also in cell proliferation and differentiation and in the regulation of cell death, including apoptotic pathways. Lowered GSH metabolism and a low GSH/GSSG ratio following oxidative stress are associated with mitochondrial dysfunctions and constitute a critical factor in the neuroinflammatory and neurodegenerative processes accompanying PD. This review provides indirect evidence that GSH redox signaling is associated with the pathophysiology of PD. Nevertheless, it has not been delineated whether GSH redox imbalances are a causative factor in PD or whether PD-associated pathways cause the GSH redox imbalances in PD. The results show that antioxidant approaches, including neuroprotective and anti-neuroinflammatory agents, which neutralize reactive oxygen species, may have therapeutic efficacy in the treatment of PD and its progression.
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Affiliation(s)
- Geir Bjørklund
- Council for Nutritional and Environmental Medicine (CONEM), Mo i Rana, Norway.
| | | | - Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Impact Research Center, Deakin University, Geelong, Australia
| | - Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Beatrice Severin
- Faculty of Medicine, Ovidius University of Constanta, Constanta, Romania
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Interaction of glutathione S-transferase polymorphisms and tobacco smoking during pregnancy in susceptibility to autism spectrum disorders. Sci Rep 2019; 9:3206. [PMID: 30824761 PMCID: PMC6397281 DOI: 10.1038/s41598-019-39885-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 01/30/2019] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASD) are a group of complex psychiatric disorders, with a proposed gene-environment interaction in their etiology. One mechanism that could explain both the genetic and environmental component is oxidative stress. The aim of our study was to investigate the potential role of common polymorphisms in genes for glutathione transferase A1, M1, T1 and P1 in susceptibility to ASD. We also aimed to explore the possible oxidative stress - specific gene-environment interaction, regarding GST polymorphisms, maternal smoking tobacco during pregnancy (TSDP) and the risk of ASD. This case-control study included 113 children with ASD and 114 age and sex-matched controls. The diagnosis was made based on ICD-10 criteria and verified by Autism Diagnostic Interview – Revised (ADI-R). We investigated GSTA1, GSTM1, GSTP1 and GSTT1 genotypes and explored their individual and combined effects in individuals with ASD. Individual effect of GST genotypes was shown for GSTM1 active genotype decreasing the risk of ASD (OR = 0.554, 95%CI: 0.313–0.983, p = 0.044), and for GSTA1 CC genotype, increasing susceptibility to ASD (OR = 4.132, 95%CI: 1.219–14.012, p = 0.023); the significance was lost when genotype-genotype interactions were added into the logistic regression model. The combination of GSTM1 active and GSTT1 active genotype decreased the risk of ASD (OR = 0.126, 95%CI: 0.029–0.547, p = 0.006), as well as combination of GSTT1 active and GSTP1 llelle (OR = 0.170, 95%CI: 0.029–0.992, p = 0.049). Increased risk of ASD was observed if combination of GSTM1 active and GSTP1 llelle was present (OR = 11.088, 95%CI: 1.745–70.456, p = 0.011). The effect of TSDP was not significant for the risk of ASD, neither individually, nor in interaction with specific GST genotypes. Specific combination of GST genotypes might be associated with susceptibility to ASD, while it appears that maternal smoking during pregnancy does not increase the risk of ASD.
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Abstract
PURPOSE OF REVIEW This review aims to provide a brief description of the complex etiology of autism spectrum disorders (ASD), with special emphasis on the recent findings of impaired redox control in ASD, and to suggest a possible model of oxidative stress-specific gene-environment interaction in this group of disorders. RECENT FINDINGS Recent findings point out to the significance of environmental, prenatal, and perinatal factors in ASD but, at the same time, are in favor of the potentially significant oxidative stress-specific gene-environment interaction in ASD. Available evidence suggests an association between both the identified environmental factors and genetic susceptibility related to the increased risk of ASD and the oxidative stress pathway. There might be a potentially significant specific gene-environment interaction in ASD, which is associated with oxidative stress. Revealing novel susceptibility genes (including those encoding for antioxidant enzymes), or environmental factors that might increase susceptibility to ASD in carriers of a specific genotype, might enable the stratification of individuals more prone to developing ASD and, eventually, the possibility of applying preventive therapeutic actions.
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