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Djihinto OY, Meacci D, Medjigodo AA, Bernardini F, Djogbénou LS. Relative expression of key genes involved in nucleic acids methylation in Anopheles gambiae sensu stricto. MEDICAL AND VETERINARY ENTOMOLOGY 2023; 37:754-766. [PMID: 37417368 DOI: 10.1111/mve.12681] [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: 04/19/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
In vertebrates, enzymes responsible for DNA methylation, one of the epigenetic mechanisms, are encoded by genes falling into the cytosine methyltransferases genes family (Dnmt1, Dnmt3a,b and Dnmt3L). However, in Diptera, only the methyltransferase Dnmt2 was found, suggesting that DNA methylation might act differently for species in this order. Moreover, genes involved in epigenetic dynamics, such as Ten-eleven Translocation dioxygenases (TET) and Methyl-CpG-binding domain (MBDs), present in vertebrates, might play a role in insects. This work aimed at investigating nucleic acids methylation in the malaria vector Anopheles gambiae (Diptera: Culicidae) by analysing the expression of Dnmt2, TET2 and MBDs genes using quantitative real-time polymerase chain reaction (qRT-PCR) at pre-immature stages and in reproductive tissues of adult mosquitoes. In addition, the effect of two DNA methylation inhibitors on larval survival was evaluated. The qPCR results showed an overall low expression of Dnmt2 at all developmental stages and in adult reproductive tissues. In contrast, MBD and TET2 showed an overall higher expression. In adult mosquito reproductive tissues, the expression level of the three genes in males' testes was significantly higher than that in females' ovaries. The chemical treatments did not affect larval survival. The findings suggest that mechanisms other than DNA methylation underlie epigenetic regulation in An. gambiae.
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Affiliation(s)
- Oswald Y Djihinto
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Dario Meacci
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Adandé A Medjigodo
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
- Institut Régional de Santé Publique (IRSP), University of Abomey-Calavi, Ouidah, Benin
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2
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Semik-Gurgul E, Szmatoła T, Gurgul A, Pawlina-Tyszko K, Gałuszka A, Pędziwiatr R, Witkowski M, Ząbek T. Methylome and transcriptome data integration reveals aberrantly regulated genes in equine sarcoids. Biochimie 2023; 213:100-113. [PMID: 37211255 DOI: 10.1016/j.biochi.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/23/2023]
Abstract
DNA methylation is a key mechanism in transcription regulation, and aberrant methylation is a common and important mechanism in tumor initiation, maintenance, and progression. To find genes that are aberrantly regulated by altered methylation in horse sarcoids, we used reduced representation bisulfite sequencing (RRBS) accompanied by RNA sequencing (RNA-Seq) for methylome (whole genome DNA methylation sequencing) and transcriptome profiling, respectively. We found that the DNA methylation level was generally lower in lesion samples than in controls. In the analyzed samples, a total of 14,692 differentially methylated sites (DMSs) in the context of CpG (where cytosine and guanine are separated by a phosphate), and 11,712 differentially expressed genes (DEGs) were identified. The integration of the methylome and transcriptome data suggests that aberrant DNA methylation may be involved in the deregulation of expression of the 493 genes in equine sarcoid. Furthermore, enrichment analysis of the genes demonstrated the activation of multiple molecular pathways related to extracellular matrix (ECM), oxidative phosphorylation (OXPHOS), immune response, and disease processes that can be related to tumor progression. The results provide further insight into the epigenetic alterations in equine sarcoids and provide a valuable resource for follow-up studies to identify biomarkers for predicting susceptibility to this common condition in horses.
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Affiliation(s)
- Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St., 32-083, Balice, Poland.
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St., 32-083, Balice, Poland; Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, 30-248, Krakow, Poland
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, 30-248, Krakow, Poland
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St., 32-083, Balice, Poland
| | - Anna Gałuszka
- Department of Animal Anatomy and Preclinical Sciences, University Centre of Veterinary Medicine JU-UA, University of Agriculture in Krakow, Mickiewicza 24/28, 30-059, Krakow, Poland
| | - Rafał Pędziwiatr
- University Centre of Veterinary Medicine JU-UA, University of Agriculture in Krakow, Mickiewicza 24/28, 30-059, Krakow, Poland; Equine Vet Clinic EQUI-VET, Stogniowice 55A St., 32-100 Stogniowice, Poland
| | - Maciej Witkowski
- University Centre of Veterinary Medicine JU-UA, University of Agriculture in Krakow, Mickiewicza 24/28, 30-059, Krakow, Poland; Equine Hospital on the Racing Truck, Sluzewiec, Pulawska 266, 02-684, Warszawa, Poland
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St., 32-083, Balice, Poland
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Zhang X, Yang L, Deng Y, Huang Z, Huang H, Wu Y, He B, Hu F. Single-cell RNA-Seq and bulk RNA-Seq reveal reliable diagnostic and prognostic biomarkers for CRC. J Cancer Res Clin Oncol 2023; 149:9805-9821. [PMID: 37247080 DOI: 10.1007/s00432-023-04882-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/19/2023] [Indexed: 05/30/2023]
Abstract
PURPOSE The potential role of epithelium-specific genes through the adenoma-carcinoma sequence in the development of colorectal cancer (CRC) remains unknown. Therefore, we integrated single-cell RNA sequencing and bulk RNA sequencing data to select diagnosis and prognosis biomarkers for CRC. METHODS The CRC scRNA-seq dataset was used to describe the cellular landscape of normal intestinal mucosa, adenoma and CRC and to further select epithelium-specific clusters. Differentially expressed genes (DEGs) of epithelium-specific clusters were identified between intestinal lesion and normal mucosa in the scRNA-seq data throughout the adenoma-carcinoma sequence. Diagnostic biomarkers and prognostic biomarker (the risk score) for CRC were selected in the bulk RNA-seq dataset based on DEGs shared by the adenoma epithelium-specific cluster and the CRC epithelium-specific cluster (shared-DEGs). RESULTS Among the 1063 shared-DEGs, we selected 38 gene expression biomarkers and 3 methylation biomarkers that had promising diagnostic power in plasma. Multivariate Cox regression identified 174 shared-DEGs as prognostic genes for CRC. We combined 1000 times LASSO-Cox regression and two-way stepwise regression to select 10 prognostic shared-DEGs to construct the risk score in the CRC meta-dataset. In the external validation dataset, the 1- and 5-year AUCs of the risk score were higher than those of stage, the pyroptosis-related genes (PRG) score and the cuproptosis-related genes (CRG) score. In addition, the risk score was closely associated with the immune infiltration of CRC. CONCLUSION The combined analysis of the scRNA-seq dataset and the bulk RNA-seq dataset in this study provides reliable biomarkers for the diagnosis and prognosis of CRC.
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Affiliation(s)
- Xing Zhang
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Longkun Yang
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Ying Deng
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Zhicong Huang
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China
| | - Hao Huang
- Department of Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen University Medical School, Shenzhen, 518061, Guangdong Province, People's Republic of China
| | - Yuying Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Baochang He
- Department of Epidemiology, The School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, People's Republic of China.
| | - Fulan Hu
- Department of Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen University Medical School, Shenzhen, 518061, Guangdong Province, People's Republic of China.
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Dema H, Videtič Paska A, Kouter K, Katrašnik M, Jensterle M, Janež A, Oblak A, Škodlar B, Bon J. Effects of Mindfulness-Based Therapy on Clinical Symptoms and DNA Methylation in Patients with Polycystic Ovary Syndrome and High Metabolic Risk. Curr Issues Mol Biol 2023; 45:2717-2737. [PMID: 37185702 PMCID: PMC10136994 DOI: 10.3390/cimb45040178] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is an endocrine and metabolic disorder affecting women of reproductive age. Research has shown that epigenetic alterations such as DNA methylation may play a role in the development and progression of abnormal ovarian function and metabolic disorders in PCOS. Studies have identified specific genes (related with insulin signaling and steroid hormone metabolism) that are methylated in women with PCOS. DNA methylation appears to respond to various interventions aimed at altering health and lifestyle factors. We tested the efficacy of a mindfulness-based stress reduction program (MBSR) in PCOS patients. We examined its effects on anthropometric measurements, mental health and wellbeing, and alterations in DNA methylation in peripheral blood. MBSR was associated with a reduction in body mass index, waist circumference and blood glucose level, an improvement in subjectively perceived general health, emotional role limitation, and levels of pain, as well as mindfulness-like traits. MBSR reduced the expression of anxious symptomatology and subjectively perceived stress. Methylation changes were observed in four genes: COMT, FST, FKBP51, and MAOA. We conclude that MBSR may be a useful supplementary therapy to mitigate the deleterious effects of PCOS on mental health.
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Affiliation(s)
- Hana Dema
- Department of Health Care Quality, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Alja Videtič Paska
- Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Katarina Kouter
- Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Mojca Katrašnik
- Institute for Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Mojca Jensterle
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Andrej Janež
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleš Oblak
- University Psychiatric Clinic Ljubljana, SI-1260 Ljubljana, Slovenia
| | - Borut Škodlar
- University Psychiatric Clinic Ljubljana, SI-1260 Ljubljana, Slovenia
- Department of Psychiatry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Bon
- University Psychiatric Clinic Ljubljana, SI-1260 Ljubljana, Slovenia
- Department of Psychiatry, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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Signaling pathways in rheumatoid arthritis: implications for targeted therapy. Signal Transduct Target Ther 2023; 8:68. [PMID: 36797236 PMCID: PMC9935929 DOI: 10.1038/s41392-023-01331-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/16/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023] Open
Abstract
Rheumatoid arthritis (RA) is an incurable systemic autoimmune disease. Disease progression leads to joint deformity and associated loss of function, which significantly impacts the quality of life for sufferers and adds to losses in the labor force. In the past few decades, RA has attracted increased attention from researchers, the abnormal signaling pathways in RA are a very important research field in the diagnosis and treatment of RA, which provides important evidence for understanding this complex disease and developing novel RA-linked intervention targets. The current review intends to provide a comprehensive overview of RA, including a general introduction to the disease, historical events, epidemiology, risk factors, and pathological process, highlight the primary research progress of the disease and various signaling pathways and molecular mechanisms, including genetic factors, epigenetic factors, summarize the most recent developments in identifying novel signaling pathways in RA and new inhibitors for treating RA. therapeutic interventions including approved drugs, clinical drugs, pre-clinical drugs, and cutting-edge therapeutic technologies. These developments will hopefully drive progress in new strategically targeted therapies and hope to provide novel ideas for RA treatment options in the future.
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Polyphenols as Potent Epigenetics Agents for Cancer. Int J Mol Sci 2022; 23:ijms231911712. [PMID: 36233012 PMCID: PMC9570183 DOI: 10.3390/ijms231911712] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 02/06/2023] Open
Abstract
Human diseases such as cancer can be caused by aberrant epigenetic regulation. Polyphenols play a major role in mammalian epigenome regulation through mechanisms and proteins that remodel chromatin. In fruits, seeds, and vegetables, as well as food supplements, polyphenols are found. Compounds such as these ones are powerful anticancer agents and antioxidants. Gallic acid, kaempferol, curcumin, quercetin, and resveratrol, among others, have potent anti-tumor effects by helping reverse epigenetic changes associated with oncogene activation and tumor suppressor gene inactivation. The role dietary polyphenols plays in restoring epigenetic alterations in cancer cells with a particular focus on DNA methylation and histone modifications was summarized. We also discussed how these natural compounds modulate gene expression at the epigenetic level and described their molecular targets in cancer. It highlights the potential of polyphenols as an alternative therapeutic approach in cancer since they modulate epigenetic activity.
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Tang D, Zheng S, Zheng Z, Liu C, Zhang J, Yan R, Wu C, Zuo N, Wu L, Xu H, Liu S, He Y. Dnmt1 is required for the development of auditory organs via cell cycle arrest and Fgf signalling. Cell Prolif 2022; 55:e13225. [PMID: 35352419 PMCID: PMC9136517 DOI: 10.1111/cpr.13225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives To explore the role of DNA methyltransferase 1 (DNMT1) in the development of auditory system using zebrafish as experimental model. Methods Morpholino oligonucleotide was used to induce Dnmt1 deficiency. RNA sequencing, in situ hybridization (ISH), whole genomic bisulfide sequencing (WGBS) and immunostaining were used to investigate the morphologic alterations and mechanisms. Results We found that downregulation of Dnmt1 induced decreased number of neuromasts and repressed cell proliferation of primordium in the developing posterior lateral line system of zebrafish. The ISH data uncovered that Fgf signalling pathway was inhibited and the expression of chemokine members cxcr4b, cxcr7b and cxcl12a were interfered, while lef1 expression was increased after inhibiting Dnmt1. Additionally, Dnmt1 downregulation led to malformed otoliths and deformed semicircular canals, and hair cell differentiation in utricle and saccule was inhibited severely. The in situ staining of otic placode markers pax2/5 and fgf 3/8/10 was decreased when Dnmt1 downregulated. The WGBS analysis demonstrated that the global methylation status was markedly downregulated, and cell cycle genes were among those most differently expressed between Dnmt1 morphants and the controls. Further ISH analysis confirmed the findings by RNA‐seq and WGBS assay that cdkn1a and tp53 were both upregulated after knockdown of Dnmt1. Conclusion Our results revealed that Dnmt1 is essential for the development of zebrafish auditory organ through regulating cell cycle genes together with Wnt and Fgf signalling pathways.
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Affiliation(s)
- Dongmei Tang
- ENT Institute and Otorhinolaryngology Department, Eye and ENT Hospital, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, China
| | - Shimei Zheng
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Zhiwei Zheng
- ENT Institute and Otorhinolaryngology Department, Eye and ENT Hospital, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, China
| | - Chang Liu
- ENT Institute and Otorhinolaryngology Department, Eye and ENT Hospital, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, China
| | - Jiner Zhang
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Renchun Yan
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Cheng Wu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Na Zuo
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Lijuan Wu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Hongfei Xu
- Department of Forensic Medicine, Soochow University, Suzhou, China
| | - Shaofeng Liu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Yingzi He
- ENT Institute and Otorhinolaryngology Department, Eye and ENT Hospital, NHC Key Laboratory of Hearing Medicine Research, Fudan University, Shanghai, China
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Komlósi ZI, van de Veen W, Kovács N, Szűcs G, Sokolowska M, O'Mahony L, Akdis M, Akdis CA. Cellular and molecular mechanisms of allergic asthma. Mol Aspects Med 2021; 85:100995. [PMID: 34364680 DOI: 10.1016/j.mam.2021.100995] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/21/2022]
Abstract
Asthma is a chronic disease of the airways, which affects more than 350 million people worldwide. It is the most common chronic disease in children, affecting at least 30 million children and young adults in Europe. Asthma is a complex, partially heritable disease with a marked heterogeneity. Its development is influenced both by genetic and environmental factors. The most common, as well as the most well characterized subtype of asthma is allergic eosinophilic asthma, which is characterized by a type 2 airway inflammation. The prevalence of asthma has substantially increased in industrialized countries during the last 60 years. The mechanisms underpinning this phenomenon are incompletely understood, however increased exposure to various environmental pollutants probably plays a role. Disease inception is thought to be enabled by a disadvantageous shift in the balance between protective and harmful lifestyle and environmental factors, including exposure to protective commensal microbes versus infection with pathogens, collectively leading to airway epithelial cell damage and disrupted barrier integrity. Epithelial cell-derived cytokines are one of the main drivers of the type 2 immune response against innocuous allergens, ultimately leading to infiltration of lung tissue with type 2 T helper (TH2) cells, type 2 innate lymphoid cells (ILC2s), M2 macrophages and eosinophils. This review outlines the mechanisms responsible for the orchestration of type 2 inflammation and summarizes the novel findings, including but not limited to dysregulated epithelial barrier integrity, alarmin release and innate lymphoid cell stimulation.
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Affiliation(s)
- Zsolt I Komlósi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary.
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Nóra Kovács
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Lung Health Hospital, Munkácsy Mihály Str. 70, 2045, Törökbálint, Hungary
| | - Gergő Szűcs
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Department of Pulmonology, Semmelweis University, Tömő Str. 25-29, 1083, Budapest, Hungary
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Liam O'Mahony
- Department of Medicine and School of Microbiology, APC Microbiome Ireland, University College Cork, Ireland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
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9
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Pichon F, Shen Y, Busato F, P Jochems S, Jacquelin B, Grand RL, Deleuze JF, Müller-Trutwin M, Tost J. Analysis and annotation of DNA methylation in two nonhuman primate species using the Infinium Human Methylation 450K and EPIC BeadChips. Epigenomics 2021; 13:169-186. [PMID: 33471557 DOI: 10.2217/epi-2020-0200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: Nonhuman primates are essential for research on many human diseases. The Infinium Human Methylation450/EPIC BeadChips are popular tools for the study of the methylation state across the human genome at affordable cost. Methods: We performed a precise evaluation and re-annotation of the BeadChip probes for the analysis of genome-wide DNA methylation patterns in rhesus macaques and African green monkeys through in silico analyses combined with functional validation by pyrosequencing. Results: Up to 165,847 of the 450K and 261,545 probes of the EPIC BeadChip can be reliably used. The annotation files are provided in a format compatible with a variety of standard bioinformatic pipelines. Conclusion: Our study will facilitate high-throughput DNA methylation analyses in Macaca mulatta and Chlorocebus sabaeus.
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Affiliation(s)
- Fabien Pichon
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Yimin Shen
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France.,Laboratory for Bioinformatics, Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Florence Busato
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Simon P Jochems
- Institut Pasteur, HIV Inflammation & Persistence Unit, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Leiden University Medical Center, Leiden, The Netherlands
| | | | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, France
| | - Jean-Francois Deleuze
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France.,Laboratory for Bioinformatics, Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | | | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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Fransquet PD, Ritchie K, Januar V, Saffery R, Ancelin ML, Ryan J. Is Peripheral BDNF Promoter Methylation a Preclinical Biomarker of Dementia? J Alzheimers Dis 2020; 73:645-655. [PMID: 31839607 DOI: 10.3233/jad-190738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Brain-derived neurotrophic factor (BDNF) has been implicated in dementia. Preliminary evidence suggests that BDNF DNA methylation may be a diagnostic biomarker of dementia, but the potential pre-clinical utility remains unclear. Participants in the ESPRIT study were assessed for cognitive function and dementia (DSM-IV criteria) over 14 years. BDNF exon 1 promoter methylation was measured in blood at baseline (n = 769) and buccal samples during follow-up (n = 1062). Genotyping was carried out for several common BDNF SNPs, including Val66Met (rs6265) and APOE ɛ4. Multivariable logistic regression analyses determined the association between BDNF methylation and both prevalent and incident dementia. Adjustment for gender, age, education, APOEɛ4 genotype, body mass index, depression, and type 2 diabetes, as well as possible effect modification by gender and genetic variation were also investigated. Weak evidence of an association between lower blood methylation and dementia was observed at one of 11 sites investigated (Δ-0.5%, 95% CI:-0.9,-0.04, p = 0.03, p = 0.22 adjusted for multiple comparisons). Buccal methylation at two other sites was associated with 14-year incident dementia cases prior to adjustment for multiple comparisons only, and the effect sizes were small (Δ+0.3%, OR:1.57, SE:0.30, p = 0.02, p = 0.14 adjusted and Δ-1.5%, OR:0.85, SE:0.06, p = 0.03, p = 0.14 adjusted). Genetic variation in the BDNF gene did not modify these associations, and no gender-specific effects were observed. There was only a weak correlation between blood and buccal BDNF log-methylation at two sites (both r=-0.11). There was no strong evidence that blood or buccal BDNF exon 1 promoter DNA methylation is associated with prevalent or incident dementia, and reported associations would not remain after adjustment for multiple testing.
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Affiliation(s)
- Peter D Fransquet
- Biological Neuropsychiatry and Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia.,Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Karen Ritchie
- Inserm U1061, Hospital La Colombiere & University Montpellier, Montpellier, France.,Center for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Vania Januar
- Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Richard Saffery
- Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Marie-Laure Ancelin
- Inserm U1061, Hospital La Colombiere & University Montpellier, Montpellier, France
| | - Joanne Ryan
- Biological Neuropsychiatry and Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia.,Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,Inserm U1061, Hospital La Colombiere & University Montpellier, Montpellier, France
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11
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Bickler SW, Prieto JM, Cauvi DM, De Cos V, Nasamran C, Ameh E, Amin S, Nicholson S, Din H, Mocumbi AO, Noormahomed EV, Tellez-Isaias G, Fisch KM, De Maio A. Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco. Cell Stress Chaperones 2020; 25:847-856. [PMID: 32319023 PMCID: PMC7591688 DOI: 10.1007/s12192-020-01108-x] [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: 01/13/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 11/25/2022] Open
Abstract
Urbanization in low-income countries represents an important inflection point in the epidemiology of disease, with rural populations experiencing high rates of chronic and recurrent infections and urban populations displaying a profile of noncommunicable diseases. To investigate if urbanization alters the expression of genes encoding mitochondrial proteins, we queried gene microarray data from rural and urban populations living in Morocco (GSE17065). The R Bioconductor packages edgeR and limma were used to identify genes with different expression. The experimental design was modeled upon location and sex. Nuclear genes encoding mitochondrial proteins were identified from the MitoCarta2.0 database. Of the 1158 genes listed in the MitoCarta2.0 database, 847 genes (73%) were available for analysis in the Moroccan dataset. The urban-rural comparison with the greatest environmental differences showed that 76.5% of the MitoCarta2.0 genes were differentially expressed, with 97% of the genes having an increased expression in the urban area. Enrichment analysis revealed 367 significantly enriched pathways (adjusted p value < 0.05), with oxidative phosphorylation, insulin secretion and glucose regulations (adj.p values = 6.93E-16) being the top three. Four significantly perturbed KEGG disease pathways were associated with urbanization-three degenerative neurological diseases (Huntington's, Alzheimer's, and Parkinson's diseases) and herpes simplex infection (false discover rate corrected p value (PGFdr) < 0.2). Mitochondrial RNA metabolic processing and translational elongation were the biological processes that had the greatest enrichment (enrichment ratios 14.0 and 14.8, respectively, FDR < 0.5). Our study links urbanization in Morocco with changes in the expression of the nuclear genes encoding mitochondrial proteins.
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Affiliation(s)
- Stephen W. Bickler
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA 92093 USA
| | - James M. Prieto
- Department of Surgery, Naval Medical Center San Diego, San Diego, CA USA
| | - David M. Cauvi
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA 92093 USA
| | - Victor De Cos
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
| | - Chanond Nasamran
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093 USA
| | - Emmanuel Ameh
- Department of Pediatric Surgery, National Hospital, Abuja, Nigeria
| | - Said Amin
- Department of Histopathology, National Hospital, Abuja, Nigeria
| | - Sneha Nicholson
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
| | - Hena Din
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
| | - Ana Olga Mocumbi
- Instituto Nacional de Saúde, Maputo, Mozambique
- Department of Microbiology, Faculty of Medicine, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | | | | | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093 USA
| | - Antonio De Maio
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA 92093 USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
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12
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Li J, Su X, Dai L, Chen N, Fang C, Dong Z, Fu J, Yu Y, Wang W, Zhang H, Wang H, Ji Y, Liu Y, Cheng L, Shi G, Zhang S, Yang Y, Deng H. Temporal DNA methylation pattern and targeted therapy in colitis-associated cancer. Carcinogenesis 2020; 41:235-244. [PMID: 31802101 DOI: 10.1093/carcin/bgz199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/19/2019] [Accepted: 12/04/2019] [Indexed: 02/05/2023] Open
Abstract
DNA methylation plays a crucial role in the pathogenesis of various diseases, including colorectal cancer (CRC). However, the global and temporal DNA methylation pattern during initiation and progression of colitis-associated cancer (CAC) are still unknown, including the potential therapeutic strategy of targeting methylation for CAC. In the present study, the global DNA methylation pattern was determined at different time points during CAC using DNA methylation sequencing, followed by the Starburst plot integrating alterations and potential functional prediction analysis. After demonstrating the regulatory role of DNA methyltransferases (DNMTs) on the expression of hub-genes in CRC cells, DNMT inhibitors were administered to treat CAC mice. Our results indicated that 811 genes were hypermethylated at different time points during initiation and progression of CAC. Genes that were downregulated and hypermethylated during CAC, including hub-genes BAD and inositol polyphosphate phosphatase-like 1 (INPPL1), were involved in MAPK signaling pathways, kit receptor signaling pathways, apoptosis and EGF/EGFR signaling pathways. Upregulated DNMTs (DNMT1, DNMT3A and DNMT3B) mediated downregulation and hypermethylation of BAD and INPPL1 in CAC and CRC cells. Low doses of DNMT inhibitors (decitabine (DAC) and azacitidine (AZA)) exerted efficient antitumor effects in CAC, accompanied with upregulation of BAD and INPPL1 expression, and apoptosis induction. In summary, the present study demonstrates the temporal DNA methylation pattern during CAC and provides a novel therapeutic strategy for treating this disease.
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Affiliation(s)
- Junshu Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Xiaolan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Lei Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Na Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Chao Fang
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Zhexu Dong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Jiamei Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yan Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Wenshuang Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Hantao Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Huiling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yanhong Ji
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yi Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Lin Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Gang Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Shuang Zhang
- Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Hongxin Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
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13
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Raut JR, Guan Z, Schrotz-King P, Brenner H. Fecal DNA methylation markers for detecting stages of colorectal cancer and its precursors: a systematic review. Clin Epigenetics 2020; 12:122. [PMID: 32778176 PMCID: PMC7418412 DOI: 10.1186/s13148-020-00904-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background DNA methylation biomarkers in stool may have applications in early colorectal cancer (CRC) detection; however, their association with stages of CRC carcinogenesis or their performance in detecting various stages is unclear. We aimed to systematically review the evidence for DNA methylation markers in stool for risk stratification or detection of specific CRC stages, as well as precursors of CRC. Methods We conducted a systematic search in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched PubMed and ISI Web of Knowledge to identify relevant studies published until 14th January 2020. Two reviewers independently extracted data on study population characteristics, candidate genes, methylation measurement methods, odds ratios (ORs), overall and stage-specific sensitivities, specificities, areas under the receiver operating characteristics curve, and p-values for statistical significance for OR and for association of methylation levels with stage. Results Twenty-seven studies that reported stage-specific associations or performances of fecal DNA methylation markers for detecting colorectal neoplasms were identified. All studies used methylation-specific polymerase chain reaction for assessing methylation levels in the promoter or exon 1 regions of targeted genes. However, most studies were underpowered and limited by their case-control design. Furthermore, the stage-specific associations or sensitivities were validated for two markers (hypermethylation of GATA4 and VIM) only. Conclusion Methylation markers in stool may be useful for detection of CRC precursors or CRC staging, but promising candidate markers need to be validated in longitudinal studies on large screening populations, performing epigenome-wide analyses. Identification of stage-specific DNA methylation biomarkers in stool could boost current strategies towards early detection and enable different approaches to precision medicine for CRC.
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Affiliation(s)
- Janhavi R Raut
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Zhong Guan
- Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany.,Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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14
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Zeggar HR, How-Kit A, Daunay A, Bettaieb I, Sahbatou M, Rahal K, Adouni O, Gammoudi A, Douik H, Deleuze JF, Kharrat M. Tumor DNA hypomethylation of LINE-1 is associated with low tumor grade of breast cancer in Tunisian patients. Oncol Lett 2020; 20:1999-2006. [PMID: 32724446 PMCID: PMC7377197 DOI: 10.3892/ol.2020.11745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
DNA hypomethylation of long interspersed repetitive DNA retrotransposon (LINE-1) and Alu repeats elements of short interspersed elements family (SINEs) is an early event in carcinogenesis that causes transcriptional activation and leads to chromosomal instability. In the current study, DNA methylation levels of LINE-1 and Alu repeats were analyzed in tumoral tissues of invasive breast cancer in a Tunisian cohort and its association with the clinicopathological features of patients was defined. DNA methylation of LINE-1 and Alu repeats were analyzed using pyrosequencing in 61 invasive breast cancers. Median values observed for DNA methylation of LINE-1 and Alu repeats were considered as the cut-off (59.81 and 18.49%, respectively). The results of the current study demonstrated a positive correlation between DNA methylation levels of LINE-1 and Alu repeats (rho=0.284; P<0.03). DNA hypomethylation of LINE-1 was also indicated to be associated with low grade (P=0.023). To the best of our knowledge, the current study is the first study regarding DNA methylation of LINE-1 and Alu repeats element in breast cancer of the Tunisian population. The results of the current study suggest that, since hypomethylation of LINE-1 is associated with low grade, it could be used as a biomarker for prognosis for patients with breast cancer.
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Affiliation(s)
- Hayet Radia Zeggar
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Antoine Daunay
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Ilhem Bettaieb
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Mourad Sahbatou
- Laboratoire de Biostatistique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Khaled Rahal
- Service de Chirurgie Carcinologique, Institut Salah Azaiz de Tunis, 1006 Tunis, Tunisia
| | - Olfa Adouni
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Amor Gammoudi
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Hayet Douik
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
- Centre National de Recherche en Génomique Humaine, CEA, Le Commissariat à l'énergie atomique et aux énergies alternatives-Institut François Jacob, 92265 Evry, France
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
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15
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Li YP, Deng HL, Wang WJ, Wang MQ, Li M, Zhang YF, Wang J, Dang SS. Vitamin D receptor gene methylation in patients with hand, foot, and mouth disease caused by enterovirus 71. Arch Virol 2020; 165:1979-1985. [PMID: 32556549 DOI: 10.1007/s00705-020-04701-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/07/2023]
Abstract
To evaluate the epigenetic regulation of the VDR gene in enterovirus 71 (EV71)-associated severe hand, foot, and mouth disease (HFMD), a total of 116 patients with EV71-HFMD, including 58 with mild EV71-HFMD and 58 with severe EV71-HFMD, as well as 60 healthy controls, were enrolled in this study. Quantitative real-time PCR was used to measure the relative levels of VDR mRNA expression, and the methylation status of the VDR promoter was assessed using a MethylTarget™ assay. The DNA methylation levels of the VDR promoter in children with EV71-associated severe HFMD were lower than those in the healthy controls and in children with mild HFMD (P < 0.05). Hypomethylation at CpG site 133 and hypermethylation at the CpG 42 sites and 68 downregulated VDR expression. Moreover, the methylation level of VDR could be used for differential diagnosis of mild and severe EV71-associated HFMD (AUC56, 0.73; AUC68, 0.699; AUC42, 0.694; AUC66, 0.693). VDR expression and promoter methylation were associated with the progression of EV71 infection. Determining the VDR promoter status might help clinicians initiate the appropriate strategy for treatment of EV71-associated HFMD.
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Affiliation(s)
- Ya-Ping Li
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Hui-Ling Deng
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China.,Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, 710003, China
| | - Wen-Jun Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Mu-Qi Wang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Mei Li
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China
| | - Yu-Feng Zhang
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, 710003, China
| | - Jun Wang
- Department of Infectious Diseases, Xi'an Children's Hospital, Xi'an, 710003, China
| | - Shuang-Suo Dang
- Department of Infectious Diseases, Xi'an Jiaotong University Second Affiliated Hospital, No. 157 Xiwu Road, Xi'an, 710004, China.
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16
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Recent findings in the genetics and epigenetics of asthma and allergy. Semin Immunopathol 2020; 42:43-60. [PMID: 32060620 PMCID: PMC7066293 DOI: 10.1007/s00281-019-00777-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/22/2019] [Indexed: 12/16/2022]
Abstract
In asthma and allergy genetics, a trend towards a few main topics developed over the last 2 years. First, a number of studies have been published recently which focus on overlapping and/or very specific phenotypes: within the allergy spectrum but also reaching beyond, looking for common genetic traits shared between different diseases or disease entities. Secondly, an urgently needed focus has been put on asthma and allergy genetics in populations genetically different from European ancestry. This acknowledges that the majority of new asthma patients today are not white and asthma is a truly worldwide disease. In epigenetics, recent years have seen several large-scale epigenome-wide association studies (EWAS) being published and a further focus was on the interaction between the environment and epigenetic signatures. And finally, the major trends in current asthma and allergy genetics and epigenetics comes from the field of pharmacogenetics, where it is necessary to understand the susceptibility for and mechanisms of current asthma and allergy therapies while at the same time, we need to have scientific answers to the recent availability of novel drugs that hold the promise for a more individualized therapy.
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17
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Abstract
Epigenetic regulatory mechanisms, encompassing diverse molecular processes including DNA methylation, histone post-translational modifications, and noncoding RNAs, are essential to numerous processes such as cell differentiation, growth and development, environmental adaptation, aging, and disease states. In many cases, epigenetic changes occur in response to environmental cues and lifestyle factors, resulting in persistent changes in gene expression that affect vascular disease risk during the lifetime of the individual. Biological aging-a powerful cardiovascular risk factor-is partly genetically determined yet strongly influenced by traditional risk factors, reflecting epigenetic modulation. Quantification of specific DNA methylation patterns may serve as an accurate predictor of biological age-a concept known as the epigenetic clock, which could help to refine cardiovascular risk assessment. Epigenetic reprogramming of monocytes rewires cellular immune signaling and induces a metabolic shift toward aerobic glycolysis, thereby increasing innate immune responses. This form of trained epigenetic memory can be maladaptive, thus augmenting vascular inflammation. Somatic mutations in epigenetic regulatory enzymes lead to clonal hematopoiesis of indeterminate potential, a precursor of hematologic malignancies and a recently recognized cardiovascular risk factor; moreover, epigenetic regulators are increasingly being targeted in cancer therapeutics. Thus, understanding epigenetic regulatory mechanisms lies at the intersection between cancer and cardiovascular disease and is of paramount importance to the burgeoning field of cardio-oncology (Graphic Abstract).
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Affiliation(s)
- Abdalrahman Zarzour
- From the Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University
| | - Ha Won Kim
- From the Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University
| | - Neal L Weintraub
- From the Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University
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18
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Vázquez-Martínez ER, Gómez-Viais YI, García-Gómez E, Reyes-Mayoral C, Reyes-Muñoz E, Camacho-Arroyo I, Cerbón M. DNA methylation in the pathogenesis of polycystic ovary syndrome. Reproduction 2019; 158:R27-R40. [DOI: 10.1530/rep-18-0449] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 04/08/2019] [Indexed: 12/12/2022]
Abstract
Polycystic ovary syndrome (PCOS) is the leading endocrine and metabolic disorder in premenopausal women characterized by hyperandrogenism and abnormal development of ovarian follicles. To date, the PCOS etiology remains unclear and has been related to insulin resistance, obesity, type 2 diabetes mellitus, cardiovascular disease and infertility, among other morbidities. Substantial evidence illustrates the impact of genetic, intrauterine and environmental factors on the PCOS etiology. Lately, epigenetic factors have garnered considerable attention in the pathogenesis of PCOS considering that changes in the content of DNA methylation, histone acetylation and noncoding RNAs have been reported in various tissues of women with this disease. DNA methylation is changed in the peripheral and umbilical cord blood, as well as in ovarian and adipose tissue of women with PCOS, suggesting the involvement of this epigenetic modification in the pathogenesis of the disease. Perhaps, these defects in DNA methylation promote the deregulation of genes involved in inflammation, hormone synthesis and signaling and glucose and lipid metabolism. Research on the role of DNA methylation in the pathogenesis of PCOS is just beginning, and several issues await investigation. This review aims to provide an overview of current research focused on DNA methylation and PCOS, as well as discuss the perspectives regarding this topic.
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19
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Noland D, Raj S. Academy of Nutrition and Dietetics: Revised 2019 Standards of Practice and Standards of Professional Performance for Registered Dietitian Nutritionists (Competent, Proficient, and Expert) in Nutrition in Integrative and Functional Medicine. J Acad Nutr Diet 2019; 119:1019-1036.e47. [DOI: 10.1016/j.jand.2019.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Indexed: 02/07/2023]
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20
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Gillespie SL, Hardy LR, Anderson CM. Patterns of DNA methylation as an indicator of biological aging: State of the science and future directions in precision health promotion. Nurs Outlook 2019; 67:337-344. [PMID: 31248628 DOI: 10.1016/j.outlook.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND A rapidly expanding literature suggests that individuals of the same chronological age show significant variation in biological age. PURPOSE The purpose of this article is to review the literature surrounding epigenetic age as estimated by DNA methylation, involving the addition or removal of methyl groups to DNA that can alter gene expression without changing the DNA sequence. METHODS This state of the science literature review summarizes current approaches in epigenetic age determination and applications of aging algorithms. FINDINGS A number of algorithms estimate epigenetic age using DNA methylation markers, primarily among adults. Algorithm application has focused on determining predictive value for risk of disease and death and identifying antecedents to age acceleration. Several studies have incorporated epigenetic age to evaluate intervention effectiveness. DISCUSSION As the research community continues to refine aging algorithms, there may be opportunity to promote health from a precision health perspective.
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Affiliation(s)
- Shannon L Gillespie
- Martha S. Pitzer Center for Women, Children, & Youth, College of Nursing, The Ohio State University, Columbus, OH.
| | - Lynda R Hardy
- Center for Research and Health Analytics, College of Nursing, The Ohio State University, Columbus, OH
| | - Cindy M Anderson
- Martha S. Pitzer Center for Women, Children, & Youth, College of Nursing, The Ohio State University, Columbus, OH
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