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Zhou JX, Li LX, Zhang H, Agborbesong E, Harris PC, Calvet JP, Li X. DNA methyltransferase 1 (DNMT1) promotes cyst growth and epigenetic age acceleration in autosomal dominant polycystic kidney disease. Kidney Int 2024; 106:258-272. [PMID: 38782200 PMCID: PMC11270650 DOI: 10.1016/j.kint.2024.04.017] [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: 06/15/2023] [Revised: 02/28/2024] [Accepted: 04/05/2024] [Indexed: 05/25/2024]
Abstract
Alteration of DNA methylation leads to diverse diseases, and the dynamic changes of DNA methylation (DNAm) on sets of CpG dinucleotides in mammalian genomes are termed "DNAm age" and "epigenetic clocks" that can predict chronological age. However, whether and how dysregulation of DNA methylation promotes cyst progression and epigenetic age acceleration in autosomal dominant polycystic kidney disease (ADPKD) remains elusive. Here, we show that DNA methyltransferase 1 (DNMT1) is upregulated in cystic kidney epithelial cells and tissues and that knockout of Dnmt1 and targeting DNMT1 with hydralazine, a safe demethylating agent, delays cyst growth in Pkd1 mutant kidneys and extends life span of Pkd1 conditional knockout mice. With methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), DNMT1 chromatin immunoprecipitation (ChIP)-sequencing and RNA-sequencing analysis, we identified two novel DNMT1 targets, PTPRM and PTPN22 (members of the protein tyrosine phosphatase family). PTPRM and PTPN22 function as mediators of DNMT1 and the phosphorylation and activation of PKD-associated signaling pathways, including ERK, mTOR and STAT3. With whole-genome bisulfide sequencing in kidneys of patients with ADPKD versus normal individuals, we found that the methylation of epigenetic clock-associated genes was dysregulated, supporting that epigenetic age is accelerated in the kidneys of patients with ADPKD. Furthermore, five epigenetic clock-associated genes, including Hsd17b14, Itpkb, Mbnl1, Rassf5 and Plk2, were identified. Thus, the diverse biological roles of these five genes suggest that their methylation status may not only predict epigenetic age acceleration but also contribute to disease progression in ADPKD.
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Affiliation(s)
- Julie Xia Zhou
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.
| | - Linda Xiaoyan Li
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Hongbing Zhang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter C Harris
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - James P Calvet
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.
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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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3
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Sun W, Wang Z, Wen S, Huang A, Li H, Jiang L, Feng Q, Fan D, Tian Q, Han D, Liu X. Technical strategy for monozygotic twin discrimination by single-nucleotide variants. Int J Legal Med 2024; 138:767-779. [PMID: 38197923 DOI: 10.1007/s00414-023-03150-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Monozygotic (MZ) twins are theoretically genetically identical. Although they are revealed to accumulate mutations after the zygote splits, discriminating between twin genomes remains a formidable challenge in the field of forensic genetics. Single-nucleotide variants (SNVs) are responsible for a substantial portion of genetic variation, thus potentially serving as promising biomarkers for the identification of MZ twins. In this study, we sequenced the whole genome of a pair of female MZ twins when they were 27 and 33 years old to approximately 30 × coverage using peripheral blood on an Illumina NovaSeq 6000 Sequencing System. Potentially discordant SNVs supported by whole-genome sequencing were validated extensively by amplicon-based targeted deep sequencing and Sanger sequencing. In total, we found nine bona fide post-twinning SNVs, all of which were identified in the younger genomes and found in the older genomes. None of the SNVs occurred within coding exons, three of which were observed in introns, supported by whole-exome sequencing results. A double-blind test was employed, and the reliability of MZ twin discrimination by discordant SNVs was endorsed. All SNVs were successfully detected when input DNA amounts decreased to 0.25 ng, and reliable detection was limited to seven SNVs below 0.075 ng input. This comprehensive analysis confirms that SNVs could serve as cost-effective biomarkers for MZ twin discrimination.
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Affiliation(s)
- Weifen Sun
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Shubo Wen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China.
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Wang J, Fu G, Wang Q, Ma G, Wang Z, Lu C, Fu L, Zhang X, Cong B, Li S. Differences of circular RNA expression profiles between monozygotic twins' blood, with the forensic application in bloodstain and saliva. Forensic Sci Int Genet 2024; 69:103001. [PMID: 38150775 DOI: 10.1016/j.fsigen.2023.103001] [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: 09/22/2023] [Revised: 11/26/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Monozygotic twins (MZTs) possess identical genomic DNA sequences and are usually indistinguishable through routine forensic DNA typing methods, which can be relevant in criminal and paternity cases. Recently, novel epigenetic methods involving DNA methylation and microRNA analysis have been introduced to differentiate MZTs. In this study, we explore the potential of using epigenetic markers, specifically circular RNAs (circRNAs), a type of non-coding RNA (ncRNA), to identify MZTs, and investigate the unique expression patterns of circRNAs within pairs of MZTs, enabling effective differentiation. Epigenetics regulates gene expression at the post-transcriptional level and plays a crucial role in cell growth and aging. CircRNAs, a recently characterized subclass of ncRNA, have a distinct covalent loop structure without the typical 5' cap or 3' tail. They have been reported to modulate various cellular processes and play roles in embryogenesis and eukaryotic development. To achieve this, we conducted a comprehensive circRNA sequencing analysis (circRNA-seq) using total RNA extracted from the blood samples of five pairs of MZTs. We identified a total of 15,257 circRNAs in all MZTs using circRNA-seq. Among them, 3, 21, 338, and 2967 differentially expressed circRNAs (DEcircRNAs) were shared among five, four, three, and two pairs of MZTs, respectively. Subsequently, we validated twelve selected DEcircRNAs using real-time quantitative polymerase chain reaction (RT-qPCR) assays, which included hsa_circ_0004724, hsa_circ_0054196, hsa_circ_004964, hsa_circ_0000591, hsa_circ_0005077, hsa_circ_0054853, hsa_circ_0054716, hsa_circ_0002302, hsa_circ_0004482, hsa_circ_0001103, novel_circ_0030288 and novel_circ_0056831. Among them, hsa_circ_0005077 and hsa_circ_0004482 exhibited the best performance, showing differences in 7 out of 10 pairs of MZTs. These twelve differentially expressed circRNAs also demonstrated strong discriminative power when tested on saliva samples from 10 pairs of MZTs. Notably, hsa_circ_0004724 displayed differential expression in 8 out of 10 pairs of MZTs in their saliva. Additionally, we evaluated the detection sensitivity, longitudinal temporal stability, and suitability for aged bloodstains of these twelve DEcircRNAs in forensic scenarios. Our findings highlight the potential of circRNAs as molecular markers for distinguishing MZTs, emphasizing their suitability for forensic application.
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Affiliation(s)
- Junyan Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
| | - Guangping Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Qian Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Zhonghua Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Chaolong Lu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Xiaojing Zhang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
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5
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Bogan SN, Yi SV. Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations. Genome Biol Evol 2024; 16:evae022. [PMID: 38324384 PMCID: PMC10899001 DOI: 10.1093/gbe/evae022] [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: 07/13/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
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6
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Geiger M, Gorica E, Mohammed SA, Mongelli A, Mengozi A, Delfine V, Ruschitzka F, Costantino S, Paneni F. Epigenetic Network in Immunometabolic Disease. Adv Biol (Weinh) 2024; 8:e2300211. [PMID: 37794610 DOI: 10.1002/adbi.202300211] [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] [Revised: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Although a large amount of data consistently shows that genes affect immunometabolic characteristics and outcomes, epigenetic mechanisms are also heavily implicated. Epigenetic changes, including DNA methylation, histone modification, and noncoding RNA, determine gene activity by altering the accessibility of chromatin to transcription factors. Various factors influence these alterations, including genetics, lifestyle, and environmental cues. Moreover, acquired epigenetic signals can be transmitted across generations, thus contributing to early disease traits in the offspring. A closer investigation is critical in this aspect as it can help to understand the underlying molecular mechanisms further and gain insights into potential therapeutic targets for preventing and treating diseases arising from immuno-metabolic dysregulation. In this review, the role of chromatin alterations in the transcriptional modulation of genes involved in insulin resistance, systemic inflammation, macrophage polarization, endothelial dysfunction, metabolic cardiomyopathy, and nonalcoholic fatty liver disease (NAFLD), is discussed. An overview of emerging chromatin-modifying drugs and the importance of the individual epigenetic profile for personalized therapeutic approaches in patients with immuno-metabolic disorders is also presented.
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Affiliation(s)
- Martin Geiger
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Era Gorica
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Shafeeq Ahmed Mohammed
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Alessia Mongelli
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Alessandro Mengozi
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Valentina Delfine
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Frank Ruschitzka
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Sarah Costantino
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- University Heart Center, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
| | - Francesco Paneni
- Center for Translational and Experimental Cardiology, University Hospital Zürich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- University Heart Center, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
- Department of Research and Education, University Hospital Zurich and University of Zürich, Wagistrasse 12, Schlieren, Zurich, 8952, Switzerland
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Chhatwal K, Smith JJ, Bola H, Zahid A, Venkatakrishnan A, Brand T. Uncovering the Genetic Basis of Congenital Heart Disease: Recent Advancements and Implications for Clinical Management. CJC PEDIATRIC AND CONGENITAL HEART DISEASE 2023; 2:464-480. [PMID: 38205435 PMCID: PMC10777202 DOI: 10.1016/j.cjcpc.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/13/2023] [Indexed: 01/12/2024]
Abstract
Congenital heart disease (CHD) is the most prevalent hereditary disorder, affecting approximately 1% of all live births. A reduction in morbidity and mortality has been achieved with advancements in surgical intervention, yet challenges in managing complications, extracardiac abnormalities, and comorbidities still exist. To address these, a more comprehensive understanding of the genetic basis underlying CHD is required to establish how certain variants are associated with the clinical outcomes. This will enable clinicians to provide personalized treatments by predicting the risk and prognosis, which might improve the therapeutic results and the patient's quality of life. We review how advancements in genome sequencing are changing our understanding of the genetic basis of CHD, discuss experimental approaches to determine the significance of novel variants, and identify barriers to use this knowledge in the clinics. Next-generation sequencing technologies are unravelling the role of oligogenic inheritance, epigenetic modification, genetic mosaicism, and noncoding variants in controlling the expression of candidate CHD-associated genes. However, clinical risk prediction based on these factors remains challenging. Therefore, studies involving human-induced pluripotent stem cells and single-cell sequencing help create preclinical frameworks for determining the significance of novel genetic variants. Clinicians should be aware of the benefits and implications of the responsible use of genomics. To facilitate and accelerate the clinical integration of these novel technologies, clinicians should actively engage in the latest scientific and technical developments to provide better, more personalized management plans for patients.
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Affiliation(s)
- Karanjot Chhatwal
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Jacob J. Smith
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Harroop Bola
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Abeer Zahid
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Ashwin Venkatakrishnan
- Imperial College School of Medicine, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
| | - Thomas Brand
- National Heart and Lung Institute, Imperial College London, Imperial Center of Clinical and Translational Medicine, London, United Kingdom
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Ng ETH, Kinjo AR. Plasticity-led evolution as an intrinsic property of developmental gene regulatory networks. Sci Rep 2023; 13:19830. [PMID: 37963964 PMCID: PMC10645858 DOI: 10.1038/s41598-023-47165-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: 06/09/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
The modern evolutionary synthesis seemingly fails to explain how a population can survive a large environmental change: the pre-existence of heritable variants adapted to the novel environment is too opportunistic, whereas the search for new adaptive mutations after the environmental change is so slow that the population may go extinct. Plasticity-led evolution, the initial environmental induction of a novel adaptive phenotype followed by genetic accommodation, has been proposed to solve this problem. However, the mechanism enabling plasticity-led evolution remains unclear. Here, we present computational models that exhibit behaviors compatible with plasticity-led evolution by extending the Wagner model of gene regulatory networks. The models show adaptive plastic response and the uncovering of cryptic mutations under large environmental changes, followed by genetic accommodation. Moreover, these behaviors are consistently observed over distinct novel environments. We further show that environmental cues, developmental processes, and hierarchical regulation cooperatively amplify the above behaviors and accelerate evolution. These observations suggest plasticity-led evolution is a universal property of complex developmental systems independent of particular mutations.
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Affiliation(s)
- Eden Tian Hwa Ng
- Department of Mathematics, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410, Brunei Darussalam
| | - Akira R Kinjo
- Department of Mathematics, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410, Brunei Darussalam.
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9
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Chiu MH, Chang CH, Tantoh DM, Hsu TW, Hsiao CH, Zhong JH, Liaw YP. Susceptibility to hypertension based on MTHFR rs1801133 single nucleotide polymorphism and MTHFR promoter methylation. Front Cardiovasc Med 2023; 10:1159764. [PMID: 37849939 PMCID: PMC10577234 DOI: 10.3389/fcvm.2023.1159764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
Background The aetio-pathologenesis of hypertension is multifactorial, encompassing genetic, epigenetic, and environmental factors. The combined effect of genetic and epigenetic changes on hypertension is not known. We evaluated the independent and interactive association of MTHFR rs1801133 single nucleotide polymorphism (SNP) and MTHFR promoter methylation with hypertension among Taiwanese adults. Methods We retrieved data including, MTHFR promoter methylation, MTHFR rs1801133 genotypes (CC, CT, and TT), basic demography, personal lifestyle habits, and disease history of 1,238 individuals from the Taiwan Biobank (TWB). Results The distributions of hypertension and MTHFR promoter methylation quartiles (β < 0.1338, 0.1338 ≤ β < 0.1385, 0.1385 ≤ β < 0.1423, and β ≥ 0.1423 corresponding to Conclusion Independently, rs1801133 TT was associated with a higher risk of hypertension, but methylation was not. Based on genotypes, lower methylation was dose-dependently associated with a higher risk of hypertension in individuals with the CC genotype. Our findings suggest that MTHFR rs1801133 and MTHFR promoter methylation could jointly influence hypertension susceptibility.
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Affiliation(s)
- Ming-Huang Chiu
- Department of Pulmonology and Respiratory Care, Cathay General Hospital, Taipei City, Taiwan
| | - Chia-Hsiu Chang
- Cardiovascular Center, Cathay General Hospital, Taipei City, Taiwan
| | - Disline Manli Tantoh
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, Taiwan
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
| | - Tsui-Wen Hsu
- Superintendent Office, Institute of Medicine, Cathay General Hospital, Taipei City, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
| | - Yung-Po Liaw
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung City, Taiwan
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung City, Taiwan
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10
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Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, Chandler D, Schramek D, Triche TJ, Pospisilik JA. Developmental priming of cancer susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557446. [PMID: 37745326 PMCID: PMC10515831 DOI: 10.1101/2023.09.12.557446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
DNA mutations are necessary drivers of cancer, yet only a small subset of mutated cells go on to cause the disease. To date, the mechanisms that determine which rare subset of cells transform and initiate tumorigenesis remain unclear. Here, we take advantage of a unique model of intrinsic developmental heterogeneity (Trim28+/D9) and demonstrate that stochastic early life epigenetic variation can trigger distinct cancer-susceptibility 'states' in adulthood. We show that these developmentally primed states are characterized by differential methylation patterns at typically silenced heterochromatin, and that these epigenetic signatures are detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential. These same genes are frequently mutated in human cancers, and their dysregulation correlates with poor prognosis. These results provide proof-of-concept that intrinsic developmental heterogeneity can prime individual, life-long cancer risk.
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Affiliation(s)
- Ilaria Panzeri
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Luca Fagnocchi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Stefanos Apostle
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Megan Tompkins
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Kristen Schaefer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Genetics and Genome Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yang Chih-Hsiang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Alexis Bergsma
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Parkinson’s Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Anne Drougard
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Erez Dror
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Darrell Chandler
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Timothy J. Triche
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - J. Andrew Pospisilik
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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11
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Kamzolas O, Papazoglou AS, Gemousakakis E, Moysidis DV, Kyriakoulis KG, Brilakis ES, Milkas A. Concomitant Coronary Artery Disease in Identical Twins: Case Report and Systematic Literature Review. J Clin Med 2023; 12:5742. [PMID: 37685809 PMCID: PMC10489011 DOI: 10.3390/jcm12175742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Coronary artery disease (CAD) is multifactorial and strongly affected by genetic, epigenetic and environmental factors. Several studies have reported development of concomitant CAD in identical twins. We report a case in which a pair of Caucasian male monozygotic twins presented almost concomitantly with acute coronary syndrome (ACS) and had concordant coronary anatomy and identical site of occlusion. We performed a systematic literature review of PubMed, Web Of Science and Scopus databases from inception until 28 February 2023 of case reports/case series reporting the concomitant development of CAD in monozygotic twins. We found 25 eligible case reports with a total of 31 monozygotic twin pairs (including the case from our center) suffering from CAD and presenting (most of them simultaneously) with ACS (mean age of presentation: 45 ± 12 years, males: 81%). Coronary angiograms demonstrated lesion and anatomy concordance in 77% and 79% of the twin pairs, respectively. Screening for disease-related genetic mutations was performed in six twin pairs leading to the identification of five CAD-related genetic polymorphisms. This is the first systematic literature review of studies reporting identical twin pairs suffering from CAD. In summary, there is high concordance of coronary anatomy and clinical presentation between monozygotic twins. Future monozygotic twin studies-unbiased by age effects-can provide insights into CAD heritability being able to disentangle the traditional dyad of genetic and environmental factors and investigate the within-pair epigenetic drift.
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Affiliation(s)
| | | | | | | | | | - Emmanouil S Brilakis
- Center for Coronary Artery Disease, Minneapolis Heart Institute and Minneapolis Heart Institute Foundation, Abbott Northwestern, Minneapolis, MN 55407, USA
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12
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Wang X, Li W, Feng X, Li J, Liu GE, Fang L, Yu Y. Harnessing male germline epigenomics for the genetic improvement in cattle. J Anim Sci Biotechnol 2023; 14:76. [PMID: 37277852 PMCID: PMC10242889 DOI: 10.1186/s40104-023-00874-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
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Affiliation(s)
- Xiao Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Konge Larsen ApS, Kongens Lyngby, 2800, Denmark
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Feng
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbing Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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13
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Caiye Z, Song S, Li M, Huang X, Luo Y, Fang S. Genome-wide DNA methylation analysis reveals different methylation patterns in Chinese indigenous sheep with different type of tail. Front Vet Sci 2023; 10:1125262. [PMID: 37215474 PMCID: PMC10196035 DOI: 10.3389/fvets.2023.1125262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Background The study was aimed to analyze the difference of genome-wide DNA differential methylation in Lanzhou Large-tailed sheep, Altay sheep and Tibetan sheep, which the typical breeds with different type tails, as to screen the differentially methylated genes (DMGs) that affect the type of tails. Methods In this study, three Lanzhou Large-tailed sheep, three Altay sheep and three Tibetan sheep were detected by whole genome bisulfite sequencing (WGBS). The degree of genome-wide DNA methylation, differentially methylated regions (DMRs) and DMGs were analyzed. The candidate genes affecting the tail type of sheep were identified by GO and KEGG pathway enrichment analysis of DMGs. Results we identified 68,603 different methylated regions (DMCs) and 75 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in biological process, cellular component and molecular function, Some of the genes in these pathways are involved in fat metabolism: NFATC4, LPIN2, MGAT2 and MAT2B. Conclusion Our results may help to further understand the epigenetic regulation mechanisms of deposition of fat in the tail of sheep and provide new basic data for the study of local sheep.
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Affiliation(s)
- Zhu Caiye
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shuzhen Song
- Institute of Animal and Pasture Science and Green Agriculture, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Minna Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xaioyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yan Luo
- Gansu Institute of Animal Science and Veterinary Medicine, Pingliang, China
| | - Suli Fang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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14
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Lee EJ, Kim JH, Choi HG, Kang HS, Lim H, Kim JH, Cho SJ, Nam ES, Park HY, Kim NY, Kwon MJ. Comparison of the Concordance of Allergic Diseases between Monozygotic and Dizygotic Twins: A Cross-Sectional Study Using KoGES HTS Data. J Pers Med 2023; 13:jpm13050721. [PMID: 37240891 DOI: 10.3390/jpm13050721] [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: 03/23/2023] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
Several epidemiological studies have demonstrated that genetic and environmental factors contribute to the development of allergic diseases. However, there is limited information on these factors in the Korean population. This study investigated the importance of genetic and environmental factors in allergic diseases, such as allergic rhinitis, asthma, allergic conjunctivitis, or atopic dermatitis, by comparing the disease incidence in Korean adult monozygotic and dizygotic twins. This cross-sectional study utilized data from 1296 twin pairs, including 1052 monozygotic and 244 dizygotic twins, aged over 20 years, from the Korean Genome and Epidemiology Study (2005-2014). The study utilized binomial and multinomial logistic regression models to compute odds ratios of disease concordance. The concordance rate (92%) of the presence or absence of atopic dermatitis in monozygotic twins was slightly higher than that in dizygotic twins (90.2%), which only had a borderline significance (p = 0.090). The concordance rates of other allergic diseases within monozygotic twins were lower compared to dizygotic twins (asthma, 94.3% vs. 95.1%; allergic rhinitis, 77.5% vs. 78.7%; allergic conjunctivitis, 90.6% vs. 91.8%), of which the differences were not statistically significant. Monozygotic twins had a higher proportion of cases in which both siblings had allergic diseases than dizygotic twins (asthma, 1.1% vs. 0.0%; allergic rhinitis, 6.7% vs. 3.3%; atopic dermatitis, 2.9% vs. 0.0%; allergic conjunctivitis, 1.5% vs. 0.0%), of which the differences were also not statistically significant. In conclusion, our results appear to indicate the relative importance of environmental factors over genetic factor in the development of allergic diseases in Korean adult monozygotic twins.
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Affiliation(s)
- Eun Jae Lee
- College of Nursing, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Joo-Hee Kim
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Hyo Geun Choi
- Suseo Seoul E.N.T. Clinic and MD Analytics, 10, Bamgogae-ro 1-gil, Gangnam-gu, Seoul 06349, Republic of Korea
| | - Ho Suk Kang
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Hyun Lim
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Ji Hee Kim
- Department of Neurosurgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Seong-Jin Cho
- Department of Pathology, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Republic of Korea
| | - Eun Sook Nam
- Department of Pathology, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Republic of Korea
| | - Ha Young Park
- Department of Pathology, Busan Paik Hospital, Inje University College of Medicine, Busan 47392, Republic of Korea
| | - Nan Young Kim
- Hallym Institute of Translational Genomics and Bioinformatics, Hallym University Medical Center, Anyang 14068, Republic of Korea
| | - Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
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15
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El-Sayed A, Aleya L, Kamel M. Epigenetics and the role of nutraceuticals in health and disease. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28480-28505. [PMID: 36694069 DOI: 10.1007/s11356-023-25236-w] [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: 08/07/2020] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
In the post-genomic era, the data provided by complete genome sequencing could not answer several fundamental questions about the causes of many noninfectious diseases, diagnostic biomarkers, and novel therapeutic approaches. The rapidly expanding understanding of epigenetic mechanisms, as well as widespread acceptance of their hypothesized role in disease induction, facilitated the development of a number of novel diagnostic markers and therapeutic concepts. Epigenetic aberrations are reversible in nature, which enables the treatment of serious incurable diseases. Therefore, the interest in epigenetic modulatory effects has increased over the last decade, so about 60,000 publications discussing the expression of epigenetics could be detected in the PubMed database. Out of these, 58,442 were published alone in the last 10 years, including 17,672 reviews (69 historical articles), 314 clinical trials, 202 case reports, 197 meta-analyses, 156 letters to the editor, 108 randomized controlled trials, 87 observation studies, 40 book chapters, 22 published lectures, and 2 clinical trial protocols. The remaining publications are either miscellaneous or a mixture of the previously mentioned items. According to the species and gender, the publications included 44,589 human studies (17,106 females, 14,509 males, and the gender is not mentioned in the remaining papers) and 30,253 animal studies. In the present work, the role of epigenetic modulations in health and disease and the influencing factors in epigenetics are discussed.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, 25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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16
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Li J, Qiu CY, Tao YJ, Cheng L. Epigenetic modifications in chronic rhinosinusitis with and without nasal polyps. Front Genet 2023; 13:1089647. [PMID: 36699454 PMCID: PMC9868256 DOI: 10.3389/fgene.2022.1089647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023] Open
Abstract
Chronic rhinosinusitis (CRS) has brought a huge socioeconomic burden. However, its mechanism is still elusive, which may involve genetic, environmental and some other factors. Epigenetic analyses have been conducted to explore the mechanisms underlying CRS. Here, we reviewed the fruits in the epigenetic studies on DNA methylation, histone modification, and non-coding RNA regulation. We concluded that the epigenetic research on CRS has made great breakthroughs, especially in the past 5 years and the field of microRNAs. "Epigenetic therapies" are expected to be designed to treat CRS in the future.
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Affiliation(s)
- Jing Li
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China,Department of Otorhinolaryngology, The Affiliated Jiangning Hospital, Nanjing Medical University, Nanjing, China
| | - Chang-Yu Qiu
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China,International Centre for Allergy Research, Nanjing Medical University, Nanjing, China
| | - Yue-Jin Tao
- Department of Otorhinolaryngology, The Affiliated Jiangning Hospital, Nanjing Medical University, Nanjing, China,*Correspondence: Yue-Jin Tao, ; Lei Cheng,
| | - Lei Cheng
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China,International Centre for Allergy Research, Nanjing Medical University, Nanjing, China,*Correspondence: Yue-Jin Tao, ; Lei Cheng,
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17
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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18
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Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL. DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. Nat Genet 2023; 55:112-122. [PMID: 36510025 PMCID: PMC10249665 DOI: 10.1038/s41588-022-01248-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/26/2022] [Indexed: 12/14/2022]
Abstract
Studies of DNA methylation (DNAm) in solid human tissues are relatively scarce; tissue-specific characterization of DNAm is needed to understand its role in gene regulation and its relevance to complex traits. We generated array-based DNAm profiles for 987 human samples from the Genotype-Tissue Expression (GTEx) project, representing 9 tissue types and 424 subjects. We characterized methylome and transcriptome correlations (eQTMs), genetic regulation in cis (mQTLs and eQTLs) across tissues and e/mQTLs links to complex traits. We identified mQTLs for 286,152 CpG sites, many of which (>5%) show tissue specificity, and mQTL colocalizations with 2,254 distinct GWAS hits across 83 traits. For 91% of these loci, a candidate gene link was identified by integration of functional maps, including eQTMs, and/or eQTL colocalization, but only 33% of loci involved an eQTL and mQTL present in the same tissue type. With this DNAm-focused integrative analysis, we contribute to the understanding of molecular regulatory mechanisms in human tissues and their impact on complex traits.
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Affiliation(s)
- Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yihao Lu
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Meytal Chernoff
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA.
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19
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Beopoulos A, Géa M, Fasano A, Iris F. RNA epitranscriptomics dysregulation: A major determinant for significantly increased risk of ASD pathogenesis. Front Neurosci 2023; 17:1101422. [PMID: 36875672 PMCID: PMC9978375 DOI: 10.3389/fnins.2023.1101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Autism spectrum disorders (ASDs) are perhaps the most severe, intractable and challenging child psychiatric disorders. They are complex, pervasive and highly heterogeneous and depend on multifactorial neurodevelopmental conditions. Although the pathogenesis of autism remains unclear, it revolves around altered neurodevelopmental patterns and their implications for brain function, although these cannot be specifically linked to symptoms. While these affect neuronal migration and connectivity, little is known about the processes that lead to the disruption of specific laminar excitatory and inhibitory cortical circuits, a key feature of ASD. It is evident that ASD has multiple underlying causes and this multigenic condition has been considered to also dependent on epigenetic effects, although the exact nature of the factors that could be involved remains unclear. However, besides the possibility for differential epigenetic markings directly affecting the relative expression levels of individual genes or groups of genes, there are at least three mRNA epitranscriptomic mechanisms, which function cooperatively and could, in association with both genotypes and environmental conditions, alter spatiotemporal proteins expression patterns during brain development, at both quantitative and qualitative levels, in a tissue-specific, and context-dependent manner. As we have already postulated, sudden changes in environmental conditions, such as those conferred by maternal inflammation/immune activation, influence RNA epitranscriptomic mechanisms, with the combination of these processes altering fetal brain development. Herein, we explore the postulate whereby, in ASD pathogenesis, RNA epitranscriptomics might take precedence over epigenetic modifications. RNA epitranscriptomics affects real-time differential expression of receptor and channel proteins isoforms, playing a prominent role in central nervous system (CNS) development and functions, but also RNAi which, in turn, impact the spatiotemporal expression of receptors, channels and regulatory proteins irrespective of isoforms. Slight dysregulations in few early components of brain development, could, depending upon their extent, snowball into a huge variety of pathological cerebral alterations a few years after birth. This may very well explain the enormous genetic, neuropathological and symptomatic heterogeneities that are systematically associated with ASD and psychiatric disorders at large.
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Affiliation(s)
| | - Manuel Géa
- Bio-Modeling Systems, Tour CIT, Paris, France
| | - Alessio Fasano
- Division of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Center for Celiac Research and Treatment, Massachusetts General Hospital for Children, Boston, MA, United States
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20
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Minskaia E, Lacerda JF. Analysis of FOXP3 DNA Methylation Patterns to Identify Functional FOXP3+ T-Cell Subpopulations. Methods Mol Biol 2023; 2559:115-136. [PMID: 36180630 DOI: 10.1007/978-1-0716-2647-4_9] [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] [Indexed: 06/16/2023]
Abstract
Human regulatory CD4+CD25+FOXP3+ T cells (Tregs) are involved in the suppression of immune responses and play important roles in the maintenance of self-tolerance and immune homeostasis. Abnormal Treg function may result in disease states of varying severity. As FOXP3-expressing Treg cells are phenotypically and functionally heterogeneous, the success of Treg therapies depends on the ability to reliably distinguish subpopulations of T cells bearing a Treg-like phenotype. Methylation of cytosines within CpG dinucleotides is an important epigenetic mechanism involved in regulation (and suppression) of gene expression. On the other hand, demethylation of regulatory DNA sequences, such as promoters and enhancers, is essential for initiation of gene transcription. This protocol shows that bisulfite sequencing (BS) distinguishes methylated and unmethylated cytosines within DNA and reveals the methylation status of individual CpGs in cells within each population, identifying functionally different FOXP3+ subpopulations.
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Affiliation(s)
- Ekaterina Minskaia
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Infection and Immunity Division, Institute of Immunity and Transplantation, University College London, Royal Free Hospital, London, UK
| | - João F Lacerda
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal.
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21
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Mijakovac A, Frkatović A, Hanić M, Ivok J, Martinić Kavur M, Pučić-Baković M, Spector T, Zoldoš V, Mangino M, Lauc G. Heritability of the glycan clock of biological age. Front Cell Dev Biol 2022; 10:982609. [PMID: 36619858 PMCID: PMC9815111 DOI: 10.3389/fcell.2022.982609] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
Immunoglobulin G is posttranslationally modified by the addition of complex N-glycans affecting its function and mediating inflammation at multiple levels. IgG glycome composition changes with age and health in a predictive pattern, presumably due to inflammaging. As a result, a novel biological aging biomarker, glycan clock of age, was developed. Glycan clock of age is the first of biological aging clocks for which multiple studies showed a possibility of clock reversal even with simple lifestyle interventions. However, none of the previous studies determined to which extent the glycan clock can be turned, and how much is fixed by genetic predisposition. To determine the contribution of genetic and environmental factors to phenotypic variation of the glycan clock, we performed heritability analysis on two TwinsUK female cohorts. IgG glycans from monozygotic and dizygotic twin pairs were analyzed by UHPLC and glycan age was calculated using the glycan clock. In order to determine additive genetic, shared, and unique environmental contributions, a classical twin design was applied. Heritability of the glycan clock was calculated for participants of one cross-sectional and one longitudinal cohort with three time points to assess the reliability of measurements. Heritability estimate for the glycan clock was 39% on average, suggesting a moderate contribution of additive genetic factors (A) to glycan clock variation. Remarkably, heritability estimates remained approximately the same in all time points of the longitudinal study, even though IgG glycome composition changed substantially. Most environmental contributions came from shared environmental factors (C), with unique environmental factors (E) having a minor role. Interestingly, heritability estimates nearly doubled, to an average of 71%, when we included age as a covariant. This intervention also inflated the estimates of unique environmental factors contributing to glycan clock variation. A complex interplay between genetic and environmental factors defines alternative IgG glycosylation during aging and, consequently, dictates the glycan clock's ticking. Apparently, environmental factors (including lifestyle choices) have a strong impact on the biological age measured with the glycan clock, which additionally clarifies why this aging clock is one of the most potent biomarkers of biological aging.
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Affiliation(s)
- Anika Mijakovac
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Maja Hanić
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Jelena Ivok
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | | | | | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Vlatka Zoldoš
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom,NIHR Biomedical Research Centre at Guy’s and St Thoma’s Foundation Trust, London, United Kingdom
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia,Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia,*Correspondence: Gordan Lauc,
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22
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Suseelan S, Pinna G. Heterogeneity in major depressive disorder: The need for biomarker-based personalized treatments. Adv Clin Chem 2022; 112:1-67. [PMID: 36642481 DOI: 10.1016/bs.acc.2022.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Major Depressive Disorder (MDD) or depression is a pathological mental condition affecting millions of people worldwide. Identification of objective biological markers of depression can provide for a better diagnostic and intervention criteria; ultimately aiding to reduce its socioeconomic health burden. This review provides a comprehensive insight into the major biomarker candidates that have been implicated in depression neurobiology. The key biomarker categories are covered across all the "omics" levels. At the epigenomic level, DNA-methylation, non-coding RNA and histone-modifications have been discussed in relation to depression. The proteomics system shows great promise with inflammatory markers as well as growth factors and neurobiological alterations within the endocannabinoid system. Characteristic lipids implicated in depression together with the endocrine system are reviewed under the metabolomics section. The chapter also examines the novel biomarkers for depression that have been proposed by studies in the microbiome. Depression affects individuals differentially and explicit biomarkers identified by robust research criteria may pave the way for better diagnosis, intervention, treatment, and prediction of treatment response.
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Affiliation(s)
- Shayam Suseelan
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - Graziano Pinna
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States; UI Center on Depression and Resilience (UICDR), Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States; Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States.
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23
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Kang HS, Kim SY, Choi HG, Lim H, Kim JH, Kim JH, Cho SJ, Nam ES, Min KW, Park HY, Kim NY, Choi Y, Kwon MJ. Comparison of the Concordance of Cardiometabolic Diseases and Physical and Laboratory Examination Findings between Monozygotic and Dizygotic Korean Adult Twins: A Cross-Sectional Study Using KoGES HTS Data. Nutrients 2022; 14:nu14224834. [PMID: 36432523 PMCID: PMC9693823 DOI: 10.3390/nu14224834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/31/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022] Open
Abstract
This study investigated the contribution of genetic and environmental factors to cardiometabolic diseases (CMDs) by comparing disease concordance in monozygotic and dizygotic twins. This cross-sectional study analyzed 1294 (1040 monozygotic and 254 dizygotic) twin pairs (>20 years) based on the Korean Genome and Epidemiology Study data (2005−2014). The odds ratios of disease concordance were calculated using binomial and multinomial logistic regression models. The occurrence of CMDs (hypertension, hyperlipidemia, type 2 diabetes, cerebral stroke, transient ischemic attack, and ischemic heart disease) and related physical and laboratory levels did not differ between the monozygotic and dizygotic twin groups. The odds for concordance of the presence/absence of CMDs and the likelihood of incident CMD within monozygotic twins were comparable to that of dizygotic twins. The absolute differences in hemoglobin A1c, insulin, low- and high-density lipoprotein cholesterol, total cholesterol, triglycerides, and systolic blood pressure were lower in monozygotic twins than in dizygotic twins. Absolute differences in fasting glucose and diastolic blood pressure did not differ between groups. Although baseline levels of several laboratory parameters related to CMD showed a strong likelihood of heritability in monozygotic twins, CMD phenotype appears to be largely affected by environmental factors.
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Affiliation(s)
- Ho Suk Kang
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - So Young Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, CHA Bundang Medical Center, CHA University College of Medicine, Seongnam 13488, Republic of Korea
| | - Hyo Geun Choi
- Department of Otorhinolaryngology-Head & Neck Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Hyun Lim
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Joo-Hee Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Ji Hee Kim
- Department of Neurosurgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
| | - Seong-Jin Cho
- Department of Pathology, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Republic of Korea
| | - Eun Sook Nam
- Department of Pathology, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Republic of Korea
| | - Kyueng-Whan Min
- Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Republic of Korea
| | - Ha Young Park
- Department of Pathology, Busan Paik Hospital, Inje University College of Medicine, Busan 47392, Republic of Korea
| | - Nan Young Kim
- Hallym Institute of Translational Genomics and Bioinformatics, Hallym University Medical Center, Anyang 14068, Republic of Korea
| | - Younghee Choi
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong 18450, Republic of Korea
- Research Insititute for Complementary & Alternative Medicine, Hallym University, Hwaseong 18450, Republic of Korea
| | - Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Republic of Korea
- Correspondence:
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24
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The emergence and development of behavioral individuality in clonal fish. Nat Commun 2022; 13:6419. [PMID: 36307437 PMCID: PMC9616841 DOI: 10.1038/s41467-022-34113-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Behavioral individuality is a ubiquitous phenomenon in animal populations, yet the origins and developmental trajectories of individuality, especially very early in life, are still a black box. Using a high-resolution tracking system, we mapped the behavioral trajectories of genetically identical fish (Poecilia formosa), separated immediately after birth into identical environments, over the first 10 weeks of their life at 3 s resolution. We find that (i) strong behavioral individuality is present at the very first day after birth, (ii) behavioral differences at day 1 of life predict behavior up to at least 10 weeks later, and (iii) patterns of individuality strengthen gradually over developmental time. Our results establish a null model for how behavioral individuality can develop in the absence of genetic and environmental variation and provide experimental evidence that later-in-life individuality can be strongly shaped by factors pre-dating birth like maternal provisioning, epigenetics and pre-birth developmental stochasticity.
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25
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Choi HG, Kim SY, Lim H, Kim JH, Kim JH, Cho SJ, Nam ES, Min KW, Park HY, Kim NY, Hong S, Choi Y, Kang HS, Kwon MJ. Comparison of Concordance of Peptic Ulcer Disease, Non-Adenomatous Intestinal Polyp, and Gallstone Disease in Korean Monozygotic and Dizygotic Twins: A Cross-Sectional Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191912708. [PMID: 36232007 PMCID: PMC9566074 DOI: 10.3390/ijerph191912708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 06/01/2023]
Abstract
Epidemiological studies have suggested the role of multiple genetic and environmental factors in the development of non-neoplastic gastrointestinal (GI) diseases; however, little information is available on these factors in the Korean population. Therefore, this cross-sectional study explored the effect of these factors by analyzing the concordance of several benign GI disorders in 525 monozygotic twins compared to that in 122 dizygotic twins aged >20 years from the Healthy Twin Study data of the Korean Genome and Epidemiology Study (2005-2014). Chi-square test, Wilcoxon rank-sum, and binomial and multinomial logistic regression models were used for statistical analysis. There was lack of concordance of gastric/duodenal ulcers and cholelithiasis/cholangitis between monozygotic twins compared to that in dizygotic twins, suggesting that environmental factors may mediate those concordant disease expressions in monozygotic twins. The concordance of intestinal polyps in monozygotic twins was 32% lower than that in dizygotic twins (p = 0.028), indicating that the effect of genetic factors on the risk for intestinal polyp development may be low. In conclusion, the lack or low concordance of several benign GI diseases between monozygotic and dizygotic twin groups suggests the relative importance of environmental factors, indicating that these are preventable diseases.
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Affiliation(s)
- Hyo Geun Choi
- Department of Otorhinolaryngology-Head & Neck Surgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea
| | - So Young Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, CHA Bundang Medical Center, CHA University College of Medicine, Seongnam 13488, Korea
| | - Hyun Lim
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea
| | - Joo-Hee Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea
| | - Ji Hee Kim
- Department of Neurosurgery, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea
| | - Seong-Jin Cho
- Department of Pathology, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea
| | - Eun Sook Nam
- Department of Pathology, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea
| | - Kyueng-Whan Min
- Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Korea
| | - Ha Young Park
- Department of Pathology, Busan Paik Hospital, Inje University College of Medicine, Busan 47392, Korea
| | - Nan Young Kim
- Hallym Institute of Translational Genomics and Bioinformatics, Hallym University Medical Center, Anyang 14068, Korea
| | - Sangkyoon Hong
- Hallym Institute of Translational Genomics and Bioinformatics, Hallym University Medical Center, Anyang 14068, Korea
| | - Younghee Choi
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong 18450, Korea
- Research Insititute for Complementary & Alternative Medicine, Hallym University, Anyang 14068, Korea
| | - Ho Suk Kang
- Division of Gastroenterology, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea
| | - Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang 14068, Korea
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26
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Barzaghi F, Cicalese MP, Zoccolillo M, Brigida I, Barcella M, Merelli I, Sartirana C, Zanussi M, Calbi V, Bernardo ME, Tucci F, Migliavacca M, Giglio F, Doglio M, Canarutto D, Ferrua F, Consiglieri G, Prunotto G, Saettini F, Bonanomi S, Rovere-Querini P, Di Colo G, Jofra T, Fousteri G, Penco F, Gattorno M, Hershfield MS, Bongiovanni L, Ponzoni M, Marktel S, Milani R, Peccatori J, Ciceri F, Mortellaro A, Aiuti A. Case Report: Consistent disease manifestations with a staggered time course in two identical twins affected by adenosine deaminase 2 deficiency. Front Immunol 2022; 13:910021. [PMID: 36248833 PMCID: PMC9557171 DOI: 10.3389/fimmu.2022.910021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/05/2022] [Indexed: 12/03/2022] Open
Abstract
Deficiency of adenosine deaminase 2 (DADA2) is an autosomal recessive disease associated with a highly variable clinical presentation, including vasculitis, immunodeficiency, and hematologic manifestations, potentially progressing over time. The present study describes the long-term evolution of the immuno-hematological features and therapeutic challenge of two identical adult twin sisters affected by DADA2. The absence of plasmatic adenosine deaminase 2 (ADA2) activity in both twins suggested the diagnosis of DADA2, then confirmed by genetic analysis. Exon sequencing revealed a missense (p.Leu188Pro) mutation on the paternal ADA2 allele. While, whole genome sequencing identified an unreported deletion (IVS6_IVS7del*) on the maternal allele predicted to produce a transcript missing exon 7. The patients experienced the disease onset during childhood with early strokes (Patient 1 at two years, Patient 2 at eight years of age), subsequently followed by other shared DADA2-associated features, including neutropenia, hypogammaglobulinemia, reduced switched memory B cells, inverted CD4:CD8 ratio, increased naïve T cells, reduced follicular regulatory T cells, the almost complete absence of NK cells, T-large granular cell leukemia, and osteoporosis. Disease evolution differed: clinical manifestations presented several years earlier and were more pronounced in Patient 1 than in Patient 2. Due to G-CSF refractory life-threatening neutropenia, Patient 1 successfully underwent an urgent hematopoietic stem cell transplantation (HSCT) from a 9/10 matched unrelated donor. Patient 2 experienced a similar, although delayed, disease evolution and is currently on anti-TNF therapy and anti-infectious prophylaxis. The unique cases confirmed that heterozygous patients with null ADA2 activity deserve deep investigation for possible structural variants on a single allele. Moreover, this report emphasizes the importance of timely recognizing DADA2 at the onset to allow adequate follow-up and detection of disease progression. Finally, the therapeutic management in these identical twins raises significant concerns as they share a similar phenotype, with a delayed but almost predictable disease evolution in one of them, who could benefit from a prompt definitive treatment like elective allogeneic HSCT. Additional data are required to assess whether the absence of enzymatic activity at diagnosis is associated with hematological involvement and is also predictive of bone marrow dysfunction, encouraging early HSCT to improve functional outcomes.
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Affiliation(s)
- Federica Barzaghi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Pia Cicalese
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Matteo Zoccolillo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Immacolata Brigida
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - Ivan Merelli
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - Claudia Sartirana
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monica Zanussi
- Clinical Genomics-Molecular Genetics Service, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Donato, San Raffaele Hospital, Milan, Italy
| | - Valeria Calbi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Ester Bernardo
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesca Tucci
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maddalena Migliavacca
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Giglio
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Matteo Doglio
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Canarutto
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesca Ferrua
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Consiglieri
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Prunotto
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Bone Marrow Transplantation Unit, Pediatric Department of Milano-Bicocca University, Monza e Brianza per il Bambino e la sua Mamma Foundation, Monza, Italy
| | - Francesco Saettini
- Bone Marrow Transplantation Unit, Pediatric Department of Milano-Bicocca University, Monza e Brianza per il Bambino e la sua Mamma Foundation, Monza, Italy
| | - Sonia Bonanomi
- Bone Marrow Transplantation Unit, Pediatric Department of Milano-Bicocca University, Monza e Brianza per il Bambino e la sua Mamma Foundation, Monza, Italy
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Internal Medicine, Diabetes, and Endocrinology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Di Colo
- Vita-Salute San Raffaele University, Milan, Italy
- Immunology, Rheumatology, Allergy and Rare Disease Unit, IRCCS San Rafaelle Hospital, Milan, Italy
| | - Tatiana Jofra
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Georgia Fousteri
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Penco
- Clinica Pediatrica – Reumatologia e Centro Malattie Autoinfiammatorie, IRCCS Giannina Gaslini, Genova, Italy
| | - Marco Gattorno
- Clinica Pediatrica – Reumatologia e Centro Malattie Autoinfiammatorie, IRCCS Giannina Gaslini, Genova, Italy
| | - Michael S. Hershfield
- Department of Medicine and Biochemistry, Duke University Medical Center, Durham, NC, United States
| | - Lucia Bongiovanni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maurilio Ponzoni
- Vita-Salute San Raffaele University, Milan, Italy
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sarah Marktel
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Raffaella Milani
- Immunohematology and Transfusion Medicine Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jacopo Peccatori
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Fabio Ciceri
- Vita-Salute San Raffaele University, Milan, Italy
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Alessandra Mortellaro
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Alessandra Mortellaro,
| | - Alessandro Aiuti
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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Guo L, Wang W, Song W, Cao H, Tian H, Wang Z, Ren J, Ning F, Zhang D, Duan H. Genome-wide DNA methylation analysis of middle-aged and elderly monozygotic twins with age-related hearing loss in Qingdao, China. Gene 2022; 849:146918. [PMID: 36179964 DOI: 10.1016/j.gene.2022.146918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To explore the differences in DNA methylation associated with age-related hearing loss in a study of 57 twin pairs from China. DESIGN Monozygotic twins were identified through the Qingdao Twin Registration system. The median age of participants was >50 years. Their hearing thresholds were measured using a multilevel pure-tone audiometry assessment. The pure-tone audiometry was calculated at low frequencies (0.5, 1.0, and 2.0 kHz), speech frequencies (0.5, 1.0, 2.0, and 4.0kHz), and high frequencies (4.0 and 8 kHz). The CpG sites were tested using a linear mixed-effects model, and the function of the cis-regulatory regions and ontological enrichments were predicted using the online Genomic Regions Enrichment of Annotations Tool. The differentially methylated regions were identified using a comb-p python library approach. RESULTS In each of the PTA categories (low-, speech-, high-frequency), age-related hearing loss was detected in 25.9%, 19.3%, and 52.8% of participants. In the low-, speech- and high-frequency categories we identified 18, 42, and 12 individual CpG sites and 6, 11, and 6 differentially methylated regions. The CpG site located near DUSP4 had the strongest association with low- and speech-frequency, while the strongest association with high-frequency was near C21orf58. We identified associations of ALG10 with high-frequency hearing, C3 and LCK with low- and speech-frequency hearing, and GBX2 with low-frequency hearing. Top pathways that may be related to hearing, such as the Notch signaling pathway, were also identified. CONCLUSION Our study is the first of its kind to identify these genes and their associated with DNA methylation may play essential roles in the hearing process. The results of our epigenome-wide association study on twins clarify the complex mechanisms underlying age-related hearing loss.
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Affiliation(s)
- Longzi Guo
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Wanxue Song
- Qingdao Maternal and Child Health and Family Planning Service Center, Qingdao, China
| | - Hainan Cao
- Department of Otorhinolaryngology, Qingdao Municipal Hospital, Qingdao, China
| | - Huimin Tian
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Zhaoguo Wang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Jifeng Ren
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Feng Ning
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China.
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28
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Yang CH, Fagnocchi L, Apostle S, Wegert V, Casaní-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Bras J, Thomasen M, Grunnet LG, Vaag AA, Gillberg L, Grundberg E, Conesa A, Körner A, Pospisilik JA. Independent phenotypic plasticity axes define distinct obesity sub-types. Nat Metab 2022; 4:1150-1165. [PMID: 36097183 PMCID: PMC9499872 DOI: 10.1038/s42255-022-00629-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Studies in genetically 'identical' individuals indicate that as much as 50% of complex trait variation cannot be traced to genetics or to the environment. The mechanisms that generate this 'unexplained' phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against UPV. We find that Nnat deficiency in isogenic mice triggers the emergence of a bi-stable polyphenism, where littermates emerge into adulthood either 'normal' or 'overgrown'. Mechanistically, this is mediated by an insulin-dependent overgrowth that arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two patterns of human UPV, one of which (Type B) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, Type-B monozygotic co-twins exhibit coordinated increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes linked to insulinemia. Critically, the Type-B UPV signature stratifies both childhood and adult cohorts into four metabolic states, including two phenotypically and molecularly distinct types of obesity.
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Affiliation(s)
- Chih-Hsiang Yang
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | | | - Vanessa Wegert
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Kathrin Landgraf
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
| | - Ilaria Panzeri
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erez Dror
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Roche Diagnostics Deutschland, Mannheim, Germany
| | - Till Wörpel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Di Lu
- Van Andel Institute, Grand Rapids, MI, USA
| | - Tao Yang
- Van Andel Institute, Grand Rapids, MI, USA
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Martin Thomasen
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Louise G Grunnet
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Allan A Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Linn Gillberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, MO, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, USA
| | - Antje Körner
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - J Andrew Pospisilik
- Van Andel Institute, Grand Rapids, MI, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Joshi RS, Rigau M, García-Prieto CA, Castro de Moura M, Piñeyro D, Moran S, Davalos V, Carrión P, Ferrando-Bernal M, Olalde I, Lalueza-Fox C, Navarro A, Fernández-Tena C, Aspandi D, Sukno FM, Binefa X, Valencia A, Esteller M. Look-alike humans identified by facial recognition algorithms show genetic similarities. Cell Rep 2022; 40:111257. [PMID: 36001980 DOI: 10.1016/j.celrep.2022.111257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/05/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022] Open
Abstract
The human face is one of the most visible features of our unique identity as individuals. Interestingly, monozygotic twins share almost identical facial traits and the same DNA sequence but could exhibit differences in other biometrical parameters. The expansion of the world wide web and the possibility to exchange pictures of humans across the planet has increased the number of people identified online as virtual twins or doubles that are not family related. Herein, we have characterized in detail a set of "look-alike" humans, defined by facial recognition algorithms, for their multiomics landscape. We report that these individuals share similar genotypes and differ in their DNA methylation and microbiome landscape. These results not only provide insights about the genetics that determine our face but also might have implications for the establishment of other human anthropometric properties and even personality characteristics.
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Affiliation(s)
- Ricky S Joshi
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Maria Rigau
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Carlos A García-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain
| | - Sebastian Moran
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Pablo Carrión
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Manuel Ferrando-Bernal
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain; Centre for Genomic Regulation (CNAG-CRG), 08003 Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | | | - Decky Aspandi
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Federico M Sukno
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Xavier Binefa
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), L'Hospitalet, 08907 Barcelona, Spain.
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30
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Silk T, Dipnall L, Wong YT, Craig JM. Epigenetics and ADHD. Curr Top Behav Neurosci 2022; 57:269-289. [PMID: 35505060 DOI: 10.1007/7854_2022_339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
There is robust evidence of genetic susceptibility to Attention-Deficit Hyperactivity Disorder (ADHD); however, there still remains significant variability that is not attributable to genetic factors. The emerging field of epigenetics is beginning to reveal how genotypic expression can be mediated by an array of variables including external environmental exposure, inter-individual developmental variation, and by the genome itself. Epigenetic modification plays a central role in neurobiological and developmental processes, and disturbances to these processes can have implications for a range of mental health problems. Although the field is still in its early days, this chapter will discuss the current standing of epigenetic research into ADHD. Firstly, key relevant epigenetic processes will be discussed. This will be followed by an overview of the key findings to date investigating the role of epigenetics in ADHD. Human studies have included the theory-driven approach of candidate-gene studies (CGS), as well as the increasingly popular exploratory approach of epigenome-wide association studies (EWAS). Overall, the findings are heterogeneous. However, it is possible that with more longitudinal studies and better characterised cohorts, both predictive and protective links between epigenetic processes and ADHD will be revealed.
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Affiliation(s)
- Timothy Silk
- Centre for Social and Early Emotional Development and School of Psychology, Deakin University, Geelong, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Lillian Dipnall
- Centre for Social and Early Emotional Development and School of Psychology, Deakin University, Geelong, VIC, Australia
| | - Yen Ting Wong
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Jeffrey M Craig
- Murdoch Children's Research Institute, Parkville, VIC, Australia.,Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia
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Hosseini S, Trakooljul N, Hirschfeld M, Wimmers K, Simianer H, Tetens J, Sharifi AR, Brenig B. Epigenetic Regulation of Phenotypic Sexual Plasticity Inducing Skewed Sex Ratio in Zebrafish. Front Cell Dev Biol 2022; 10:880779. [PMID: 35912111 PMCID: PMC9334531 DOI: 10.3389/fcell.2022.880779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
The plasticity of sexual phenotype in response to environmental conditions results in biased sex ratios, and their variation has an effect on population dynamics. Epigenetic modifications can modulate sex ratio variation in species, where sex is determined by genetic and environmental factors. However, the role of epigenetic mechanisms underlying skewed sex ratios is far from being clear and is still an object of debate in evolutionary developmental biology. In this study, we used zebrafish as a model animal to investigate the effect of DNA methylation on sex ratio variation in sex-biased families in response to environmental temperature. Two sex-biased families with a significant difference in sex ratio were selected for genome-wide DNA methylation analysis using reduced representation bisulfite sequencing (RRBS). The results showed significant genome-wide methylation differences between male-biased and female-biased families, with a greater number of methylated CpG sites in testes than ovaries. Likewise, pronounced differences between testes and ovaries were identified within both families, where the male-biased family exhibited a higher number of methylated sites than the female-biased family. The effect of temperature showed more methylated positions in the high incubation temperature than the control temperature. We found differential methylation of many reproduction-related genes (e.g., sox9a, nr5a2, lhx8a, gata4) and genes involved in epigenetic mechanisms (e.g., dnmt3bb.1, dimt1l, hdac11, h1m) in both families. We conclude that epigenetic modifications can influence the sex ratio variation in zebrafish families and may generate skewed sex ratios, which could have a negative consequence for population fitness in species with genotype-environment interaction sex-determining system under rapid environmental changes.
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Affiliation(s)
- Shahrbanou Hosseini
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Functional Breeding Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- *Correspondence: Shahrbanou Hosseini, ; Nares Trakooljul,
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany
- *Correspondence: Shahrbanou Hosseini, ; Nares Trakooljul,
| | - Marc Hirschfeld
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany
| | - Henner Simianer
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
| | - Jens Tetens
- Functional Breeding Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
| | - Ahmad Reza Sharifi
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
| | - Bertram Brenig
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
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32
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Sun J, Cheng B, Su Y, Li M, Ma S, Zhang Y, Zhang A, Cai S, Bao Q, Wang S, Zhu P. The Potential Role of m6A RNA Methylation in the Aging Process and Aging-Associated Diseases. Front Genet 2022; 13:869950. [PMID: 35518355 PMCID: PMC9065606 DOI: 10.3389/fgene.2022.869950] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/31/2022] [Indexed: 12/15/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common and conserved internal eukaryotic mRNA modification. m6A modification is a dynamic and reversible post-transcriptional regulatory modification, initiated by methylase and removed by RNA demethylase. m6A-binding proteins recognise the m6A modification to regulate gene expression. Recent studies have shown that altered m6A levels and abnormal regulator expression are crucial in the ageing process and the occurrence of age-related diseases. In this review, we summarise some key findings in the field of m6A modification in the ageing process and age-related diseases, including cell senescence, autophagy, inflammation, oxidative stress, DNA damage, tumours, neurodegenerative diseases, diabetes, and cardiovascular diseases (CVDs). We focused on the biological function and potential molecular mechanisms of m6A RNA methylation in ageing and age-related disease progression. We believe that m6A modification may provide a new target for anti-ageing therapies.
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Affiliation(s)
- Jin Sun
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Bokai Cheng
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Yongkang Su
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Man Li
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Shouyuan Ma
- Department of Geriatric Cardiology, The Second Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yan Zhang
- Department of Outpatient, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Anhang Zhang
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Shuang Cai
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Qiligeer Bao
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Shuxia Wang
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Ping Zhu
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
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Tsai HH, Shen CY, Ho CC, Hsu SY, Tantoh DM, Nfor ON, Chiu SL, Chou YH, Liaw YP. Interaction between a diabetes-related methylation site (TXNIP cg19693031) and variant (GLUT1 rs841853) on fasting blood glucose levels among non-diabetics. J Transl Med 2022; 20:87. [PMID: 35164795 PMCID: PMC8842527 DOI: 10.1186/s12967-022-03269-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is caused by a combination of environmental, genetic, and epigenetic factors including, fasting blood glucose (FBG), genetic variant rs841853, and cg19693031 methylation. We evaluated the interaction between rs841853 and cg19693031 on the FBG levels of non-diabetic Taiwanese adults. Methods We used Taiwan Biobank (TWB) data collected between 2008 and 2016. The TWB data source contains information on basic demographics, personal lifestyles, medical history, methylation, and genotype. The study participants included 1300 people with DNA methylation data. The association of cg19693031 methylation (stratified into quartiles) with rs841853 and FBG was determined using multiple linear regression analysis. The beta-coefficients (β) and p-values were estimated. Results The mean ± standard deviation (SD) of FBG in rs841853-CC individuals (92.07 ± 7.78) did not differ significantly from that in the CA + AA individuals (91.62 ± 7.14). However, the cg19693031 methylation levels were significantly different in the two groups (0.7716 ± 0.05 in CC individuals and 0.7631 ± 0.05 in CA + AA individuals (p = 0.002). The cg19693031 methylation levels according to quartiles were β < 0.738592 (< Q1), 0.738592 ≤ 0.769992 (Q1–Q2), 0.769992 ≤ 0.800918 (Q2–Q3), and β ≥ 0.800918 (≥ Q3). FBG increased with decreasing cg19693031 methylation levels in a dose–response manner (ptrend = 0.005). The β-coefficient was − 0.0236 (p = 0.965) for Q2–Q3, 1.0317 (p = 0.058) for Q1–Q2, and 1.3336 (p = 0.019 for < Q1 compared to the reference quartile (≥ Q3). The genetic variant rs841853 was not significantly associated with FBG. However, its interaction with cg19693031 methylation was significant (p-value = 0.036). Based on stratification by rs841853 genotypes, only the CC group retained the inverse and dose–response association between FBG and cg19693031 methylation. The β (p-value) was 0.8082 (0.255) for Q2–Q3, 1.6930 (0.022) for Q1–Q2, and 2.2190 (0.004) for < Q1 compared to the reference quartile (≥ Q3). The ptrend was 0.002. Conclusion Summarily, methylation at cg19693031 was inversely associated with fasting blood glucose in a dose-dependent manner. The inverse association was more prominent in rs841853-CC individuals, suggesting that rs841853 could modulate the association between cg19693031 methylation and FBG. Our results suggest that genetic variants may be involved in epigenetic mechanisms associated with FBG, a hallmark of diabetes. Therefore, integrating genetic and epigenetic data may provide more insight into the early-onset of diabetes. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03269-y.
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34
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Zhao E, Tait C, Minacapelli CD, Catalano C, Rustgi VK. Circadian Rhythms, the Gut Microbiome, and Metabolic Disorders. GASTRO HEP ADVANCES 2022; 1:93-105. [PMID: 39129932 PMCID: PMC11307590 DOI: 10.1016/j.gastha.2021.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/15/2021] [Indexed: 08/13/2024]
Abstract
The circadian clock and gut microbiome play integral roles in preserving metabolic homeostasis. Circadian rhythms represent an endogenous time-keeping system that regulates cell and organ functions and synchronizes physiology with external cues to establish metabolic homeostasis. A variety of functions throughout the gastrointestinal tract and liver are under circadian control, including nutrient transport, processing, and detoxification. The gut microbiota also plays an essential role in host metabolism, regulating processes such as digestion, inflammatory modulation, and bile acid metabolism. Both the circadian clock and the gut microbiota influence each other in a reciprocal fashion, as gut dysbiosis can precipitate circadian asynchrony, and vice-versa. Disruption of either system impacts homeostasis in a bidirectional manner and can contribute to metabolic dysfunction. Evidence suggests such disruptions can lead to the development of metabolic diseases, including obesity, diabetes, nonalcoholic fatty liver disease, cirrhosis, and hepatocellular carcinoma. This review will provide a basic overview of the circadian and gut microbial systems, how they are intertwined, and their impact on the liver and gastrointestinal tract and in the development of metabolic disease. Particular areas of discussion include epigenetic regulation of circadian pathways as well as a mechanistic overview of microbial dysbiosis. In addition, therapeutic targets of these systems, including dietary modifications, behavioral modifications, and microbial-directed therapies, will be explored.
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Affiliation(s)
- Eric Zhao
- Department of Internal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Christopher Tait
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Center for Liver Diseases and Masses, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, New Jersey
| | - Carlos D. Minacapelli
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Center for Liver Diseases and Masses, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, New Jersey
| | - Carolyn Catalano
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Center for Liver Diseases and Masses, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, New Jersey
| | - Vinod K. Rustgi
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Center for Liver Diseases and Masses, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, New Jersey
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35
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Fujisawa TX, Nishitani S, Makita K, Yao A, Takiguchi S, Hamamura S, Shimada K, Okazawa H, Matsuzaki H, Tomoda A. Association of Epigenetic Differences Screened in a Few Cases of Monozygotic Twins Discordant for Attention-Deficit Hyperactivity Disorder With Brain Structures. Front Neurosci 2022; 15:799761. [PMID: 35145374 PMCID: PMC8823258 DOI: 10.3389/fnins.2021.799761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
The present study examined the relationship between DNA methylation differences and variations in brain structures involved in the development of attention-deficit hyperactivity disorder (ADHD). First, we used monozygotic (MZ) twins discordant (2 pairs of 4 individuals, 2 boys, mean age 12.5 years) for ADHD to identify candidate DNA methylation sites involved in the development of ADHD. Next, we tried to replicate these candidates in a case-control study (ADHD: N = 18, 15 boys, mean age 10.0 years; Controls: N = 62, 40 boys, mean age 13.9 years). Finally, we examined how methylation rates at those sites relate to the degree of local structural alterations where significant differences were observed between cases and controls. As a result, we identified 61 candidate DNA methylation sites involved in ADHD development in two pairs of discordant MZ twins, among which elevated methylation at a site in the sortilin-related Vps10p domain containing receptor 2 (SorCS2) gene was replicated in the case-control study. We also observed that the ADHD group had significantly reduced gray matter volume (GMV) in the precentral and posterior orbital gyri compared to the control group and that this volume reduction was positively associated with SorCS2 methylation. Furthermore, the reduced GMV regions in children with ADHD are involved in language processing and emotional control, while SorCS2 methylation is also negatively associated with emotional behavioral problems in children. These results indicate that SorCS2 methylation might mediate a reduced GMV in the precentral and posterior orbital gyri and therefore influence the pathology of children with ADHD.
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Affiliation(s)
- Takashi X. Fujisawa
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- *Correspondence: Takashi X. Fujisawa,
| | - Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
| | - Kai Makita
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
| | - Akiko Yao
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
| | - Shinichiro Takiguchi
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Shoko Hamamura
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Koji Shimada
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Hidehiko Okazawa
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Hideo Matsuzaki
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
- *Correspondence: Takashi X. Fujisawa,
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Jung M, Ahn YS, Chang SJ, Kim CB, Jeong KS, Koh SB, Gim JA. Variation in Genotype and DNA Methylation Patterns Based on Alcohol Use and CVD in the Korean Genome and Epidemiology Study (KoGES). Genes (Basel) 2022; 13:genes13020172. [PMID: 35205218 PMCID: PMC8871634 DOI: 10.3390/genes13020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 12/14/2022] Open
Abstract
Alcohol consumption can increase the risk of chronic diseases, such as myocardial infarction, coronary artery disease, hyperlipidemia, and hypertension. We aimed to assess the association between genotype, DNA methylation patterns, alcohol consumption, and chronic diseases in Korean population. We analyzed 8840 subjects for genotypes and 446 for DNA methylation among the 9351 subjects from the Korean Genome and Epidemiology Study (KoGES). We further divided both groups into two sub-groups according to the presence/absence of chronic diseases. We selected genes whose methylation varied significantly with alcohol consumption, and visualized genotype and DNA methylation patterns specific to each group. Genome-wide association study (GWAS) revealed single nucleotide polymorphisms (SNPs) rs2074356 and rs11066280 in HECT domain E3 ubiquitin protein ligase 4 (HECTD4) to be significantly associated with alcohol consumption in both the presence. The rs12229654 genotype also displayed significantly different patterns with alcohol consumption. Furthermore, we retrieved differentially methylated regions (DMRs) from four groups based on sex and chronic diseases and compared them by drinking status. In genotype analysis, cardiovascular diseases (CVDs) showed a higher proportion in drinker than in non-drinker, but not in DMR analysis. Additionally, we analyzed the enriched Gene Ontology terms and Kyoto Gene and Genome Encyclopedia (KEGG) pathways and visualized the network, heatmap, and upset plot. We show that the pattern of DNA methylation associated with CVD is strongly influenced by alcoholism. Overall, this study identified genetic and epigenetic variants influenced by alcohol consumption and chronic diseases.
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Affiliation(s)
- Myoungjee Jung
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
| | - Yeon-Soon Ahn
- Department of Preventive Medicine and Genomic Cohort Institute, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea;
| | - Sei-Jin Chang
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
| | - Chun-Bae Kim
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
| | - Kyoung Sook Jeong
- Department of Occupational and Environmental Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea;
| | - Sang-Baek Koh
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
- Institute of Genomic Cohort, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea
- Correspondence: (S.-B.K.); (J.-A.G.); Tel.: +82-33-741-0345 (S.-B.K.); +82-2-2626-2362 (J.-A.G.)
| | - Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University, 8 Gamasan-ro 20-gil, Guro-gu, Seoul 08308, Korea
- Correspondence: (S.-B.K.); (J.-A.G.); Tel.: +82-33-741-0345 (S.-B.K.); +82-2-2626-2362 (J.-A.G.)
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37
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Chakravarti R, Lenka SK, Gautam A, Singh R, Ravichandiran V, Roy S, Ghosh D. A Review on CRISPR-Mediated Epigenome Editing: A Future Directive for Therapeutic Management of Cancer. Curr Drug Targets 2022; 23:836-853. [DOI: 10.2174/1389450123666220117105531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Recent studies have shed light on the role of epigenetic marks in certain diseases like cancer, type II diabetes mellitus (T2DM), obesity, and cardiovascular dysfunction, to name a few. Epigenetic marks like DNA methylation and histone acetylation are randomly altered in the disease state. It has been seen that methylation of DNA and histones can result in down-regulation of gene expression, whereas histone acetylation, ubiquitination, and phosphorylation are linked to enhanced expression of genes. How can we precisely target such epigenetic aberrations to prevent the advent of diseases? The answer lies in the amalgamation of the efficient genome editing technique, CRISPR, with certain effector molecules that can alter the status of epigenetic marks as well as employ certain transcriptional activators or repressors. In this review, we have discussed the rationale of epigenetic editing as a therapeutic strategy and how CRISPR-Cas9 technology coupled with epigenetic effector tags can efficiently edit epigenetic targets. In the later part, we have discussed how certain epigenetic effectors are tagged with dCas9 to elicit epigenetic changes in cancer. Increased interest in exploring the epigenetic background of cancer and non-communicable diseases like type II diabetes mellitus and obesity accompanied with technological breakthroughs has made it possible to perform large-scale epigenome studies.
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Affiliation(s)
- Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Swadhin Kumar Lenka
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Syamal Roy
- CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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Zou Y, Li JJ, Xue W, Kong X, Duan H, Li Y, Wei L. Epigenetic Modifications and Therapy in Uveitis. Front Cell Dev Biol 2021; 9:758240. [PMID: 34869347 PMCID: PMC8636745 DOI: 10.3389/fcell.2021.758240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Uveitis is a sight-threatening intraocular inflammation, and the exact pathogenesis of uveitis is not yet clear. Recent studies, including multiple genome-wide association studies (GWASs), have identified genetic variations associated with the onset and progression of different types of uveitis, such as Vogt–Koyanagi–Harada (VKH) disease and Behcet’s disease (BD). However, epigenetic regulation has been shown to play key roles in the immunoregulation of uveitis, and epigenetic therapies are promising treatments for intraocular inflammation. In this review, we summarize recent advances in identifying epigenetic programs that cooperate with the physiology of intraocular immune responses and the pathology of intraocular inflammation. These attempts to understand the epigenetic mechanisms of uveitis may provide hope for the future development of epigenetic therapies for these devastating intraocular inflammatory conditions.
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Affiliation(s)
- Yanli Zou
- Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China.,State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Wei Xue
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Xiangbin Kong
- Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Hucheng Duan
- Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Yiqun Li
- Department of Orthopaedics, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
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Changes in DNA methylation in APOE and ACKR3 genes in multiple sclerosis patients and the relationship with their heavy metal blood levels. Neurotoxicology 2021; 87:182-187. [PMID: 34624384 DOI: 10.1016/j.neuro.2021.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/12/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease with demyelinated lesions in the central nervous system caused by genetic and environmental factors. DNA methylation as an epigenetic change influenced by environmental factors, including heavy metals has been implemented in MS disease. We investigated the correlation of DNA methylation changes in APOE and ACKR3 genes in MS patients and the possible association with blood concentration of arsenic (As), cadmium (Cd) and lead (Pb) as major heavy metal pollutants. This study included 69 relapsing-remitting multiple sclerosis (RR-MS) patients and 69 age/gender-matched healthy subjects. The HRM real-time PCR method was used to investigate the changes in DNA methylation and heavy metal concentrations were measured by electrothermal atomic absorption spectrometry. Our results showed that the methylation pattern in the ACKR3 gene of the patient group was more hypomethylated, while in the case of the APOE gene, this pattern was more towards hypermethylation compared to healthy subjects. Moreover, the blood levels of As and Cd metals, but not Pb, were significantly higher in the patient group compare to the control group (p ≤ 0.05). The data indicate that the increase in expression of ACKR3 gene by hypomethylation and the decrease in expression of APOE gene via hypermethylation are possibly involved in the onset and progression of inflammatory processes in MS patients. The level of As can also lead to hypomethylation by disrupting the methylation patterns of the ACKR3 gene, resulting in increased expression in MS patients. Finally, we have shown that epigenetic changes can be an important factor in increasing and decreasing the expression of genes involved in the onset and/or progression of inflammatory processes in MS. Furthermore, exposure to heavy metals, especially As, by changing the natural patterns of DNA methylation can be effective in this disease.
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40
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Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk. Nat Commun 2021; 12:5251. [PMID: 34475392 PMCID: PMC8413445 DOI: 10.1038/s41467-021-25517-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/12/2021] [Indexed: 11/28/2022] Open
Abstract
DNA methylation (DNAm) is an epigenetic regulator of gene expression and a hallmark of gene-environment interaction. Using whole-genome bisulfite sequencing, we have surveyed DNAm in 344 samples of human postmortem brain tissue from neurotypical subjects and individuals with schizophrenia. We identify genetic influence on local methylation levels throughout the genome, both at CpG sites and CpH sites, with 86% of SNPs and 55% of CpGs being part of methylation quantitative trait loci (meQTLs). These associations can further be clustered into regions that are differentially methylated by a given SNP, highlighting the genes and regions with which these loci are epigenetically associated. These findings can be used to better characterize schizophrenia GWAS-identified variants as epigenetic risk variants. Regions differentially methylated by schizophrenia risk-SNPs explain much of the heritability associated with risk loci, despite covering only a fraction of the genomic space. We provide a comprehensive, single base resolution view of association between genetic variation and genomic methylation, and implicate schizophrenia GWAS-associated variants as influencing the epigenetic plasticity of the brain. The authors provide a comprehensive, single base resolution view of association between genetic variation and DNA methylation in human brain. They also show that heritability attributed to schizophrenia GWAS-associated variants reflects the epigenetic plasticity of the brain.
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Schamschula E, Lahnsteiner A, Assenov Y, Hagmann W, Zaborsky N, Wiederstein M, Strobl A, Stanke F, Muley T, Plass C, Tümmler B, Risch A. Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in PKP3 in lung epithelial cells. Epigenetics 2021; 17:837-860. [PMID: 34415821 PMCID: PMC9423854 DOI: 10.1080/15592294.2021.1959976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the Plakophilin-3 (PKP3) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of PKP3 which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
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Affiliation(s)
| | | | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hagmann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria.,Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Anna Strobl
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Frauke Stanke
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik Heidelberg, University of Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Burkhard Tümmler
- Clinical Research Group, Clinic for Pediatric Pneumology, Allergology and NeonatologyClinic for Pediatric Pneumology, Allergology and Neonatology, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Angela Risch
- Department of Biosciences, University of Salzburg, Salzburg, Austria.,Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Cancer Cluster Salzburg, Salzburg, Austria.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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42
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Qi Z, Li J, Li M, Du X, Zhang L, Wang S, Xu B, Liu W, Xu Z, Deng Y. The Essential Role of Epigenetic Modifications in Neurodegenerative Diseases with Dyskinesia. Cell Mol Neurobiol 2021; 42:2459-2472. [PMID: 34383231 DOI: 10.1007/s10571-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022]
Abstract
Epigenetics play an essential role in the occurrence and improvement of many diseases. Evidence shows that epigenetic modifications are crucial to the regulation of gene expression. DNA methylation is closely linked to embryonic development in mammalian. In recent years, epigenetic drugs have shown unexpected therapeutic effects on neurological diseases, leading to the study of the epigenetic mechanism in neurodegenerative diseases. Unlike genetics, epigenetics modify the genome without changing the DNA sequence. Research shows that epigenetics is involved in all aspects of neurodegenerative diseases. The study of epigenetic will provide valuable insights into the molecular mechanism of neurodegenerative diseases, which may lead to new treatments and diagnoses. This article reviews the role of epigenetic modifications neurodegenerative diseases with dyskinesia, and discusses the therapeutic potential of epigenetic drugs in neurodegenerative diseases.
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Affiliation(s)
- Zhipeng Qi
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Jiashuo Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Minghui Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Xianchao Du
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Lei Zhang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Shuang Wang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Zhaofa Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China.
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43
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Milošević M, Arsić A, Cvetković Z, Vučić V. Memorable Food: Fighting Age-Related Neurodegeneration by Precision Nutrition. Front Nutr 2021; 8:688086. [PMID: 34422879 PMCID: PMC8374314 DOI: 10.3389/fnut.2021.688086] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Healthcare systems worldwide are seriously challenged by a rising prevalence of neurodegenerative diseases (NDDs), which mostly, but not exclusively, affect the ever-growing population of the elderly. The most known neurodegenerative diseases are Alzheimer's (AD) and Parkinson's disease, multiple sclerosis, and amyotrophic lateral sclerosis, but some viral infections of the brain and traumatic brain injury may also cause NDD. Typical for NDD are the malfunctioning of neurons and their irreversible loss, which often progress irreversibly to dementia and ultimately to death. Numerous factors are involved in the pathogenesis of NDD: genetic variability, epigenetic changes, extent of oxidative/nitrosative stress, mitochondrial dysfunction, and DNA damage. The complex interplay of all the above-mentioned factors may be a fingerprint of neurodegeneration, with different diseases being affected to different extents by particular factors. There is a voluminous body of evidence showing the benefits of regular exercise to brain health and cognitive functions. Moreover, the importance of a healthy diet, balanced in macro- and micro-nutrients, in preventing neurodegeneration and slowing down a progression to full-blown disease is evident. Individuals affected by NDD almost inevitably have low-grade inflammation and anomalies in lipid metabolism. Metabolic and lipid profiles in NDD can be improved by the Mediterranean diet. Many studies have associated the Mediterranean diet with a decreased risk of dementia and AD, but a cause-and-effect relationship has not been deduced. Studies with caloric restriction showed neuroprotective effects in animal models, but the results in humans are inconsistent. The pathologies of NDD are complex and there is a great inter-individual (epi)genetic variance within any population. Furthermore, the gut microbiome, being deeply involved in nutrient uptake and lipid metabolism, also represents a pillar of the gut microbiome-brain axis and is linked with the pathogenesis of NDD. Numerous studies on the role of different micronutrients (omega-3 fatty acids, bioactive polyphenols from fruit and medicinal plants) in the prevention, prediction, and treatment of NDD have been conducted, but we are still far away from a personalized diet plan for individual NDD patients. For this to be realized, large-scale cohorts that would include the precise monitoring of food intake, mapping of genetic variants, epigenetic data, microbiome studies, and metabolome, lipidome, and transcriptome data are needed.
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Affiliation(s)
- Maja Milošević
- Department of Neuroendocrinology, Institute for Medical Research, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Arsić
- Department of Nutritional Biochemistry and Dietology, Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, University of Belgrade, Belgrade, Serbia
| | - Zorica Cvetković
- Department of Hematology, Clinical Hospital Center Zemun, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vesna Vučić
- Department of Nutritional Biochemistry and Dietology, Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, University of Belgrade, Belgrade, Serbia
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44
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Lu M, Xueying Q, Hexiang P, Wenjing G, Hägg S, Weihua C, Chunxiao L, Canqing Y, Jun L, Zengchang P, Liming C, Hua W, Xianping W, Yunzhang W, Liming L. Genome-wide associations between alcohol consumption and blood DNA methylation: evidence from twin study. Epigenomics 2021; 13:939-951. [PMID: 33993705 DOI: 10.2217/epi-2021-0039] [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: 11/21/2022] Open
Abstract
Aim: Alcohol intake alters DNA methylation profiles and methylation might mediate the association between alcohol and disease, but limited number of positive CpG sites repeatedly replicated. Materials & methods: In total, 57 monozygotic (MZ) twin pairs discordant for alcohol drinking from the Chinese National Twin Registry and 158 MZ and dizygotic twin pairs in the Swedish Adoption/Twin Study of Aging were evaluated. DNA methylation was detected using the Infinium HumanMethylation450 BeadChip. Results: Among candidate CpG sites, cg07326074 was significantly correlated with drinking after adjusting for covariates in MZ twins in both datasets but not in the entire sample or dizygotic twins. Conclusion: The hypermethylation of cg07326074, located in the tumor-promoting gene C16orf59, was associated with alcohol consumption.
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Affiliation(s)
- Meng Lu
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Qin Xueying
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China.,Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Peng Hexiang
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Gao Wenjing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Cao Weihua
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Li Chunxiao
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Yu Canqing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Lv Jun
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Pang Zengchang
- Qingdao Center for Disease Control & Prevention, Qingdao 266033, PR China
| | - Cong Liming
- Zhejiang Center for Disease Control & Prevention, Hangzhou 310051, PR China
| | - Wang Hua
- Jiangsu Center for Disease Control & Prevention, Nanjing 210009, PR China
| | - Wu Xianping
- Sichuan Center for Disease Control & Prevention, Chengdu 610041, PR China
| | - Wang Yunzhang
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Li Liming
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
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45
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Young JI, Slifer S, Hecht JT, Blanton SH. DNA Methylation Variation Is Identified in Monozygotic Twins Discordant for Non-syndromic Cleft Lip and Palate. Front Cell Dev Biol 2021; 9:656865. [PMID: 34055787 PMCID: PMC8149607 DOI: 10.3389/fcell.2021.656865] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCLP) is the most common craniofacial birth defect. The etiology of NSCLP is complex with multiple genes and environmental factors playing causal roles. Although studies have identified numerous genetic markers associated with NSCLP, the role of epigenetic variation remains relatively unexplored. Because of their identical DNA sequences, monozygotic (MZ) twins discordant for NSCLP are an ideal model for examining the potential contribution of DNA methylation to non-syndromic orofacial clefting. In this study, we compared the patterns of whole genome DNA methylation in six MZ twin pairs discordant for NSCLP. Differentially methylated positions (DMPs) and regions (DMRs) were identified in NSCLP candidate genes, including differential methylation in MAFB and ZEB2 in two independent MZ twin pairs. In addition to DNA methylation differences in NSCLP candidate genes, we found common differential methylation in genes belonging to the Hippo signaling pathway, implicating this mechanosensory pathway in the etiology of NSCLP. The results of this novel approach using MZ twins discordant for NSCLP suggests that differential methylation is one mechanism contributing to NSCLP, meriting future studies on the role of DNA methylation in familial and sporadic NSCLP.
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Affiliation(s)
- Juan I. Young
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Susan Slifer
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Jacqueline T. Hecht
- McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Susan H. Blanton
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
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Shi X, Wang Q, Sun C, Guo Q, Song T. Study on the role of methylation in nonsyndromic cleft lip with or without cleft palate using a monozygotic twin model. Int J Pediatr Otorhinolaryngol 2021; 143:110659. [PMID: 33667834 DOI: 10.1016/j.ijporl.2021.110659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/19/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The research on the etiology of nonsyndromic cleft lip with or without cleft palate(NSCL/P) is challenging, and DNA methylation has an impact on the formation of cleft lip and palate. SUBJECTS In this study, one of a pair of monozygotic twins (T1) had nonsyndromic cleft lip (NSCL), and one of a pair of monozygotic twins (T2) had nonsyndromic cleft lip and palate (NSCLP). We determined the methylation profiles of more than 850,000 CpGs in the DNA of the blood samples from the two pairs of monozygotic twins. RESULT Methylation data indicated that 1184 differentially methylated CpG sites were found in the T1 group (651 hypermethylated and 533 hypomethylated) and 8099 differentially methylated CpG sites in the T2 group (1713 hypermethylated and 6386 hypomethylated) compared with the healthy twin.The common difference was 107 methylation sites.GO enrichment analysis showed that regulation of smooth muscle cell migration and actin cytoskeleton reorganization were the most prominent classes.KEGG pathway enrichment analysis showed that the TGF-β signaling pathway, Notch signaling pathway and Wnt signaling pathway are relevant to the formation of NSCL/P.Two selected genes (NTN1 and PLEKHA7) are involved in the formation of NSCL/P. CONCLUSION These findings provide some support for the hypothesis that abnormal DNA methylation may influence the formation of clefts.
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Affiliation(s)
- Xuheng Shi
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Qi Wang
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Changsheng Sun
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Qiang Guo
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Tao Song
- Department of Stomatology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China.
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Discordant phenotypes in twins with infantile nystagmus. Sci Rep 2021; 11:2826. [PMID: 33531592 PMCID: PMC7854608 DOI: 10.1038/s41598-021-82368-0] [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: 12/18/2020] [Accepted: 01/18/2021] [Indexed: 11/08/2022] Open
Abstract
Infantile nystagmus (IN) may result from aetiologies including albinism and FRMD7 mutations. IN has low prevalence, and twins with IN are rare. Whilst discordant presentation has been previously reported for IN, we present for the first time the comprehensive assessment of diagnostically discordant monozygotic twins. From a cohort of over 2000 patients, we identified twins and triplets discordant for nystagmus. Using next-generation sequencing, high-resolution infra-red pupil tracking and optical coherence tomography, we characterised differences in genotype and phenotype. Monozygotic twins (n = 1), dizygotic twins (n = 3) and triplets (n = 1) were included. The monozygotic twins had concordant TYR variants. No causative variants were identified in the triplets. Dizygotic twins had discordant variants in TYR, OCA2 and FRMD7. One unaffected co-twin demonstrated sub-clinical nystagmus. Foveal hypoplasia (FH) was noted in four of five probands. Both co-twins of the monozygotic pair and triplets displayed FH. In three families, at least one parent had FH without nystagmus. FH alone may be insufficient to develop nystagmus. Whilst arrested optokinetic reflex pathway development is implicated in IN, discordant twins raise questions regarding where differences in development have arisen. In unaffected monozygotes therefore, genetic variants may predispose to oculomotor instability, with variable expressivity possibly responsible for the discordance observed.
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48
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Romanos P, Borjac J. Epigenetic Discrimination of Lebanese Monozygotic Twins as a Promising Forensic Approach. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group. Mol Psychiatry 2021; 26:3884-3895. [PMID: 31811260 PMCID: PMC8550939 DOI: 10.1038/s41380-019-0605-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation, which is modulated by both genetic factors and environmental exposures, may offer a unique opportunity to discover novel biomarkers of disease-related brain phenotypes, even when measured in other tissues than brain, such as blood. A few studies of small sample sizes have revealed associations between blood DNA methylation and neuropsychopathology, however, large-scale epigenome-wide association studies (EWAS) are needed to investigate the utility of DNA methylation profiling as a peripheral marker for the brain. Here, in an analysis of eleven international cohorts, totalling 3337 individuals, we report epigenome-wide meta-analyses of blood DNA methylation with volumes of the hippocampus, thalamus and nucleus accumbens (NAcc)-three subcortical regions selected for their associations with disease and heritability and volumetric variability. Analyses of individual CpGs revealed genome-wide significant associations with hippocampal volume at two loci. No significant associations were found for analyses of thalamus and nucleus accumbens volumes. Cluster-based analyses revealed additional differentially methylated regions (DMRs) associated with hippocampal volume. DNA methylation at these loci affected expression of proximal genes involved in learning and memory, stem cell maintenance and differentiation, fatty acid metabolism and type-2 diabetes. These DNA methylation marks, their interaction with genetic variants and their impact on gene expression offer new insights into the relationship between epigenetic variation and brain structure and may provide the basis for biomarker discovery in neurodegeneration and neuropsychiatric conditions.
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Joshi AD, Chan AT. Racial Differences in Epigenetic Aging of the Colon: Implications for Colorectal Cancer. J Natl Cancer Inst 2020; 113:1618-1619. [PMID: 33377963 PMCID: PMC8634465 DOI: 10.1093/jnci/djaa207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Amit D Joshi
- Clinical and Translational Epidemiology, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew T Chan
- Clinical and Translational Epidemiology, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Correspondence to: Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, 100 Cambridge Street, 15th Floor, Boston, MA 02114, USA (e-mail: )
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