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Chaar DL, Nguyen K, Wang YZ, Ratliff SM, Mosley TH, Kardia SLR, Smith JA, Zhao W. SNP-by-CpG Site Interactions in ABCA7 Are Associated with Cognition in Older African Americans. Genes (Basel) 2022; 13:2150. [PMID: 36421824 PMCID: PMC9691156 DOI: 10.3390/genes13112150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 06/28/2024] Open
Abstract
SNPs in ABCA7 confer the largest genetic risk for Alzheimer's Disease (AD) in African Americans (AA) after APOE ε4. However, the relationship between ABCA7 and cognitive function has not been thoroughly examined. We investigated the effects of five known AD risk SNPs and 72 CpGs in ABCA7, as well as their interactions, on general cognitive function (cognition) in 634 older AA without dementia from Genetic Epidemiology Network of Arteriopathy (GENOA). Using linear mixed models, no SNP or CpG was associated with cognition after multiple testing correction, but five CpGs were nominally associated (p < 0.05). Four SNP-by-CpG interactions were associated with cognition (FDR q < 0.1). Contrast tests show that methylation is associated with cognition in some genotype groups (p < 0.05): a 1% increase at cg00135882 and cg22271697 is associated with a 0.68 SD decrease and 0.14 SD increase in cognition for those with the rs3764647 GG/AG (p = 0.004) and AA (p = 2 × 10-4) genotypes, respectively. In addition, a 1% increase at cg06169110 and cg17316918 is associated with a 0.37 SD decrease (p = 2 × 10-4) and 0.33 SD increase (p = 0.004), respectively, in cognition for those with the rs115550680 GG/AG genotype. While AD risk SNPs in ABCA7 were not associated with cognition in this sample, some have interactions with proximal methylation on cognition.
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Affiliation(s)
- Dima L. Chaar
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kim Nguyen
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Zhe Wang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas H. Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MI 39216, USA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
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2
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Starnawska A, Demontis D. Role of DNA Methylation in Mediating Genetic Risk of Psychiatric Disorders. Front Psychiatry 2021; 12:596821. [PMID: 33868039 PMCID: PMC8049112 DOI: 10.3389/fpsyt.2021.596821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/16/2021] [Indexed: 12/28/2022] Open
Abstract
Psychiatric disorders are common, complex, and heritable conditions estimated to be the leading cause of disability worldwide. The last decade of research in genomics of psychiatry, performed by multinational, and multicenter collaborative efforts on hundreds of thousands of mental disorder cases and controls, provided invaluable insight into the genetic risk variants of these conditions. With increasing cohort sizes, more risk variants are predicted to be identified in the near future, but there appears to be a knowledge gap in understanding how these variants contribute to the pathophysiology of psychiatric disorders. Majority of the identified common risk single-nucleotide polymorphisms (SNPs) are non-coding but are enriched in regulatory regions of the genome. It is therefore of great interest to study the impact of identified psychiatric disorders' risk SNPs on DNA methylation, the best studied epigenetic modification, playing a pivotal role in the regulation of transcriptomic processes, brain development, and functioning. This work outlines the mechanisms through which risk SNPs can impact DNA methylation levels and provides a summary of current evidence on the role of DNA methylation in mediating the genetic risk of psychiatric disorders.
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Affiliation(s)
- Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
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3
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An introduction to EpiPol (Epigenetic affecting Polymorphism) concept with an in silico identification of CpG-affecting SNPs in the upstream regulatory sequences of human AHR gene. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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4
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Wang Y, Mao JM, Wang GD, Luo ZP, Yang L, Yao Q, Chen KP. Human SARS-CoV-2 has evolved to reduce CG dinucleotide in its open reading frames. Sci Rep 2020; 10:12331. [PMID: 32704018 PMCID: PMC7378049 DOI: 10.1038/s41598-020-69342-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
The outbreak of COVID-19 has brought great threat to human health. Its causative agent is a severe acute respiratory syndrome-related coronavirus which has been officially named SARS-CoV-2. Here we report the discovery of extremely low CG abundance in its open reading frames. We found that CG reduction in SARS-CoV-2 is achieved mainly through mutating C/G into A/T, and CG is the best target for mutation. Meanwhile, 5'-untranslated region of SARS-CoV-2 has high CG content and is capable of forming an internal ribosome entry site (IRES) to recruit host ribosome for translating its RNA. These features allow SARS-CoV-2 to reproduce efficiently in host cells, because less energy is consumed in disrupting the stem-loops formed by its genomic RNA. Notably, genomes of cellular organisms also have very low CG abundance, suggesting that mutating C/G into A/T occurs universally in all life forms. Moreover, CG is the dinucleotide related to CpG island, mutational hotspot and single nucleotide polymorphism in cellular organisms. The relationship between these features is worthy of further investigations.
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Affiliation(s)
- Yong Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Jun-Ming Mao
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Guang-Dong Wang
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Zhi-Peng Luo
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Liu Yang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Qin Yao
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Ke-Ping Chen
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
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5
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Identification of novel functional CpG-SNPs associated with type 2 diabetes and coronary artery disease. Mol Genet Genomics 2020; 295:607-619. [PMID: 32162118 DOI: 10.1007/s00438-020-01651-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/03/2020] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D) and coronary artery disease (CAD), respectively. Nevertheless, these studies were generally performed for single-trait/disease and failed to assess the pleiotropic role of the identified variants. To identify novel functional loci and the pleiotropic relationship between CAD and T2D, the targeted cFDR analysis on CpG-SNPs was performed by integrating two independent large and multi-centered GWASs with summary statistics of T2D (26,676 cases and 132,532 controls) and CAD (60,801 cases and 123,504 controls). Applying the cFDR significance threshold of 0.05, we observed a pleiotropic enrichment between T2D and CAD by incorporating pleiotropic effects into a conditional analysis framework. We identified 79 novel CpG-SNPs for T2D, 61 novel CpG-SNPs for CAD, and 18 novel pleiotropic loci for both traits. Among these novel CpG-SNPs, 33 of them were annotated as methylation quantitative trait locus (meQTL) in whole blood, and ten of them showed expression QTL (eQTL), meQTL, and metabolic QTL (metaQTL) effects simultaneously. To the best of our knowledge, we performed the first targeted cFDR analysis on CpG-SNPs, and our findings provided novel insights into the shared biological mechanisms and overlapped genetic heritability between T2D and CAD.
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6
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Qiu C, Shen H, Fu X, Xu C, Deng H. Meta-Analysis of Genome-Wide Association Studies Identifies Novel Functional CpG-SNPs Associated with Bone Mineral Density at Lumbar Spine. Int J Genomics 2018; 2018:6407257. [PMID: 30159320 PMCID: PMC6109501 DOI: 10.1155/2018/6407257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/19/2018] [Indexed: 12/16/2022] Open
Abstract
Osteoporosis is a serious public health issue, which is mostly characterized by low bone mineral density (BMD). To search for additional genetic susceptibility loci underlying BMD variation, an effective strategy is to focus on testing of specific variants with high potential of functional effects. Single nucleotide polymorphisms (SNPs) that introduce or disrupt CpG dinucleotides (CpG-SNPs) may alter DNA methylation levels and thus represent strong candidate functional variants. Here, we performed a targeted GWAS for 63,627 potential functional CpG-SNPs that may affect DNA methylation in bone-related cells, in five independent cohorts (n = 5905). By meta-analysis, 9 CpG-SNPs achieved a genome-wide significance level (p < 7.86 × 10-7) for association with lumbar spine BMD and additional 15 CpG-SNPs showed suggestive significant (p < 5.00 × 10-5) association, of which 2 novel SNPs rs7231498 (NFATC1) and rs7455028 (ESR1) also reached a genome-wide significance level in the joint analysis. Several identified CpG-SNPs were mapped to genes that have not been reported for association with BMD in previous GWAS, such as NEK3 and NFATC1 genes, highlighting the enhanced power of targeted association analysis for identification of novel associations that were missed by traditional GWAS. Interestingly, several genomic regions, such as NEK3 and LRP5 regions, contained multiple significant/suggestive CpG-SNPs for lumbar spine BMD, suggesting that multiple neighboring CpG-SNPs may synergistically mediate the DNA methylation level and gene expression pattern of target genes. Furthermore, functional annotation analyses suggested a strong regulatory potential of the identified BMD-associated CpG-SNPs and a significant enrichment in biological processes associated with protein localization and protein signal transduction. Our results provided novel insights into the genetic basis of BMD variation and highlighted the close connections between genetic and epigenetic mechanisms of complex disease.
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Affiliation(s)
- Chuan Qiu
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Hui Shen
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Xiaoying Fu
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Chao Xu
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
| | - Hongwen Deng
- Department of Global Biostatistics and Data Science, Center for Bioinformatics and Genomics, School of Public Health and Tropical Medicine, New Orleans 70112, USA
- School of Basic Medical Science, Central South University, Changsha 410013, China
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7
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Schwarz E. A gene-based review of RGS4 as a putative risk gene for psychiatric illness. Am J Med Genet B Neuropsychiatr Genet 2018; 177:267-273. [PMID: 28544755 DOI: 10.1002/ajmg.b.32547] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/10/2017] [Indexed: 12/15/2022]
Abstract
Considerable efforts have been made to characterize RGS4 as a potential candidate gene for schizophrenia. Investigations span across numerous modalities and include explorations of genetic risk associations, mRNA and protein levels in the brain, and functionally relevant interactions with other candidate genes as well as links to schizophrenia relevant neural phenotypes. While these lines of investigations have yielded partially inconsistent findings, they provide a perspective on RGS4 as an important part of a larger biological system contributing to schizophrenia risk. This gene-based review aims to provide a comprehensive overview of published data from different experimental modalities and discusses the current knowledge of RGS4's systems-biological impact on the schizophrenia pathology.
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Affiliation(s)
- Emanuel Schwarz
- Medical Faculty Mannheim, Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Heidelberg University, Mannheim, Germany
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8
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Bani-Fatemi A, Howe AS, Matmari M, Koga A, Zai C, Strauss J, De Luca V. Interaction between Methylation and CpG Single-Nucleotide Polymorphisms in the HTR2A Gene: Association Analysis with Suicide Attempt in Schizophrenia. Neuropsychobiology 2016; 73:10-5. [PMID: 26812280 DOI: 10.1159/000441191] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/09/2015] [Indexed: 11/19/2022]
Abstract
Dysfunctional mechanisms in the serotonergic system have been implicated in suicidal behavior among patients with schizophrenia. However, previous association analyses of major serotonin genes have provided inconsistent findings regarding their role in suicidal behavior. The goal of the current study was to identify single-nucleotide polymorphisms (SNP) within HTR2A that directly affect CpG methylation sites in schizophrenic patients with suicidal behavior. Furthermore, direct methylation analysis was performed using genomic DNA from peripheral leukocytes employing bisulfite pyrosequencing to assess the contributions of six CpG sites in HTR2A exon I in 67 schizophrenia patients assessed for lifetime suicide attempt. Potential methylation in 25 CpG SNPs across the entire HTR2A gene was analyzed considering their direct contribution to methylation. When we compared direct methylation between attempters and nonattempters, we found that only the polymorphic T102C (rs6313) was significantly different between the two groups (p = 0.02). Furthermore, in the potential methylation analysis, we found a nominal association with suicide attempt for six of the 25 SNPs analyzed, i.e. rs2770293 (p = 0.045), rs6313 (p = 0.033), rs17068986 (p = 0.029), rs4942578 (p = 0.024), rs1728872 (p = 0.014), and rs9534511 (p = 0.003). The results of this investigation provide preliminary evidence that the combined analysis of CpG SNPs and methylation may be useful for investigating the genetic and epigenetic factors involved in suicidal behavior.
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Affiliation(s)
- Ali Bani-Fatemi
- Group for Suicide Studies, Centre for Addiction and Mental Health, Department of Psychiatry, University of Toronto, Toronto, Ont., Canada
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9
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Chen X, Chen X, Xu Y, Yang W, Wu N, Ye H, Yang JY, Hong Q, Xin Y, Yang MQ, Deng Y, Duan S. Association of six CpG-SNPs in the inflammation-related genes with coronary heart disease. Hum Genomics 2016; 10 Suppl 2:21. [PMID: 27461004 PMCID: PMC4965732 DOI: 10.1186/s40246-016-0067-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Chronic inflammation has been widely considered to be the major risk factor of coronary heart disease (CHD). The goal of our study was to explore the possible association with CHD for inflammation-related single nucleotide polymorphisms (SNPs) involved in cytosine-phosphate-guanine (CpG) dinucleotides. A total of 784 CHD patients and 739 non-CHD controls were recruited from Zhejiang Province, China. Using the Sequenom MassARRAY platform, we measured the genotypes of six inflammation-related CpG-SNPs, including IL1B rs16944, IL1R2 rs2071008, PLA2G7 rs9395208, FAM5C rs12732361, CD40 rs1800686, and CD36 rs2065666). Allele and genotype frequencies were compared between CHD and non-CHD individuals using the CLUMP22 software with 10,000 Monte Carlo simulations. Results Allelic tests showed that PLA2G7 rs9395208 and CD40 rs1800686 were significantly associated with CHD. Moreover, IL1B rs16944, PLA2G7 rs9395208, and CD40 rs1800686 were shown to be associated with CHD under the dominant model. Further gender-based subgroup tests showed that one SNP (CD40 rs1800686) and two SNPs (FAM5C rs12732361 and CD36 rs2065666) were associated with CHD in females and males, respectively. And the age-based subgroup tests indicated that PLA2G7 rs9395208, IL1B rs16944, and CD40 rs1800686 were associated with CHD among individuals younger than 55, younger than 65, and over 65, respectively. Conclusions In conclusion, all the six inflammation-related CpG-SNPs (rs16944, rs2071008, rs12732361, rs2065666, rs9395208, and rs1800686) were associated with CHD in the combined or subgroup tests, suggesting an important role of inflammation in the risk of CHD.
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Affiliation(s)
- Xiaomin Chen
- Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, 315010, China
| | - Xiaoying Chen
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yan Xu
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - William Yang
- Texas Advanced Computing Center, University of Texas at Austin, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Nan Wu
- Cardiovascular Center of Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, 315010, China.,School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huadan Ye
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Jack Y Yang
- MidSouth Bioinformatics Center, Department of Information Science, George Washington Donaghey College of Engineering and Information Science, and Joint Bioinformatics Graduate Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2881 S. University Ave, Little Rock, AR, 72204, USA
| | - Qingxiao Hong
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yanfei Xin
- Center of Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310007, China
| | - Mary Qu Yang
- MidSouth Bioinformatics Center, Department of Information Science, George Washington Donaghey College of Engineering and Information Science, and Joint Bioinformatics Graduate Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2881 S. University Ave, Little Rock, AR, 72204, USA
| | - Youping Deng
- Medical College, Wuhan University of Science and Technology, Wuhan, 430064, China.,Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Shiwei Duan
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China.
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10
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Woodard GE, Jardín I, Berna-Erro A, Salido GM, Rosado JA. Regulators of G-protein-signaling proteins: negative modulators of G-protein-coupled receptor signaling. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 317:97-183. [PMID: 26008785 DOI: 10.1016/bs.ircmb.2015.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Regulators of G-protein-signaling (RGS) proteins are a category of intracellular proteins that have an inhibitory effect on the intracellular signaling produced by G-protein-coupled receptors (GPCRs). RGS along with RGS-like proteins switch on through direct contact G-alpha subunits providing a variety of intracellular functions through intracellular signaling. RGS proteins have a common RGS domain that binds to G alpha. RGS proteins accelerate GTPase and thus enhance guanosine triphosphate hydrolysis through the alpha subunit of heterotrimeric G proteins. As a result, they inactivate the G protein and quickly turn off GPCR signaling thus terminating the resulting downstream signals. Activity and subcellular localization of RGS proteins can be changed through covalent molecular changes to the enzyme, differential gene splicing, and processing of the protein. Other roles of RGS proteins have shown them to not be solely committed to being inhibitors but behave more as modulators and integrators of signaling. RGS proteins modulate the duration and kinetics of slow calcium oscillations and rapid phototransduction and ion signaling events. In other cases, RGS proteins integrate G proteins with signaling pathways linked to such diverse cellular responses as cell growth and differentiation, cell motility, and intracellular trafficking. Human and animal studies have revealed that RGS proteins play a vital role in physiology and can be ideal targets for diseases such as those related to addiction where receptor signaling seems continuously switched on.
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Affiliation(s)
- Geoffrey E Woodard
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Isaac Jardín
- Department of Physiology, University of Extremadura, Caceres, Spain
| | - A Berna-Erro
- Department of Physiology, University of Extremadura, Caceres, Spain
| | - Gines M Salido
- Department of Physiology, University of Extremadura, Caceres, Spain
| | - Juan A Rosado
- Department of Physiology, University of Extremadura, Caceres, Spain
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11
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Sokolowski M, Wasserman J, Wasserman D. An overview of the neurobiology of suicidal behaviors as one meta-system. Mol Psychiatry 2015; 20:56-71. [PMID: 25178164 DOI: 10.1038/mp.2014.101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/19/2014] [Accepted: 07/22/2014] [Indexed: 12/12/2022]
Abstract
Suicidal behaviors (SB) may be regarded as the outmost consequence of mental illnesses, or as a distinct entity per se. Regardless, the consequences of SB are very large to both society and affected individuals. The path leading to SB is clearly a complex one involving interactions between the subject's biology and environmental influences throughout life. With the aim to generate a representative and diversified overview of the different neurobiological components hypothesized or shown implicated across the entire SB field up to date by any approach, we selected and compiled a list of 212 gene symbols from the literature. An increasing number of novel gene (products) have been introduced as candidates, with half being implicated in SB in only the last 4 years. These candidates represent different neuro systems and functions and might therefore be regarded as competing or redundant explanations. We then adopted a unifying approach by treating them all as parts of the same meta-system, using bioinformatic tools. We present a network of all components connected by physical protein-protein interactions (the SB interactome). We proceeded by exploring the differences between the highly connected core (~30% of the candidate genes) and its peripheral parts, observing more functional homogeneity at the core, with multiple signal transduction pathways and actin-interacting proteins connecting a subset of receptors in nerve cell compartments as well as development/morphology phenotypes and the stress-sensitive synaptic plasticity processes of long term potentiation/depression. We suggest that SB neurobiology might also be viewed as one meta-system and perhaps be explained as intrinsic unbalances acting within the core or as imbalances arising between core and specific peripheral components.
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Affiliation(s)
- M Sokolowski
- National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm, Sweden
| | - J Wasserman
- National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm, Sweden
| | - D Wasserman
- 1] National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm, Sweden [2] WHO Collaborating Centre for Research, Methods Development and Training in Suicide Prevention, Stockholm, Sweden
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12
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Mansego ML, Milagro FI, Zulet MA, Martinez JA. SH2B1 CpG-SNP is associated with body weight reduction in obese subjects following a dietary restriction program. ANNALS OF NUTRITION AND METABOLISM 2014; 66:1-9. [PMID: 25471250 DOI: 10.1159/000368425] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 09/15/2014] [Indexed: 11/19/2022]
Abstract
UNLABELLED The objective of this study was to examine whether 7 SNPs previously associated with obesity-related traits that add or remove potential sites of DNA methylation are accompanied by differential DNA methylation and subsequently affect adiposity variables or body weight reduction in WBC from obese subjects under an energy-restricted program. MATERIAL AND METHODS Anthropometric measurements were assessed in 47 volunteers recruited within the RESMENA study (Spain). At baseline, DNA from white blood cells was isolated and 7 obesity-related trait CpG-SNPs were genotyped by TaqMan-PCR. Then, methylation levels of CpG-SNP sites were quantified by MassArray® EpiTyper™ or MS-HRM approaches. RESULTS Differential DNA methylation levels were observed by genotypes in all of the CpG-SNPs analyzed. The FTO and BDNF methylation levels were further correlated with baseline body weight and, BDNF mRNA levels and body weight change, respectively. Moreover, the rs7359397 (SH2B1) was associated with the body weight, body mass index, and truncal fat mass reduction. CONCLUSIONS Our results reveal the interaction of epigenetic and genetic variations in CpG-SNPs, especially in BDNF and SH2B1 genes, and how allele-specific methylation may contribute to elucidate the possible molecular mechanisms as these SNPs are affecting the decrease of mRNA levels and contributing to a lower body weight reduction.
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Affiliation(s)
- Maria Luisa Mansego
- CIBERobn, Physiopathology of Obesity and Nutrition, Institute of Health Carlos III, Madrid, Spain
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13
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Guintivano J, Brown T, Newcomer A, Jones M, Cox O, Maher BS, Eaton WW, Payne JL, Wilcox HC, Kaminsky ZA. Identification and replication of a combined epigenetic and genetic biomarker predicting suicide and suicidal behaviors. Am J Psychiatry 2014; 171:1287-96. [PMID: 25073599 PMCID: PMC7081376 DOI: 10.1176/appi.ajp.2014.14010008] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Considerable research suggests that suicide involves effects of genes, the environment, and their interaction. Analysis of three independent data sets of post-mortem brains revealed signs of increased methylation in one particular gene, SKA2, a finding that was extended to peripheral blood samples from other cohorts of prospectively followed individuals.
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Affiliation(s)
- Jerry Guintivano
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287
| | - Tori Brown
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287
| | - Alison Newcomer
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287
| | - Marcus Jones
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287
| | - Olivia Cox
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA, 21287
| | - William W. Eaton
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA, 21287
| | - Jennifer L. Payne
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287
| | - Holly C. Wilcox
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA, 21287
| | - Zachary A. Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, 21287,Correspondence to: Zachary Kaminsky, The Mood Disorder Center, Johns Hopkins University, 720 Rutland Avenue, Ross Research Building 1070, Baltimore. MD, 21205, Ph: 443-287-0093,
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