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Jin YY, Liang YP, Wei ZY, Sui WJ, Chen JH. Hippocampal adenosine-to-inosine RNA editing in sepsis: dynamic changes and influencing factors. Brain Commun 2024; 6:fcae260. [PMID: 39135964 PMCID: PMC11317967 DOI: 10.1093/braincomms/fcae260] [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: 12/10/2023] [Revised: 06/05/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Sepsis-associated encephalopathy is a diffuse brain dysfunction secondary to infection. It has been established that factors such as age and sex can significantly contribute to the development of sepsis-associated encephalopathy. Our recent study implicated a possible link between adenosine-to-inosine RNA editing and sepsis-associated encephalopathy, yet the dynamics of adenosine-to-inosine RNA editing during sepsis-associated encephalopathy and how it could be influenced by factors such as age, sex and antidepressants remain uninvestigated. Our current study analysed and validated transcriptome-wide changes in adenosine-to-inosine RNA editing in the hippocampus of different septic mouse models. Seventy-four sites in 64 genes showed significant differential RNA editing over time in septic mice induced by caecal ligation and perforation. The differential RNA editing might contribute to the RNA expression regulation of the edited genes, with 42.2% differentially expressed. These differentially edited genes, especially those with missense editing, such as glutamate receptor, ionotropic, kainate 2 (Grik2, p.M620V), filamin A (Flna, p.S2331G) and capicua transcriptional repressor (Cic, p.E2270G), were mainly involved in abnormal social behaviour and neurodevelopmental and psychiatric disorders. Significant effects of age and sex were also observed on sepsis-associated RNA editing. Further comparison highlighted 40 common differential RNA editing sites that caecal ligation and perforation-induced and lipopolysaccharide-induced septic mouse models shared. Interestingly, these findings demonstrate temporal dynamics of adenosine-to-inosine RNA editing in the mouse hippocampus during sepsis, add to the understanding of age and sex differences in the disease and underscore the role of the epigenetic process in sepsis-associated encephalopathy.
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Affiliation(s)
- Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Jiangnan University Brain Institute, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ya-Ping Liang
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Jiangnan University Brain Institute, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhi-Yuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Jiangnan University Brain Institute, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei-Jia Sui
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Jiangnan University Brain Institute, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Jiangnan University Brain Institute, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
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Toli EA, Kemppainen P, Bounas A, Sotiropoulos K. Genetic insight into a polygenic trait using a novel genome-wide association approach in a wild amphibian population. Mol Ecol 2024; 33:e17344. [PMID: 38597332 DOI: 10.1111/mec.17344] [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: 06/21/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Body size variation is central in the evolution of life-history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness-related traits in small data sets from natural populations in non-model species.
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Affiliation(s)
- Elisavet-Aspasia Toli
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
| | - Petri Kemppainen
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong City, Hong Kong SAR
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, Helsinki, Finland
| | - Anastasios Bounas
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
| | - Konstantinos Sotiropoulos
- Molecular Ecology & Conservation Genetics Lab, Department of Biological Applications & Technology, University of Ioannina, Ioannina, Greece
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Imrie G, Gray MB, Raghuraman V, Farhy-Tselnicker I. Gene Expression at the Tripartite Synapse: Bridging the Gap Between Neurons and Astrocytes. ADVANCES IN NEUROBIOLOGY 2024; 39:95-136. [PMID: 39190073 DOI: 10.1007/978-3-031-64839-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Astrocytes, a major class of glial cells, are an important element at the synapse where they engage in bidirectional crosstalk with neurons to regulate numerous aspects of neurotransmission, circuit function, and behavior. Mutations in synapse-related genes expressed in both neurons and astrocytes are central factors in a vast number of neurological disorders, making the proteins that they encode prominent targets for therapeutic intervention. Yet, while the roles of many of these synaptic proteins in neurons are well established, the functions of the same proteins in astrocytes are largely unknown. This gap in knowledge must be addressed to refine therapeutic approaches. In this chapter, we integrate multiomic meta-analysis and a comprehensive overview of current literature to show that astrocytes express an astounding number of genes that overlap with the neuronal and synaptic transcriptomes. Further, we highlight recent reports that characterize the expression patterns and potential novel roles of these genes in astrocytes in both physiological and pathological conditions, underscoring the importance of considering both cell types when investigating the function and regulation of synaptic proteins.
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Affiliation(s)
- Gillian Imrie
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Madison B Gray
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Vishnuvasan Raghuraman
- Department of Biology, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Isabella Farhy-Tselnicker
- Department of Biology, Texas A&M University, College Station, TX, USA.
- Texas A&M Institute for Neuroscience (TAMIN), Texas A&M University, College Station, TX, USA.
- Center for Biological Clocks Research, Texas A&M University, College Station, TX, USA.
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Chen J, Hui Q, Wang Z, Wilson FP, So-Armah K, Freiberg MS, Justice AC, Xu K, Zhao W, Ammous F, Smith JA, Kardia SL, Gwinn M, Marconi VC, Sun YV. Epigenome-Wide Meta-Analysis Reveals Differential DNA Methylation Associated With Estimated Glomerular Filtration Rate Among African American Men With HIV. Kidney Int Rep 2023; 8:1076-1086. [PMID: 37180517 PMCID: PMC10166785 DOI: 10.1016/j.ekir.2023.02.1085] [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: 11/26/2022] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction People with HIV (PWH) of African ancestry have faster decline of kidney function and faster progression to end-stage renal disease than PWH of European ancestry. DNA methylation have been associated with kidney function in the general population, however, their relationships are unclear for PWH of African ancestry. Methods We performed epigenome-wide association studies (EWAS) of estimated glomerular filtration rate (eGFR) among PWH of African ancestry in 2 subsets of the Veterans Aging Cohort Study cohort (N = 885), followed by a meta-analysis to combine the results. Replication was conducted among independent African American samples without HIV. Results DNA methylation sites cg17944885 near Zinc Finger Family Member 788 (ZNF788) and Zinc Finger Protein 20 (ZNF20), and cg06930757 in SHANK1 were significantly associated with eGFR among PWH of African ancestry (false discovery rate < 0.05). DNA methylation site cg17944885 was also associated with eGFR among different populations including African Americans without HIV. Conclusions Our study attempted to address an important gap in the literature and to understand the role of DNA methylation in renal diseases in PWH of African ancestry. Replication of cg17944885 among different populations suggests there may be a common pathway for renal diseases progression among PWH and people without HIV, and across different ancestral groups. Our results suggest that genes ZNF788/ZNF20 and SHANK1 could be involved in a pathway linking DNA methylation to renal diseases among PWH and are worth further investigation.
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Affiliation(s)
- Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Qin Hui
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Zeyuan Wang
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Francis P. Wilson
- Department of Medicine, Yale University School of Medicine, Connecticut, USA
| | - Kaku So-Armah
- Boston University School of Medicine, Massachusetts, USA
| | - Matthew S. Freiberg
- Cardiovascular Medicine Division, Vanderbilt University School of Medicine and Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Amy C. Justice
- Connecticut Veteran Health System, West Haven, Connecticut, USA
- Schools of Medicine and Public Health, Yale University, New Haven, Connecticut, USA
| | - Ke Xu
- Connecticut Veteran Health System, West Haven, Connecticut, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Marta Gwinn
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Vincent C. Marconi
- Hubert Department of Global Health, Rollins School of Public Health, Atlanta, Georgia, USA
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
- Atlanta Veterans Affairs Health Care System, Decatur, Georgia, USA
| | - Yan V. Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Atlanta Veterans Affairs Health Care System, Decatur, Georgia, USA
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Perini S, Filosi M, Domenici E. Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs. Transl Psychiatry 2023; 13:109. [PMID: 37012247 PMCID: PMC10070641 DOI: 10.1038/s41398-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
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Affiliation(s)
- Samuel Perini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
- EURAC Research, Bolzano, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy.
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.
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Genome-wide tandem repeat expansions contribute to schizophrenia risk. Mol Psychiatry 2022; 27:3692-3698. [PMID: 35546631 PMCID: PMC9708556 DOI: 10.1038/s41380-022-01575-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 02/08/2023]
Abstract
Tandem repeat expansions (TREs) can cause neurological diseases but their impact in schizophrenia is unclear. Here we analyzed genome sequences of adults with schizophrenia and found that they have a higher burden of TREs that are near exons and rare in the general population, compared with non-psychiatric controls. These TREs are disproportionately found at loci known to be associated with schizophrenia from genome-wide association studies, in individuals with clinically-relevant genetic variants at other schizophrenia loci, and in families where multiple individuals have schizophrenia. We showed that rare TREs in schizophrenia may impact synaptic functions by disrupting the splicing process of their associated genes in a loss-of-function manner. Our findings support the involvement of genome-wide rare TREs in the polygenic nature of schizophrenia.
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Paprocka J, Ziętkiewicz S, Kosińska J, Kaczorowska E, Płoski R. Case Report: Lennox-Gastaut Epileptic Encephalopathy Responsive to Cannabidiol Treatment Associated With a Novel de novo Mosaic SHANK1 Variant. Front Genet 2021; 12:735292. [PMID: 34912368 PMCID: PMC8667173 DOI: 10.3389/fgene.2021.735292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
The SH3 and multiple ankyrin repeat domains (SHANKs) are a family of scaffolding proteins located in excitatory synapses required for their development and function. Molecular defects of SHANK3 are a well-known cause of several neurodevelopmental entities, in particular autism spectrum disorders and epilepsy, whereas relatively little is known about disease associations of SHANK1. Here, we propose a novel de novo mosaic p.(Gly126Arg) SHANK1 variant as the monogenic cause of disease in a patient who presented, from the age of 2 years, moderate intellectual disability, autism, and refractory epilepsy of the Lennox–Gastaut type. The epilepsy responded remarkably well to cannabidiol add-on therapy. In silico analyses including homology modeling and molecular dynamics simulations indicated the deleterious effect of SHANK1 p.(Gly126Arg) on the protein structure and the related function associated with protein–protein interactions. In particular, the variant was predicted to disrupt a hitherto unknown conserved region of SHANK1 protein with high homology to a recently recognized functionally relevant domain in SHANK3 implicated in ligand binding, including the “non-canonical” binding of Rap1.
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Affiliation(s)
- Justyna Paprocka
- Department of Pediatric Neurologsluy, Faculty of Medical Science in Katowice, Medical University of Silesia, Katowice, Poland
| | - Szymon Ziętkiewicz
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Intercollegiate Faculty of Biotechnology, University of Gdansk, Gdańsk, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Kaczorowska
- Department of Biology and Medical Genetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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