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Huang K, Fan X, Jiang Y, Jin S, Huang J, Pang L, Wang Y, Wu Y, Sun X. Integrative identification of hub genes in development of atrial fibrillation related stroke. PLoS One 2023; 18:e0283617. [PMID: 36952494 PMCID: PMC10035830 DOI: 10.1371/journal.pone.0283617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND As the most common arrhythmia, atrial fibrillation (AF) is associated with a significantly increased risk of stroke, which causes high disability and mortality. To date, the underlying mechanism of stroke occurring after AF remains unclear. Herein, we studied hub genes and regulatory pathways involved in AF and secondary stroke and aimed to reveal biomarkers and therapeutic targets of AF-related stroke. METHODS The GSE79768 and GSE58294 datasets were used to analyze AF- and stroke-related differentially expressed genes (DEGs) to obtain a DEG1 dataset. Weighted correlation network analysis (WGCNA) was used to identify modules associated with AF-related stroke in GSE66724 (DEG2). DEG1 and DEG2 were merged, and hub genes were identified based on protein-protein interaction networks. Gene Ontology terms were used to analyze the enriched pathways. The GSE129409 and GSE70887 were applied to construct a circRNA-miRNA-mRNA network in AF-related stroke. Hub genes were verified in patients using quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS We identified 3,132 DEGs in blood samples and 253 DEGs in left atrial specimens. Co-expressed hub genes of EIF4E3, ZNF595, ZNF700, MATR3, ACKR4, ANXA3, SEPSECS-AS1, and RNF166 were significantly associated with AF-related stroke. The hsa_circ_0018657/hsa-miR-198/EIF4E3 pathway was explored as the regulating axis in AF-related stroke. The qRT-PCR results were consistent with the bioinformatic analysis. CONCLUSIONS Hub genes EIF4E3, ZNF595, ZNF700, MATR3, ACKR4, ANXA3, SEPSECS-AS1, and RNF166 have potential as novel biomarkers and therapeutic targets in AF-related stroke. The hsa_circ_0018657/hsa-miR-198/EIF4E3 axis could play an important role regulating the development of AF-related stroke.
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Affiliation(s)
- Kai Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Xi Fan
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yuwen Jiang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Sheng Jin
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Jiechun Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Liewen Pang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yiqing Wang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yuming Wu
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Xiaotian Sun
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, Shanghai, China
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Henneman P, Mul AN, Li Yim AY, Krzyzewska IM, Alders M, Adelia A, Mizee MR, Mannens MM. Prenatal NeuN+ neurons of Down syndrome display aberrant integrative DNA methylation and gene expression profiles. Epigenomics 2022; 14:375-390. [PMID: 35232286 DOI: 10.2217/epi-2021-0523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To detect expression quantitative trait methylation (eQTM) loci within the cerebrum of prenatal Down syndrome (DS) and controls. Material & methods: DNA methylation gene expression profiles were acquired from NeuN+ nuclei, obtained from cerebrum sections of DS and controls. Linear regression models were applied to both datasets and were subsequently applied in an integrative analysis model to detect DS-associated eQTM loci. Results & conclusion: Widespread aberrant DNA methylation and gene expression were observed in DS. A substantial number of differentially methylated loci were replicated according to a previously reported study. Subsequent integrative analyses (eQTM) yielded numerous associated DS loci. the authors associated DNA methylation, gene expression and eQTM loci with DS that may underlie particular DS phenotypical characteristics.
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Affiliation(s)
- Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Adri N Mul
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Andrew Yf Li Yim
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Izabela M Krzyzewska
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Adelia Adelia
- Neuroimmunology Research Group & Netherlands Brain Bank, Netherlands Institute for Neuroscience, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Mark R Mizee
- Neuroimmunology Research Group & Netherlands Brain Bank, Netherlands Institute for Neuroscience, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
| | - Marcel M Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, Amsterdam, AZ, 1105, The Netherlands
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Yi X, Li M, He G, Du H, Li X, Cao D, Wang L, Wu X, Yang F, Chen X, He L, Ping Y, Zhou D. Genetic and functional analysis reveals TENM4 contributes to schizophrenia. iScience 2021; 24:103063. [PMID: 34568788 PMCID: PMC8449235 DOI: 10.1016/j.isci.2021.103063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/23/2021] [Accepted: 08/26/2021] [Indexed: 12/09/2022] Open
Abstract
TENM4, encoding a member of the teneurin protein family, is a risk gene shared by many types of mental diseases and is implicated in neuronal plasticity and signaling. However, the role and the mechanisms of TENM4 in schizophrenia (SCZ) remain unclear. We identified possible pathogenic mutations in the TENM4 gene through target sequencing of TENM4 in 68 SCZ families. We further demonstrated that aberrant expression of Ten-m leads to lower learning ability, sleep reduction, and increased aggressiveness in animal models. RNA sequencing showed that aberrant expression of Ten-m was related to stimulus perception and metabolic process, and Gene Ontology enrichment terms were neurogenesis and ATPase activity. This study provides strong evidence that TENM4 contributes to SCZ, and its functional mutations might be responsible for the impaired neural circuits and behaviors observed in SCZ. Possible pathogenic rare missense mutations in TENM4 gene contribute to SCZ Aberrant expression of Ten-m leads to behavioral disturbances related to SCZ symptoms Ten-m affects stimulation, metabolic process, neurogenesis, and ATPase activity
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Affiliation(s)
- Xin Yi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
| | - Minzhe Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huihui Du
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongmei Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
| | - Lu Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
| | - Fengping Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
| | - Xu Chen
- Department of Neurology, Shanghai Eighth People's Hospital, Shanghai Sixth People's Hospital Xuhui Branch, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong Ping
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Daizhan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Rd., Shanghai 200030, PR China
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