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Wagner AH, Klersy A, Sultan CS, Hecker M. Potential role of soluble CD40 receptor in chronic inflammatory diseases. Biochem Pharmacol 2023; 217:115858. [PMID: 37863325 DOI: 10.1016/j.bcp.2023.115858] [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: 08/07/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
The CD40 receptor and its ligand CD154 are widely expressed in various immune-competent cells. Interaction of CD154 with CD40 is essential for B-cell growth, differentiation, and immunoglobulin class switching. Many other immune-competent cells involved in innate and adaptive immunity communicate through this co-stimulatory ligand-receptor dyad. CD40-CD154 interaction is involved in the pathogenesis of numerous inflammatory and autoimmune diseases. While CD40 and CD154 are membrane-bound proteins, their soluble counterparts are generated by proteolytic cleavage or alternative splicing. This review summarises current knowledge about the impact of single nucleotide polymorphisms in the human CD40 gene and compensatory changes in the plasma level of the soluble CD40 receptor (sCD40) isoform in related pro-inflammatory diseases. It discusses regulation patterns of the disintegrin metalloprotease ADAM17 function leading to ectodomain shedding of transmembrane proteins, such as pro-inflammatory adhesion molecules or CD40. The role of sCD40 as a potential biomarker for chronic inflammatory diseases will also be discussed.
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Affiliation(s)
- A H Wagner
- Department of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany.
| | - A Klersy
- Department of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany
| | - C S Sultan
- Department of Medical Chemistry, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Hecker
- Department of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany
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Fu Y, Xu L, Zhang H, Ding N, Zhang J, Ma S, Yang A, Hao Y, Gao Y, Jiang Y. Identification and Validation of Immune-Related Genes Diagnostic for Progression of Atherosclerosis and Diabetes. J Inflamm Res 2023; 16:505-521. [PMID: 36798871 PMCID: PMC9926990 DOI: 10.2147/jir.s393788] [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: 10/20/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
Background Atherosclerosis and type 2 diabetes mellitus contribute to a large part of cardiovascular events, but the underlying mechanism remains unclear. In this study, we focused on identifying the linking genes of the diagnostic biomarkers and effective therapeutic targets associated with these two diseases. Methods The transcriptomic datasets of atherosclerosis and type 2 diabetes mellitus were obtained from the GEO database. Differentially expressed genes analysis was performed by R studio software, and differential analysis including functional enrichment, therapeutic small molecular agents prediction, and protein-protein interaction analysis were applied to the common shared differentially expressed genes. Hub genes were identified and further validated using an independent dataset and clinical samples. Furthermore, we measured the expression correlations, immune cell infiltration, and diagnostic capability of the three key genes. Results We screened out 28 up-regulated and six down-regulated common shared differentially expressed genes. Functional enrichment analysis showed that cytokines and immune activation were involved in the development of these two diseases. Six small molecules with the highest absolute enrichment value were identified. Three critical genes (CD4, PLEK, and THY1) were further validated both in validation sets and clinical samples. The gene correlation analysis showed that CD4 was strongly positively correlated with PLEK, and ROC curves confirmed the good discriminatory capacity of CD4 and PLEK in two diseases. We have established the co-expression network between atherosclerosis lesions progressions and type 2 diabetes mellitus, and identified CD4 and PLEK as key genes in the two diseases, which may facilitate both development of diagnosis and therapeutic strategies.
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Affiliation(s)
- Yajuan Fu
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Lingbo Xu
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Hui Zhang
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Ning Ding
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Juan Zhang
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Shengchao Ma
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Anning Yang
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Yinjv Hao
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Yujing Gao
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Correspondence: Yujing Gao; Yideng Jiang, Email ;
| | - Yideng Jiang
- National Health Commission Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University, Yinchuan, People’s Republic of China,Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan, People’s Republic of China,School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, People’s Republic of China
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Yoon E, Zhang W, Cai Y, Peng C, Zhou D. Identification and Validation of Key Gene Modules and Pathways in Coronary Artery Disease Development and Progression. Crit Rev Eukaryot Gene Expr 2023; 33:81-90. [PMID: 37602455 DOI: 10.1615/critreveukaryotgeneexpr.2023039631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
The development and progression of atherosclerosis represent a chronic process involving complex molecular interactions. Therefore, identifying the potential hub genes and pathways contributing to coronary artery disease (CAD) development is essential for understanding its underlying molecular mechanisms. To this end, we performed transcriptome analysis of peripheral venous blood collected from 100 patients who were divided into four groups according to disease severity, including 27 patients in the atherosclerosis group, 22 patients in the stable angina group, 35 patients in the acute myocardial infarction group, and 16 controls. Weighted gene co-expression network analysis was performed using R programming. Significant module-trait correlations were identified according to module membership and genetic significance. Metascape was used for the functional enrichment of differentially expressed genes between groups, and the hub genes were identified via protein-protein interaction network analysis. The hub genes were further validated by analyzing Gene Expression Omnibus (GSE48060 and GSE141512) datasets. A total of 9,633 messenger ribonucleic acids were detected in three modules, among which the blue module was highly correlated with the Gensini score. The hub genes were significantly enriched in the myeloid leukocyte activation pathway, suggesting its important role in the progression of atherosclerosis. Among these genes, the Mediterranean fever gene (MEFV) may play a key role in the progression of atherosclerosis and CAD severity.
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Affiliation(s)
- Ewnji Yoon
- Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Guangdong, 518057, PR China; Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, PR China
| | - Wenjing Zhang
- Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Guangdong, 518057, PR China
| | - Yunpeng Cai
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, PR China
| | - Changnong Peng
- Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, Guangdong, 518057, PR China
| | - Daxin Zhou
- Department of Cardiology, Shanghai Institute of Cardiovascular Disease, Zhongshan Hospital, Fudan University, Shanghai, China
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Kumar S, Shih CM, Tsai LW, Dubey R, Gupta D, Chakraborty T, Sharma N, Singh AV, Swarup V, Singh HN. Transcriptomic Profiling Unravels Novel Deregulated Gene Signatures Associated with Acute Myocardial Infarction: A Bioinformatics Approach. Genes (Basel) 2022; 13:genes13122321. [PMID: 36553589 PMCID: PMC9777571 DOI: 10.3390/genes13122321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Acute myocardial infarction (AMI) is a severe disease with elevated morbidity and mortality rate worldwide. This is attributed to great losses of cardiomyocytes, which can trigger the alteration of gene expression patterns. Although several attempts have been made to assess the AMI biomarkers, to date their role in rescuing myocardial injury remains unclear. Therefore, the current study investigated three independent microarray-based gene expression datasets from AMI patients (n = 85) and their age-sex-matched healthy controls (n = 70), to identify novel gene signatures that might be involved in cardioprotection. The differentially expressed genes (DEGs) were analyzed using 'GEO2R', and weighted gene correlation network analysis (WGCNA) was performed to identify biomarkers/modules. We found 91 DEGs, of which the number of upregulated and downregulated genes were 22 and 5, respectively. Specifically, we found that the deregulated genes such as ADOR-A3, BMP6, VPS8, and GPx3, may be associated with AMI. WGCNA revealed four highly preserved modules among all datasets. The 'Enrichr' unveiled the presence of miR-660 and STAT1, which is known to affect AMI severity. Conclusively, these genes and miRNA might play a crucial role the rescue of cardiomyocytes from severe damage, which could be helpful in developing appropriate therapeutic strategies for the management of AMI.
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Affiliation(s)
- Sanjay Kumar
- Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park-III, Greater Noida 201310, India
| | - Chun-Ming Shih
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 111031, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 111031, Taiwan
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei 111031, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei 11031, Taiwan
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 111031, Taiwan
| | - Deepika Gupta
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tanmoy Chakraborty
- Department of Chemistry and Biochemistry, Sharda School of Basic Sciences and Research, Sharda University, Knowledge Park-III, Greater Noida 201310, India
| | - Naveen Sharma
- Biomedical Informatics Division, Indian Council of Medical Research, New Delhi 110029, India
| | | | - Vishnu Swarup
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India
- Correspondence: (V.S.); or (H.N.S.)
| | - Himanshu Narayan Singh
- Department of System Biology, University of Columbia Irving Medical Center, New York, NY 10032, USA
- Correspondence: (V.S.); or (H.N.S.)
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Relationship between the Soluble F11 Receptor and Annexin A5 in African Americans Patients with Type-2 Diabetes Mellitus. Biomedicines 2022; 10:biomedicines10081818. [PMID: 36009365 PMCID: PMC9405000 DOI: 10.3390/biomedicines10081818] [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: 04/25/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by endothelial dysfunction, increased thrombogenicity, and inflammation. The soluble human F11 receptor (sF11R) and annexin A5 (ANXA5) play crucial roles in inflammatory thrombosis and atherosclerosis. We examined the relationship between circulating sF11R and ANXA5 and their impact on endothelial function. The study included 125 patients with T2DM. Plasma levels of sF11R and ANXA5 were quantified by ELISA. Microvascular function was assessed using the vascular reactivity index (VRI). Large artery stiffness was assessed by carotid-femoral pulse wave velocity (PWV). Carotid intima-media thickness (CIMT) was assessed by B-mode ultrasound imaging. The mean age of patients in the study was 59.7 ± 7.8 years, 78% had hypertension, 76% had dyslipidemia, and 12% had CKD. sF11R correlated positively with ANXA5 levels (β = 0.250, p = 0.005), and correlated inversely with VRI and total nitic oxide (NO), (β = −0.201, p = 0.024; β = −0.357, p = 0.0001, respectively). Multivariate regression analysis revealed that sF11R was independently associated with ANXA5 in the total population and in patients with HbA1c > 6.5% (β = 0.366, p = 0.007; β = 0.425, p = 0.0001, respectively). sF11R and ANXA5 were not associated with vascular outcome, suggesting that they may not be reliable markers of vascular dysfunction in diabetes. The clinical significance of sF11R/ANXA5 association in diabetes warrants further investigation in a larger population.
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Zhu X, Liu Y, Cui J, Lv J, Li C, Lu J, Huo X, Dou J, Bai Z, Chen Z, Du X. LncRNA LYPLAL1-DT screening from type 2 diabetes with macrovascular complication contributes protective effects on human umbilical vein endothelial cells via regulating the miR-204-5p/SIRT1 axis. Cell Death Dis 2022; 8:245. [PMID: 35508613 PMCID: PMC9068612 DOI: 10.1038/s41420-022-01019-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 12/18/2022]
Abstract
Long noncoding RNAs (lncRNAs) are involved in diabetes related diseases. However, the role of lncRNAs in the pathogenesis of type 2 diabetes with macrovascular complication (DMC) has seldomly been recognized. This study screened lncRNA profiles of leukocytes from DMC patients and explored protective role of lncRNA LYPLAL1-DT in endothelial cells (EC) under high glucose (HG) and inflammatory conditions (IS). Between DMC and healthy controls, 477 differential expression lncRNAs (DE-lncRNAs) were identified. The enrichment and pathway analysis showed that most of the DE-lncRNAs belonged to inflammatory, metabolic, and vascular diseases. A total of 12 lncRNAs was validated as significant DE-lncRNAs in expanding cohorts. Furthermore, these DE-lncRNAs were shown to be significantly related to hypoxia, HG, and IS in EC, especially lncRNA LYPLAL1-DT. LYPLAL1-DT overexpression results in the promotion of the proliferation, and migration of EC, as well as an elevation of autophagy. Overexpressed LYPLAL1-DT reduces the adhesion of monocytes to EC, boosts anti-inflammation, and suppresses inflammatory molecules secreted in the medium. Mechanistically, LYPLAL1-DT acts as competing endogenous RNA (ceRNA) by downregulating miR-204-5p, therefore enhancing SIRT1 and protecting EC autophagy function; thus, alleviating apoptosis. Finally, exosome sequencing revealed LYPLAL1-DT expression was 4 times lower in DMC cells than in healthy samples. In general, we identified LYPLAL1-DT having protective effects on EC as ceRNA mediated through the miR-204-5p/SIRT1 pathway. Therefore, it inhibits the autophagy of EC as well as modulating systemic inflammation. This approach could be regarded as a new potential therapeutic target in DMC.
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Affiliation(s)
- Xiao Zhu
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Yihan Liu
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China.,Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jia Cui
- Department of Endocrinology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jianyi Lv
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Changlong Li
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Jing Lu
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Xueyun Huo
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Jingtao Dou
- Department of Endocrinology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Zhigang Bai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Zhenwen Chen
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Xiaoyan Du
- Department of medical genetics and biological development, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China.
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Dang R, Qu B, Guo K, Zhou S, Sun H, Wang W, Han J, Feng K, Lin J, Hu Y. Weighted Co-Expression Network Analysis Identifies RNF181 as a Causal Gene of Coronary Artery Disease. Front Genet 2022; 12:818813. [PMID: 35222523 PMCID: PMC8867041 DOI: 10.3389/fgene.2021.818813] [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: 11/20/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Coronary artery disease (CAD) exerts a global challenge to public health. Genetic heritability is one of the most vital contributing factors in the pathophysiology of CAD. Co-expression network analysis is an applicable and robust method for the interpretation of biological interaction from microarray data. Previous CAD studies have focused on peripheral blood samples since the processes of CAD may vary from tissue to blood. It is therefore necessary to find biomarkers for CAD in heart tissues; their association also requires further illustration. Materials and Methods: To filter for causal genes, an analysis of microarray expression profiles, GSE12504 and GSE22253, was performed with weighted gene co-expression network analysis (WGCNA). Co-expression modules were constructed after batch effect removal and data normalization. The results showed that 7 co-expression modules with 8,525 genes and 1,210 differentially expressed genes (DEGs) were identified. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Four major pathways in CAD tissue and hub genes were addressed in the Hybrid Mouse Diversity Panel (HMDP) and Human Protein Atlas (HPA), and isoproterenol (ISO)/doxycycline (DOX)-induced heart toxicity models were used to validate the hub genes. Lastly, the hub genes and risk variants were verified in the CAD cohort and in genome-wide association studies (GWAS). Results: The results showed that RNF181 and eight other hub genes are perturbed during CAD in heart tissues. Additionally, the expression of RNF181 was validated using RT-PCR and immunohistochemistry (IHC) staining in two cardiotoxicity mouse models. The association was further verified in the CAD patient cohort and in GWAS. Conclusion: Our findings illustrated for the first time that the E3 ubiquitination ligase protein RNF181 may serve as a potential biomarker in CAD, but further in vivo validation is warranted.
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Affiliation(s)
- Ruoyu Dang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Bojian Qu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Pharmaceutical Intelligence Platform, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Kaimin Guo
- GeneNet Pharmaceuticals Co. Ltd., Tianjin, China
| | - Shuiping Zhou
- The State Key Laboratory of Core Technology in Innovative Chinese Medicine, Tasly Academy, Tasly Holding Group Co., Ltd, Tianjin, China
| | - He Sun
- GeneNet Pharmaceuticals Co. Ltd., Tianjin, China
| | - Wenjia Wang
- GeneNet Pharmaceuticals Co. Ltd., Tianjin, China
| | - Jihong Han
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education, Nankai University, Tianjin, China
| | - Ke Feng
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education, Nankai University, Tianjin, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Pharmaceutical Intelligence Platform, Tianjin International Joint Academy of Biomedicine, Tianjin, China
- *Correspondence: Jianping Lin, ; Yunhui Hu,
| | - Yunhui Hu
- GeneNet Pharmaceuticals Co. Ltd., Tianjin, China
- *Correspondence: Jianping Lin, ; Yunhui Hu,
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Clark KC, Kwitek AE. Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome. Compr Physiol 2021; 12:3045-3084. [PMID: 34964118 PMCID: PMC9373910 DOI: 10.1002/cphy.c210010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Metabolic syndrome (MetS) is a highly heritable disease and a major public health burden worldwide. MetS diagnosis criteria are met by the simultaneous presence of any three of the following: high triglycerides, low HDL/high LDL cholesterol, insulin resistance, hypertension, and central obesity. These diseases act synergistically in people suffering from MetS and dramatically increase risk of morbidity and mortality due to stroke and cardiovascular disease, as well as certain cancers. Each of these component features is itself a complex disease, as is MetS. As a genetically complex disease, genetic risk factors for MetS are numerous, but not very powerful individually, often requiring specific environmental stressors for the disease to manifest. When taken together, all sequence variants that contribute to MetS disease risk explain only a fraction of the heritable variance, suggesting additional, novel loci have yet to be discovered. In this article, we will give a brief overview on the genetic concepts needed to interpret genome-wide association studies (GWAS) and quantitative trait locus (QTL) data, summarize the state of the field of MetS physiological genomics, and to introduce tools and resources that can be used by the physiologist to integrate genomics into their own research on MetS and any of its component features. There is a wealth of phenotypic and molecular data in animal models and humans that can be leveraged as outlined in this article. Integrating these multi-omic QTL data for complex diseases such as MetS provides a means to unravel the pathways and mechanisms leading to complex disease and promise for novel treatments. © 2022 American Physiological Society. Compr Physiol 12:1-40, 2022.
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Affiliation(s)
- Karen C Clark
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Williams AL, Walton CB, Pinell B, Khadka VS, Dunn B, Lee K, Anagaran MCT, Avelar A, Shohet RV. Ischemic heart injury leads to HIF1-dependent differential splicing of CaMK2γ. Sci Rep 2021; 11:13116. [PMID: 34162925 PMCID: PMC8222303 DOI: 10.1038/s41598-021-92426-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/19/2021] [Indexed: 12/04/2022] Open
Abstract
Ischemic heart disease is a leading cause of heart failure and hypoxia inducible factor 1 (HIF1) is a key transcription factor in the response to hypoxic injury. Our lab has developed a mouse model in which a mutated, oxygen-stable form of HIF1α (HIF-PPN) can be inducibly expressed in cardiomyocytes. We observed rapid cardiac dilation and loss of contractility in these mice due to lower expression of excitation-contraction coupling genes and reduced calcium flux. As alternative splicing plays an underappreciated role in transcriptional regulation, we used RNA sequencing to search for splicing changes in calcium-handling genes of HIF-PPN hearts and compared them to previous sequencing data from a model of myocardial infarction (MI) to select for transcripts that are modified in a pathological setting. We found overlap between genes differentially expressed in HIF-PPN and post-MI mice (54/131 genes upregulated in HIF-PPN hearts at 1 day and/or 3 days post-MI, and 45/78 downregulated), as well as changes in alternative splicing. Interestingly, calcium/calmodulin dependent protein kinase II, gamma (CAMK2G) was alternatively spliced in both settings, with variant 1 (v1) substantially decreased compared to variants 2 (v2) and 3 (v3). These findings were also replicated in vitro when cells were transfected with HIF-PPN or exposed to hypoxia. Further analysis of CAMK2γ protein abundance revealed only v1 was detectable and substantially decreased up to 7 days post-MI. Rbfox1, a splicing factor of CAMK2G, was also decreased in HIF-PPN and post-MI hearts. Subcellular fractionation showed CAMK2γ v1 was found in the nuclear and cytoplasmic fractions, and abundance decreased in both fractions post-MI. Chromatin immunoprecipitation analysis of HIF1 in post-MI hearts also demonstrated direct HIF1 binding to CAMK2G. CaMK2 is a key transducer of calcium signals in both physiological and pathological settings. The predominantly expressed isoform in the heart, CaMK2δ, has been extensively studied in cardiac injury, but the specific role of CaMK2γ is not well defined. Our data suggest that loss of CaMK2γ after MI is HIF1-dependent and may play an important role in the heart's calcium signaling and transcriptional response to hypoxia.
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Affiliation(s)
- Allison Lesher Williams
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Chad B Walton
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Blake Pinell
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Vedbar S Khadka
- Bioinformatics Core, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Brandyn Dunn
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Katie Lee
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - M C Therese Anagaran
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Abigail Avelar
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA
| | - Ralph V Shohet
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB 311, Honolulu, HI, 96813, USA.
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Qi L, Wang W, Zhao G, Jiang H, Zhang Y, Zhao D, Jin H, Yu H, Xu H. Circular RNA circitga7 accelerates glioma progression via miR-34a-5p/VEGFA axis. Aging (Albany NY) 2021; 13:13138-13152. [PMID: 33962397 PMCID: PMC8148479 DOI: 10.18632/aging.202996] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/08/2020] [Indexed: 12/24/2022]
Abstract
Circular RNAs (circRNAs) are a group of noncoding RNAs derived from back-splicing events. CircRNA is reported to be involved in various tumor progressions, including glioma. Although there are a few reports of circular RNAs participating in gliomas, it is still unclear whether circular RNAs regulate the occurrence of gliomas. In our research, we found that the expression of circITGA7 in glioma tissues and glioma cells increased significantly. Knocking down circITGA7 can significantly inhibit the proliferation of glioma cells and reduce cell metastasis. Through analysis and dual-luciferase report assay, we found that circITGA7 acts as a sponge for miR-34a-5p targeting VEGFA in glioma. Our study showed that circITGA7 regulates the proliferation and metastasis of glioma cell lines (SW1783&U373) by regulating the miR-34a-5p/VEGFA pathway. In conclusion, our study revealed a regulatory loop for the circITGA7/miR-34a-5p/VEGFA axis to regulate glioma development.
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Affiliation(s)
- Ling Qi
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China.,Department of Pathophysiology, Jilin Medical University, Jilin 132013, Jilin, China
| | - Weiyao Wang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China.,Department of Pathophysiology, Jilin Medical University, Jilin 132013, Jilin, China
| | - Guifang Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, Guangdong, China.,Department of Pathology, Jilin Medical University, Jilin 132013, China
| | - Hong Jiang
- Department of Ophthalmology, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yu Zhang
- Department of Neurovascular, First Hospital of Jilin University, Changchun 130021, China
| | - Donghai Zhao
- Department of Pathology, Jilin Medical University, Jilin 132013, China
| | - Hong Jin
- Department of Pathology, Jilin Medical University, Jilin 132013, China
| | - Hongquan Yu
- Department of Oncological Neurosurgery, First Hospital of Jilin University, Changchun 130021, China
| | - Haiyang Xu
- Department of Oncological Neurosurgery, First Hospital of Jilin University, Changchun 130021, China
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11
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Haisma S, Weersma RK, Joosse ME, de Koning BAE, de Meij T, Koot BGP, Wolters V, Norbruis O, Daly MJ, Stevens C, Xavier RJ, Koskela J, Rivas MA, Visschedijk MC, Verkade HJ, Barbieri R, Jansen DBH, Festen EAM, van Rheenen PF, van Diemen CC. Exome sequencing in patient-parent trios suggests new candidate genes for early-onset primary sclerosing cholangitis. Liver Int 2021; 41:1044-1057. [PMID: 33590606 PMCID: PMC8252477 DOI: 10.1111/liv.14831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/29/2021] [Accepted: 02/07/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS Primary sclerosing cholangitis (PSC) is a rare bile duct disease strongly associated with inflammatory bowel disease (IBD). Whole-exome sequencing (WES) has contributed to understanding the molecular basis of very early-onset IBD, but rare protein-altering genetic variants have not been identified for early-onset PSC. We performed WES in patients diagnosed with PSC ≤ 12 years to investigate the contribution of rare genetic variants to early-onset PSC. METHODS In this multicentre study, WES was performed on 87 DNA samples from 29 patient-parent trios with early-onset PSC. We selected rare (minor allele frequency < 2%) coding and splice-site variants that matched recessive (homozygous and compound heterozygous variants) and dominant (de novo) inheritance in the index patients. Variant pathogenicity was predicted by an in-house developed algorithm (GAVIN), and PSC-relevant variants were selected using gene expression data and gene function. RESULTS In 22 of 29 trios we identified at least 1 possibly pathogenic variant. We prioritized 36 genes, harbouring a total of 54 variants with predicted pathogenic effects. In 18 genes, we identified 36 compound heterozygous variants, whereas in the other 18 genes we identified 18 de novo variants. Twelve of 36 candidate risk genes are known to play a role in transmembrane transport, adaptive and innate immunity, and epithelial barrier function. CONCLUSIONS The 36 candidate genes for early-onset PSC need further verification in other patient cohorts and evaluation of gene function before a causal role can be attributed to its variants.
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Affiliation(s)
- Sjoukje‐Marije Haisma
- Department of Paediatric Gastroenterology Hepatology and NutritionUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Maria E. Joosse
- Department of Paediatric GastroenterologyErasmus University Medical CenterSophia Children's HospitalRotterdamThe Netherlands
| | - Barbara A. E. de Koning
- Department of Paediatric GastroenterologyErasmus University Medical CenterSophia Children's HospitalRotterdamThe Netherlands
| | - Tim de Meij
- Department of Pediatric GastroenterologyVU University Medical CenterAmsterdamThe Netherlands
| | - Bart G. P. Koot
- Pediatric GastroenterologyEmma Children's HospitalAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Victorien Wolters
- Department of Pediatric GastroenterologyUniversity Medical Center Utrecht – Wilhelmina Children's HospitalUtrechtThe Netherlands
| | - Obbe Norbruis
- Department of PediatricsIsala HospitalZwolleThe Netherlands
| | - Mark J. Daly
- Broad Institute of Harvard and Massachusetts Institute of TechnologyBostonMAUSA
| | - Christine Stevens
- Broad Institute of Harvard and Massachusetts Institute of TechnologyBostonMAUSA
| | | | - Jukka Koskela
- Massachusetts General Hospital, GastroenterologyBostonMAUSA,Institute for Molecular Medicine Finland (FIMM)University of HelsinkiHelsinkiFinland,Clinic of Gastroenterology HelsinkiHelsinki University and Helsinki University HospitalHelsinkiFinland
| | | | - Marijn C. Visschedijk
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Henkjan J. Verkade
- Department of Paediatric Gastroenterology Hepatology and NutritionUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Ruggero Barbieri
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands,Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Dianne B. H. Jansen
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Eleonora A. M. Festen
- Department of Gastroenterology and HepatologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands,Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Patrick F. van Rheenen
- Department of Paediatric Gastroenterology Hepatology and NutritionUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Cleo C. van Diemen
- Department of GeneticsUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
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12
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Liu C, Zhang H, Chen Y, Wang S, Chen Z, Liu Z, Wang J. Identifying RBM47, HCK, CD53, TYROBP, and HAVCR2 as Hub Genes in Advanced Atherosclerotic Plaques by Network-Based Analysis and Validation. Front Genet 2021; 11:602908. [PMID: 33519905 PMCID: PMC7844323 DOI: 10.3389/fgene.2020.602908] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Atherosclerotic cardiovascular diseases accounted for a quarter of global deaths. Most of these fatal diseases like coronary atherosclerotic disease (CAD) and stroke occur in the advanced stage of atherosclerosis, during which candidate therapeutic targets have not been fully established. This study aims to identify hub genes and possible regulatory targets involved in treatment of advanced atherosclerotic plaques. Material/Methods: Microarray dataset GSE43292 and GSE28829, both containing advanced atherosclerotic plaques group and early lesions group, were obtained from the Gene Expression Omnibus database. Weighted gene co-expression network analysis (WGCNA) was conducted to identify advanced plaque-related modules. Module conservation analysis was applied to assess the similarity of advanced plaque-related modules between GSE43292 and GSE28829. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of these modules were performed by Metascape. Differentially expressed genes (DEGs) were mapped into advanced plaque-related modules and module membership values of DEGs in each module were calculated to identify hub genes. Hub genes were further validated for expression in atherosclerotic samples, for distinguishing capacity of CAD and for potential functions in advanced atherosclerosis. Results: The lightgreen module (MElightgreen) in GSE43292 and the brown module (MEbrown) in GSE28829 were identified as advanced plaque-related modules. Conservation analysis of these two modules showed high similarity. GO and KEGG enrichment analysis revealed that genes in both MElightgreen and MEbrown were enriched in immune cell activation, secretory granules, cytokine activity, and immunoinflammatory signaling. RBM47, HCK, CD53, TYROBP, and HAVCR2 were identified as common hub genes, which were validated to be upregulated in advanced atherosclerotic plaques, to well distinguish CAD patients from non-CAD people and to regulate immune cell function-related mechanisms in advanced atherosclerosis. Conclusions: We have identified RBM47, HCK, CD53, TYROBP, and HAVCR2 as immune-responsive hub genes related to advanced plaques, which may provide potential intervention targets to treat advanced atherosclerotic plaques.
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Affiliation(s)
- Chiyu Liu
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of Cardiac Electrophysiology and Arrhythmia in Guangdong Province, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haifeng Zhang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of Cardiac Electrophysiology and Arrhythmia in Guangdong Province, Guangzhou, China
| | - Yangxin Chen
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of Cardiac Electrophysiology and Arrhythmia in Guangdong Province, Guangzhou, China
| | - Shaohua Wang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of Cardiac Electrophysiology and Arrhythmia in Guangdong Province, Guangzhou, China
| | - Zhiteng Chen
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of Cardiac Electrophysiology and Arrhythmia in Guangdong Province, Guangzhou, China
| | - Zhaoyu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jingfeng Wang
- Department of Cardiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of Cardiac Electrophysiology and Arrhythmia in Guangdong Province, Guangzhou, China
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