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Zhang Q, Lan X. Assessment of causal association between autoimmune thyroiditis and thyroid cancer: A Mendelian randomization study. Medicine (Baltimore) 2025; 104:e41633. [PMID: 40020149 PMCID: PMC11875592 DOI: 10.1097/md.0000000000041633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 02/04/2025] [Indexed: 03/05/2025] Open
Abstract
Currently, the precise interplay between autoimmune thyroiditis, particularly Hashimoto thyroiditis, and thyroid cancer remains ambiguous. While certain observational studies suggest autoimmune thyroiditis (including Hashimoto thyroiditis) as a predisposing factor for thyroid cancer. Nevertheless, it is still uncertain whether autoimmune thyroiditis is independently associated with thyroid cancer. We employed Mendelian randomization (MR) study methodology, a genetic analysis approach, to evaluate the causal impact of autoimmune thyroiditis on the occurrence of thyroid cancer. We obtained and synthesized statistical data by utilizing public available genome-wide association studies (GWAS). Our study utilized GWAS summary statistics datasets associated with autoimmune thyroiditis (including Hashimoto thyroiditis) as the exposure data source and selected GWAS summary statistics datasets related to thyroid cancer as the outcome data source. Single nucleotide polymorphisms closely associated with autoimmune thyroiditis were chosen as instrumental variables. We conducted 2-sample MR analyses to elucidate the causal association between autoimmune thyroiditis and thyroid cancer. The inverse variance-weighted (IVW) method was employed as the primary methodology, supplemented by additional MR methods including MR-Egger regression, weighted median, simple mode, and weighted mode analyses, to bolster the robustness of our findings. The MR analysis conducted using the IVW method did not confirm a causal relationship between autoimmune thyroiditis and thyroid cancer (odds ratio [OR] = 0.8554, 95% confidence interval [CI]: 0.7193 to 1.0172, P = .0772; OR = 0.8477, 95% CI: 0.7159 to 1.0039, P = .0555; and OR = 1.1324, 95% CI: 0.9342 to 1.3725, P = .2052, from 3 eligible dataset analyses, respectively). Additionally, MR analysis did not observe a causal association between Hashimoto thyroiditis and thyroid cancer (OR = 1.0449, 95% CI: 0.9400 to 1.1615, P = .4155; and OR = 0.9897, 95% CI: 0.8174 to 1.1984, P = .9159, from 2 eligible dataset analyses, respectively). Consistency in results across alternative MR methods was observed. This study employing MR methodology indicates the absence of significant causal relationship between exposure to autoimmune thyroiditis (including Hashimoto thyroiditis) and thyroid cancer. Further validation through larger-scale studies with increased sample sizes is warranted in future investigations.
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Affiliation(s)
- Qihong Zhang
- Department of Anorectal Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Xiabin Lan
- Department of Thyroid Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
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2
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Ruotsalainen AK, Kettunen S, Suoranta T, Kaikkonen MU, Ylä-Herttuala S, Aherrahrou R. The mechanisms of Chr.9p21.3 risk locus in coronary artery disease: where are we today? Am J Physiol Heart Circ Physiol 2025; 328:H196-H208. [PMID: 39656484 DOI: 10.1152/ajpheart.00580.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 11/22/2024] [Accepted: 11/22/2024] [Indexed: 01/15/2025]
Abstract
Despite the advancements and release of new therapeutics in the past few years, cardiovascular diseases (CVDs) have remained the number one cause of death worldwide. Genetic variation of a 9p21.3 genomic locus has been identified as the most significant and robust genetic CVD risk marker on the population level, with the strongest association with coronary artery disease (CAD) and other diseases, including diabetes and cancer. Several mechanisms of 9p21.3 in CVDs have been proposed, but their effects on CVDs have remained elusive. Moreover, most of the single nucleotide polymorphisms (SNPs) associated with CAD are located on a sequence of a long noncoding RNA (lncRNA) called ANRIL. ANRIL has several linear and circular splicing isoforms, which seem to have different effects and implications for CVDs. The mechanisms of the 9p21.3 locus and the interplay of its coding and noncoding transcripts in different diseases require further research. Circular RNAs have generally raised interest due to their beneficial features as biomarkers and therapeutic molecules. Here, we review the literature of 9p21.3 from its identification in 2007 and draw the current knowledge on its function, implications in CVDs, and therapeutic potential.
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Affiliation(s)
- Anna-Kaisa Ruotsalainen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Sanna Kettunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tuisku Suoranta
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Centre, Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Rédouane Aherrahrou
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Institute for Cardiogenetics, Universität zu Lübeck, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Heart Centre Lübeck, Lübeck, Germany
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3
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Chignon A, Lettre G. Using omics data and genome editing methods to decipher GWAS loci associated with coronary artery disease. Atherosclerosis 2025; 401:118621. [PMID: 39909615 DOI: 10.1016/j.atherosclerosis.2024.118621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/18/2024] [Accepted: 10/03/2024] [Indexed: 02/07/2025]
Abstract
Coronary artery disease (CAD) is due to atherosclerosis, a pathophysiological process that involves several cell-types and results in the accumulation of lipid-rich plaque that disrupt the normal blood flow through the coronary arteries to the heart. Genome-wide association studies have identified 1000s of genetic variants robustly associated with CAD or its traditional risk factors (e.g. blood pressure, blood lipids, type 2 diabetes, smoking). However, gaining biological insights from these genetic discoveries remain challenging because of linkage disequilibrium and the difficulty to interpret the functions of non-coding regulatory elements in the human genome. In this review, we present different statistical methods (e.g. Mendelian randomization) and molecular datasets (e.g. expression or protein quantitative trait loci) that have helped connect CAD-associated variants with genes, biological pathways, and cell-types or tissues. We emphasize that these various strategies make predictions, which need to be validated in orthologous systems. We discuss specific examples where the integration of omics data with GWAS results has prioritized causal CAD variants and genes. Finally, we review how targeted and genome-wide genome editing experiments using the CRISPR/Cas9 toolbox have been used to characterize new CAD genes in human cells. Researchers now have the statistical and bioinformatic methods, the molecular datasets, and the experimental tools to dissect comprehensively the loci that contribute to CAD risk in humans.
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Affiliation(s)
- Arnaud Chignon
- Montreal Heart Institute, Montreal, Quebec, Canada; Faculté de Médecine, Université de Montréal, Montreal, Quebec, Canada
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada; Faculté de Médecine, Université de Montréal, Montreal, Quebec, Canada.
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Li J, Li B, Zhang X, Ma X, Li Z. MDMNI-DGD: A novel graph neural network approach for druggable gene discovery based on the integration of multi-omics data and the multi-view network. Comput Biol Med 2025; 185:109511. [PMID: 39644579 DOI: 10.1016/j.compbiomed.2024.109511] [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: 10/08/2024] [Revised: 11/14/2024] [Accepted: 11/29/2024] [Indexed: 12/09/2024]
Abstract
Accurately predicting druggable genes is of paramount importance for enhancing the efficacy of targeted therapies, reducing drug-related toxicities and improving patients' survival rates. Nevertheless, accurately predicting candidate cancer-druggable genes remains a critical challenge in translational medicine due to the high heterogeneity and complexity of cancer data. In this study, we proposed a novel graph neural approach called Druggable Gene Discovery based on the Integration of Multi-omics Data and the Multi-view Network (MDMNI-DGD), aiming to predict and evaluate cancer-druggable genes. MDMNI-DGD integrated a comprehensive set of multi-omics data, including copy number variations, DNA methylation, somatic mutations, and gene expression profiles. Simultaneously, it constructed the multi-view gene association network based on protein-protein interactions (PPI), protein structural domains, gene co-expression, pathway co-occurrence, gene sequence and gene ontology. Compared to other state-of-the-art approaches, MDMNI-DGD exhibits excellent performance in key evaluation metrics such as AUROC and AUPR. Moreover, the case study has also demonstrated the efficacy of our approach in discovering potentially druggable genes. Among more than 20,000 protein-coding genes, MDMNI-DGD successfully identified 872 potentially druggable genes. The findings from this investigation may serve to bolster the assessment of pan-cancer druggable genes, potentially catalyzing the development of more personalized and efficacious therapeutic interventions.
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Affiliation(s)
- Jianwei Li
- School of Artificial Intelligence, Hebei University of Technology, 300401, Tianjin, China.
| | - Bing Li
- School of Artificial Intelligence, Hebei University of Technology, 300401, Tianjin, China
| | - Xukun Zhang
- School of Artificial Intelligence, Hebei University of Technology, 300401, Tianjin, China
| | - Xuxu Ma
- School of Artificial Intelligence, Hebei University of Technology, 300401, Tianjin, China
| | - Ziyu Li
- School of Artificial Intelligence, Hebei University of Technology, 300401, Tianjin, China
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Wang Y, Shi Y, Wu Z, Gao J, Wang J, Li L, Wan Y, Lang A M, Zhang J, Wang H, Hou Y. The Association of PLA2G7 Gene Polymorphisms with Serum Lp-PLA2 Activity and Lipid Profile in Han Chinese Patients with Coronary Heart Disease. Pharmgenomics Pers Med 2024; 17:563-572. [PMID: 39723113 PMCID: PMC11669343 DOI: 10.2147/pgpm.s474494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 12/02/2024] [Indexed: 12/28/2024] Open
Abstract
Purpose This study aimed to investigate the distribution patterns of PLA2G7 gene variants in Han Chinese patients with coronary heart disease (CHD), and their relationships with serum lipoprotein-associated phospholipase A2 (Lp-PLA2) levels and lipid profiles. Methods A total of 93 han Chinese CHD patients were recruited. Serum Lp-PLA2 levels were determined using enzyme-linked immunosorbent assay (ELISA), while comprehensive analysis of PLA2G7 gene polymorphisms was conducted through whole-exome sequencing. Concurrently, multiple lipid parameters were measured and analyzed. Results Among these Han Chinese CHD patients, the PLA2G7 gene rs1051931 (c.1136T>C p.Val379Ala) rare variant was highly prevalent (variant rate: 94.62%) among the study population, and showed negative correlation with serum Lp-PLA2 activity. The rs1765208290 (c.233G>A p.Gly78Asp) rare variant showed positive correlation with TG, ApoA, ApoB, HDL, LDL and TCHO levels in the serum. Strong linkage disequilibrium was observed between the rs1805018 (c.593T>C p.Ile198Thr) and rs76863441 (c.835G>T p.Val279Phe), both of which were related to lower Lp-PLA2 activity. Conclusion In these Han Chinese CHD patients, the rs1051931 (c.1136T>C p.Val379Ala) rare variant in the PLA2G7 gene is closely linked to decreased Lp-PLA2 activity, whereas the rs1765208290 (c.233G>A p.Gly78Asp) rare variant influences lipid homeostasis. The strong LD between rs1805018 (c.593T>C p.Ile198Thr) and rs76863441 (c.835G>T p.Val279Phe) loci may act synergistically to reduce Lp-PLA2 activity.
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Affiliation(s)
- Yanhai Wang
- Department of Clinical Laboratory, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Yupeng Shi
- Zhejiang Digena Diagnosis Technology CO., LTD, Zhejiang, 310030, People’s Republic of China
| | - Zhongwei Wu
- Department of Clinical Laboratory, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Jiangfeng Gao
- Cardiology Department, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Jing Wang
- Cardiology Department, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Lei Li
- Network Management, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Yugang Wan
- Network Management, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - MuGu Lang A
- Department of Clinical Laboratory, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Jianwen Zhang
- Department of Clinical Laboratory, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Hongbo Wang
- Cardiology Department, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
| | - Yu Hou
- Cardiology Department, Hohhot First Hospital, Hohhot, 010030, People’s Republic of China
- Cardiology Department, Inner Mongolia People’s Hospital, Hohhot, 010017, People’s Republic of China
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Qin GT, Zhao Q, Fujita A, Damiani I, Easwaran M, Basu S, Gu W, Li DY, Worssam M, Palmisano B, Monteiro JP, Ramste M, Kundu R, Nguyen T, Park C, Weldy CS, Cheng P, Kim JB. Aryl-hydrocarbon receptor in smooth muscle cells protect against dioxin induced adverse remodeling of atherosclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614572. [PMID: 39569142 PMCID: PMC11577244 DOI: 10.1101/2024.09.24.614572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2024]
Abstract
Introduction Environmental exposure to dioxin has been linked to increased myocardial infarction. Smooth muscle cells (SMC) in the coronary vasculature play a critical role in atherosclerotic plaque remodeling due to their phenotypic plasticity, however, the detailed mechanism linking dioxin exposure to adverse SMC modulation is not well understood. Methods Single-cell RNA and ATAC sequencing and histological analyses were performed on the aorta from mouse models of atherosclerosis exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or control. Primary human coronary artery SMC (HCASMC) treated in culture with TCDD were used to perform RNA-Seq, ATAC-Seq, and functional phenotypic assays. ChIP-Seq was performed with antibodies against Aryl-hydrocarbon receptor (AHR) and TCF21, two of known SMC modulating transcription factors. Results Modulated SMC were the most transcriptionally responsive cell type to dioxin in the atherosclerotic aorta. Dioxin accelerated disease phenotype by promoting a modulated SMC phenotype early, resulting in increased lesion size, migration of SMC, and macrophage recruitment to the lesion. We found C3 expressing modulated SMCs to be likely contributing to the increased macrophage recruitment and inflammation. Analysis of the RNA-Seq data from HCASMC treated with TCDD showed differential enrichment of biological pathways related to cell migration, localization, and inflammation. Furthermore, ATAC-Seq data showed a significant activation for pathways regulating vascular development, cell migration, inflammation, and apoptosis. With TCDD treatment, there was also enrichment of AHR ChIP-Seq peaks, while the TCF21 enrichment decreased significantly. The SMC-specific Ahr knockout resulted in increased oxidative stress in SMC, increased lesion size and macrophage content, and loss of SMC lineage cells in the lesion cap when exposed to TCDD, consistent with a more vulnerable plaque phenotype. Conclusion Dioxin adversely remodels atherosclerotic plaque by accelerating the SMC- phenotypic modulation, and increasing inflammation and oxidative stress resulting in increased macrophage recruitment and lesion size. Dioxin may adversely affect the SMC phenotype and disease state by affecting the TCF21 occupancy in the open chromatin regions. Furthermore, we observed that SMC-specific deletion of Ahr in mice resulted in worsening of dioxin mediated SMC modulation and atherosclerosis, suggesting that Ahr in SMC confers protection against dioxin by promoting a stable plaque phenotype and reducing dioxin induced oxidative stress. Summary Exposure to dioxin, an environmental pollutant present in tobacco smoke and air pollution, accelerates smooth muscle cell modulation, and atherosclerosis.Dioxin exposure leads to inflammatory smooth muscle cell phenotype characterized by complement pathway activation and increased macrophage recruitment to plaqueAryl-hydrocarbon receptor in SMC protects against oxidative stress, and promotes a stable plaque phenotype.
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7
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Yang Y, Dong L, Li Y, Huang Y, Zeng X. Summary data-based Mendelian randomization and single-cell RNA sequencing analyses identify immune associations with low-level LGALS9 in sepsis. J Cell Mol Med 2024; 28:e18559. [PMID: 39044269 PMCID: PMC11265992 DOI: 10.1111/jcmm.18559] [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: 05/02/2024] [Revised: 06/15/2024] [Accepted: 07/08/2024] [Indexed: 07/25/2024] Open
Abstract
Sepsis is one of the major challenges in intensive care units, characterized by the complexity of the host immune status. To gain a deeper understanding of the pathogenesis of sepsis, it is crucial to study the phenotypic changes in immune cells and their underlying molecular mechanisms. We conducted Summary data-based Mendelian randomization analysis by integrating genome-wide association studies data for sepsis with expression quantitative trait locus data, revealing a significant decrease in the expression levels of 17 biomarkers in sepsis patients. Furthermore, based on single-cell RNA sequencing data, we elucidated potential molecular mechanisms at single-cell resolution and identified that LGALS9 inhibition in sepsis patients leads to the activation and differentiation of monocyte and T-cell subtypes. These findings are expected to assist researchers in gaining a more in-depth understanding of the immune dysregulation in sepsis.
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Affiliation(s)
- Yongsan Yang
- Intensive Care Unit and West China Biomedical Big Data CenterWest China Hospital, Sichuan UniversityChengduChina
- Med‐X Center for InformaticsSichuan UniversityChengduChina
| | - Lei Dong
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Yanguo Li
- Institute of Drug Discovery Technology, Ningbo UniversityNingboChina
| | - Ye Huang
- Department of Emergency MedicineXiyuan Hospital of China Academy of Chinese Medical SciencesBeijingChina
| | - Xiaoxi Zeng
- Med‐X Center for InformaticsSichuan UniversityChengduChina
- West China Biomedical Big Data CenterWest China Hospital, Sichuan UniversityChengduChina
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8
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La Chica Lhoëst MT, Martinez A, Claudi L, Garcia E, Benitez-Amaro A, Polishchuk A, Piñero J, Vilades D, Guerra JM, Sanz F, Rotllan N, Escolà-Gil JC, Llorente-Cortés V. Mechanisms modulating foam cell formation in the arterial intima: exploring new therapeutic opportunities in atherosclerosis. Front Cardiovasc Med 2024; 11:1381520. [PMID: 38952543 PMCID: PMC11215187 DOI: 10.3389/fcvm.2024.1381520] [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: 02/20/2024] [Accepted: 05/28/2024] [Indexed: 07/03/2024] Open
Abstract
In recent years, the role of macrophages as the primary cell type contributing to foam cell formation and atheroma plaque development has been widely acknowledged. However, it has been long recognized that diffuse intimal thickening (DIM), which precedes the formation of early fatty streaks in humans, primarily consists of lipid-loaded smooth muscle cells (SMCs) and their secreted proteoglycans. Recent studies have further supported the notion that SMCs constitute the majority of foam cells in advanced atherosclerotic plaques. Given that SMCs are a major component of the vascular wall, they serve as a significant source of microvesicles and exosomes, which have the potential to regulate the physiology of other vascular cells. Notably, more than half of the foam cells present in atherosclerotic lesions are of SMC origin. In this review, we describe several mechanisms underlying the formation of intimal foam-like cells in atherosclerotic plaques. Based on these mechanisms, we discuss novel therapeutic approaches that have been developed to regulate the generation of intimal foam-like cells. These innovative strategies hold promise for improving the management of atherosclerosis in the near future.
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Affiliation(s)
- M. T. La Chica Lhoëst
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), Barcelona, Spain
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
| | - A. Martinez
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), Barcelona, Spain
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
| | - L. Claudi
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), Barcelona, Spain
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
| | - E. Garcia
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), Barcelona, Spain
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
| | - A. Benitez-Amaro
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), Barcelona, Spain
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
| | - A. Polishchuk
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), Barcelona, Spain
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
| | - J. Piñero
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - D. Vilades
- Department of Cardiology, Hospital de la Santa Creu I Sant Pau, Biomedical Research Institute Sant Pau (IIB-SANTPAU), Universitat Autonoma de Barcelona, Barcelona, Spain
- Department of Cardiovascular, CIBERCV, Institute of Health Carlos III, Madrid, Spain
| | - J. M. Guerra
- Department of Cardiology, Hospital de la Santa Creu I Sant Pau, Biomedical Research Institute Sant Pau (IIB-SANTPAU), Universitat Autonoma de Barcelona, Barcelona, Spain
- Department of Cardiovascular, CIBERCV, Institute of Health Carlos III, Madrid, Spain
| | - F. Sanz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - N. Rotllan
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
- Department of Cardiovascular, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
| | - J. C. Escolà-Gil
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
- Department of Cardiovascular, CIBERDEM, Institute of Health Carlos III, Madrid, Spain
| | - V. Llorente-Cortés
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona (IIBB)-Spanish National Research Council (CSIC), Barcelona, Spain
- Department of Cardiovascular, Institut de Recerca Sant Pau (IR SANT PAU), Barcelona, Spain
- Department of Cardiovascular, CIBERCV, Institute of Health Carlos III, Madrid, Spain
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McVey DG, Andreadi C, Gong P, Stanczyk PJ, Solomon CU, Turner L, Yan L, Chen R, Cao J, Nelson CP, Thompson JR, Yu H, Webb TR, Samani NJ, Ye S. Genetic influence on vascular smooth muscle cell apoptosis. Cell Death Dis 2024; 15:402. [PMID: 38851795 PMCID: PMC11162461 DOI: 10.1038/s41419-024-06799-z] [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: 10/02/2023] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Vascular smooth muscle cell (VSMC) proliferation, migration, and apoptosis play important roles in many physiological processes and pathological conditions. To identify genetic influences on VSMC behavior, we measured these traits and undertook genome-wide association studies in primary umbilical artery-derived VSMCs from >2000 individuals. Although there were no genome-wide significant associations for VSMC proliferation or migration, genetic variants at two genomic loci (7p15.3 and 7q32.3) showed highly significant associations with VSMC apoptosis (P = 1.95 × 10-13 and P = 7.47 × 10-9, respectively). The lead variant at the 7p51.3 locus was associated with increased expression of the GSDME and PALS2 genes in VSMCs. Knockdown of GSDME or PALS2 in VSMCs attenuated apoptotic cell death. A protein co-immunoprecipitation assay indicated that GSDME complexed with PALS2. PALS2 knockdown attenuated activated caspase-3 and GSDME fragmentation, whilst GSDME knockdown also reduced activated caspase-3. These findings provide new insights into the genetic regulation of VSMC apoptosis, with potential utility for therapeutic development.
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Affiliation(s)
- David G McVey
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Catherine Andreadi
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Peng Gong
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Paulina J Stanczyk
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Charles U Solomon
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Lenka Turner
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Liu Yan
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore
| | - Runji Chen
- Shantou University Medical College, Shantou, China
| | - Junjun Cao
- Shantou University Medical College, Shantou, China
| | - Christopher P Nelson
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - John R Thompson
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Haojie Yu
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore
| | - Tom R Webb
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Shu Ye
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore.
- Shantou University Medical College, Shantou, China.
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10
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Lambert J, Oc S, Worssam MD, Häußler D, Solomon CU, Figg NL, Baxter R, Imaz M, Taylor JCK, Foote K, Finigan A, Mahbubani KT, Webb TR, Ye S, Bennett MR, Krüger A, Spivakov M, Jørgensen HF. Network-based prioritization and validation of regulators of vascular smooth muscle cell proliferation in disease. NATURE CARDIOVASCULAR RESEARCH 2024; 3:714-733. [PMID: 39215134 PMCID: PMC11182749 DOI: 10.1038/s44161-024-00474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 04/18/2024] [Indexed: 06/21/2024]
Abstract
Aberrant vascular smooth muscle cell (VSMC) homeostasis and proliferation characterize vascular diseases causing heart attack and stroke. Here we elucidate molecular determinants governing VSMC proliferation by reconstructing gene regulatory networks from single-cell transcriptomics and epigenetic profiling. We detect widespread activation of enhancers at disease-relevant loci in proliferation-predisposed VSMCs. We compared gene regulatory network rewiring between injury-responsive and nonresponsive VSMCs, which suggested shared transcription factors but differing target loci between VSMC states. Through in silico perturbation analysis, we identified and prioritized previously unrecognized regulators of proliferation, including RUNX1 and TIMP1. Moreover, we showed that the pioneer transcription factor RUNX1 increased VSMC responsiveness and that TIMP1 feeds back to promote VSMC proliferation through CD74-mediated STAT3 signaling. Both RUNX1 and the TIMP1-CD74 axis were expressed in human VSMCs, showing low levels in normal arteries and increased expression in disease, suggesting clinical relevance and potential as vascular disease targets.
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MESH Headings
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/cytology
- Humans
- Cell Proliferation/genetics
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Gene Regulatory Networks
- Tissue Inhibitor of Metalloproteinase-1/metabolism
- Tissue Inhibitor of Metalloproteinase-1/genetics
- STAT3 Transcription Factor/metabolism
- STAT3 Transcription Factor/genetics
- Signal Transduction/genetics
- Cells, Cultured
- Single-Cell Analysis
- Epigenesis, Genetic
- Transcriptome
- Animals
- Core Binding Factor Alpha 2 Subunit
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Affiliation(s)
- Jordi Lambert
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Sebnem Oc
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Functional Gene Control Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK
| | - Matthew D Worssam
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Häußler
- TUM School of Medicine and Health, Institute of Experimental Oncology and Therapy Research, Technical University of Munich, Munich, Germany
| | - Charles U Solomon
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, UK
| | - Nichola L Figg
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Ruby Baxter
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Maria Imaz
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - James C K Taylor
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Kirsty Foote
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Alison Finigan
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Krishnaa T Mahbubani
- Collaborative Biorepository for Translational Medicine, Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Tom R Webb
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, UK
| | - Shu Ye
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, UK
- Shantou University Medical College, Shantou, China
- Cardiovascular and Metabolic Disease Translational Research Programme, National University of Singapore, Singapore, Singapore
| | - Martin R Bennett
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Achim Krüger
- TUM School of Medicine and Health, Institute of Experimental Oncology and Therapy Research, Technical University of Munich, Munich, Germany
| | - Mikhail Spivakov
- Functional Gene Control Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, UK
| | - Helle F Jørgensen
- Section of Cardiorespiratory Medicine, Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
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11
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Tian Q, Chen JH, Ding Y, Wang XY, Qiu JY, Cao Q, Zhuang LL, Jin R, Zhou GP. EGR1 transcriptionally regulates SVEP1 to promote proliferation and migration in human coronary artery smooth muscle cells. Mol Biol Rep 2024; 51:365. [PMID: 38409611 DOI: 10.1007/s11033-024-09322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024]
Abstract
A low-frequency variant of sushi, von Willebrand factor type A, EGF, and pentraxin domain-containing protein 1 (SVEP1) is associated with the risk of coronary artery disease, as determined by a genome-wide association study. SVEP1 induces vascular smooth muscle cell proliferation and an inflammatory phenotype to promote atherosclerosis. In the present study, qRT‒PCR demonstrated that the mRNA expression of SVEP1 was significantly increased in atherosclerotic plaques compared to normal tissues. Bioinformatics revealed that EGR1 was a transcription factor for SVEP1. The results of the luciferase reporter assay, siRNA interference or overexpression assay, mutational analysis and ChIP confirmed that EGR1 positively regulated the transcriptional activity of SVEP1 by directly binding to its promoter. EGR1 promoted human coronary artery smooth muscle cell (HCASMC) proliferation and migration via SVEP1 in response to oxidized low-density lipoprotein (ox-LDL) treatment. Moreover, the expression level of EGR1 was increased in atherosclerotic plaques and showed a strong linear correlation with the expression of SVEP1. Our findings indicated that EGR1 binding to the promoter region drive SVEP1 transcription to promote HCASMC proliferation and migration.
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Affiliation(s)
- Qiang Tian
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jia-He Chen
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi Ding
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin-Yu Wang
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jia-Yun Qiu
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qian Cao
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li-Li Zhuang
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Jin
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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12
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Luo L, Fu C, Bell CF, Wang Y, Leeper NJ. Role of vascular smooth muscle cell clonality in atherosclerosis. Front Cardiovasc Med 2023; 10:1273596. [PMID: 38089777 PMCID: PMC10713728 DOI: 10.3389/fcvm.2023.1273596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/24/2023] [Indexed: 02/01/2024] Open
Abstract
Atherosclerotic cardiovascular disease remains the leading cause of death worldwide. While many cell types contribute to the growing atherosclerotic plaque, the vascular smooth muscle cell (SMC) is a major contributor due in part to its remarkable plasticity and ability to undergo phenotype switching in response to injury. SMCs can migrate into the fibrous cap, presumably stabilizing the plaque, or accumulate within the lesional core, possibly accelerating vascular inflammation. How SMCs expand and react to disease stimuli has been a controversial topic for many decades. While early studies relying on X-chromosome inactivation were inconclusive due to low resolution and sensitivity, recent advances in multi-color lineage tracing models have revitalized the concept that SMCs likely expand in an oligoclonal fashion during atherogenesis. Current efforts are focused on determining whether all SMCs have equal capacity for clonal expansion or if a "stem-like" progenitor cell may exist, and to understand how constituents of the clone decide which phenotype they will ultimately adopt as the disease progresses. Mechanistic studies are also beginning to dissect the processes which confer cells with their overall survival advantage, test whether these properties are attributable to intrinsic features of the expanding clone, and define the role of cross-talk between proliferating SMCs and other plaque constituents such as neighboring macrophages. In this review, we aim to summarize the historical perspectives on SMC clonality, highlight unanswered questions, and identify translational issues which may need to be considered as therapeutics directed against SMC clonality are developed as a novel approach to targeting atherosclerosis.
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Affiliation(s)
- Lingfeng Luo
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford, CA, United States
| | - Changhao Fu
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford, CA, United States
| | - Caitlin F. Bell
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford, CA, United States
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Ying Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nicholas J. Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford, CA, United States
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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13
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Francis GA. The Greatly Under-Represented Role of Smooth Muscle Cells in Atherosclerosis. Curr Atheroscler Rep 2023; 25:741-749. [PMID: 37665492 PMCID: PMC10564813 DOI: 10.1007/s11883-023-01145-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
PURPOSE OF REVIEW This article summarizes previous and recent research on the fundamental role of arterial smooth muscle cells (SMCs) as drivers of initial and, along with macrophages, later stages of human atherosclerosis. RECENT FINDINGS Studies using human tissues and SMC lineage-tracing mice have reinforced earlier observations that SMCs drive initial atherogenesis in humans and contribute a multitude of phenotypes including foam cell formation hitherto attributed primarily to macrophages in atherosclerosis. Arterial smooth muscle cells (SMCs) are the primary cell type in human pre-atherosclerotic intima and are responsible for the retention of lipoproteins that drive the development of atherosclerosis. Despite this, images of atherogenesis still depict the process as initially devoid of SMCs, primarily macrophage driven, and indicate only relatively minor roles such as fibrous cap formation to intimal SMCs. This review summarizes historical and recent observations regarding the importance of SMCs in the formation of a pre-atherosclerotic intima, initial and later foam cell formation, and the phenotypic changes that give rise to multiple different roles for SMCs in human and mouse lesions. Potential SMC-specific therapies in atherosclerosis are presented.
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Affiliation(s)
- Gordon A Francis
- Centre for Heart Lung Innovation, Providence Research, St. Paul's Hospital, University of British Columbia, Vancouver, Canada.
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14
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Quaye LNK, Dalzell CE, Deloukas P, Smith AJP. The Genetics of Coronary Artery Disease: A Vascular Perspective. Cells 2023; 12:2232. [PMID: 37759455 PMCID: PMC10527262 DOI: 10.3390/cells12182232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified a large number of genetic loci for coronary artery disease (CAD), with many located close to genes associated with traditional CAD risk pathways, such as lipid metabolism and inflammation. It is becoming evident with recent CAD GWAS meta-analyses that vascular pathways are also highly enriched and present an opportunity for novel therapeutics. This review examines GWAS-enriched vascular gene loci, the pathways involved and their potential role in CAD pathogenesis. The functionality of variants is explored from expression quantitative trait loci, massively parallel reporter assays and CRISPR-based gene-editing tools. We discuss how this research may lead to novel therapeutic tools to treat cardiovascular disorders.
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Affiliation(s)
| | | | - Panos Deloukas
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; (L.N.K.Q.); (C.E.D.); (A.J.P.S.)
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15
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Pelisek J, Yundung Y, Reutersberg B, Meuli L, Rössler F, Rabin L, Kopp R, Zimmermann A. Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue. J Clin Med 2023; 12:5109. [PMID: 37568514 PMCID: PMC10420000 DOI: 10.3390/jcm12155109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (ACTB, GAPDH), ribosomal genes (18S, 28S), and long non-coding RNAs (MALAT1, H19). Our results show that RINs from diseased vascular tissue are low (2-4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA's disintegration state, is a better decision-making aid in choosing samples for omics analyses.
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Affiliation(s)
- Jaroslav Pelisek
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Yankey Yundung
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Benedikt Reutersberg
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Lorenz Meuli
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Fabian Rössler
- Department of Surgery and Transplantation, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Laetitia Rabin
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Reinhard Kopp
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Alexander Zimmermann
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
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16
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Solomon CU, Yang W, Ye S. Effector Genes at the Coronary Artery Disease Risk Locus Harboring PDGFD and LncRNA AP002989.1. J Am Heart Assoc 2023; 12:e031012. [PMID: 37489770 PMCID: PMC10492982 DOI: 10.1161/jaha.123.031012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Affiliation(s)
- Charles U. Solomon
- Department of Cardiovascular SciencesUniversity of LeicesterUnited Kingdom
| | - Wei Yang
- Shantou University Medical CollegeShantouChina
| | - Shu Ye
- Department of Cardiovascular SciencesUniversity of LeicesterUnited Kingdom
- Shantou University Medical CollegeShantouChina
- Cardiovascular‐Metabolic Disease Translational Research ProgrammeNational University of SingaporeSingapore
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17
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López Rodríguez M, Arasu UT, Kaikkonen MU. Exploring the genetic basis of coronary artery disease using functional genomics. Atherosclerosis 2023; 374:87-98. [PMID: 36801133 DOI: 10.1016/j.atherosclerosis.2023.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Genome-wide Association Studies (GWAS) have identified more than 300 loci associated with coronary artery disease (CAD), defining the genetic risk map of the disease. However, the translation of the association signals into biological-pathophysiological mechanisms constitute a major challenge. Through a group of examples of studies focused on CAD, we discuss the rationale, basic principles and outcomes of the main methodologies implemented to prioritize and characterize causal variants and their target genes. Additionally, we highlight the strategies as well as the current methods that integrate association and functional genomics data to dissect the cellular specificity underlying the complexity of disease mechanisms. Despite the limitations of existing approaches, the increasing knowledge generated through functional studies helps interpret GWAS maps and opens novel avenues for the clinical usability of association data.
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Affiliation(s)
- Maykel López Rodríguez
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland; Department of Pathology and Laboratory Medicine, University of California, UCLA, Los Angeles, USA.
| | - Uma Thanigai Arasu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland.
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18
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Aherrahrou R, Lue D, Perry RN, Aberra YT, Khan MD, Soh JY, Örd T, Singha P, Yang Q, Gilani H, Benavente ED, Wong D, Hinkle J, Ma L, Sheynkman GM, den Ruijter HM, Miller CL, Björkegren JLM, Kaikkonen MU, Civelek M. Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes. Circ Res 2023; 132:323-338. [PMID: 36597873 PMCID: PMC9898186 DOI: 10.1161/circresaha.122.321586] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Coronary artery disease (CAD) is the leading cause of death worldwide. Recent meta-analyses of genome-wide association studies have identified over 175 loci associated with CAD. The majority of these loci are in noncoding regions and are predicted to regulate gene expression. Given that vascular smooth muscle cells (SMCs) play critical roles in the development and progression of CAD, we aimed to identify the subset of the CAD loci associated with the regulation of transcription in distinct SMC phenotypes. METHODS We measured gene expression in SMCs isolated from the ascending aortas of 151 heart transplant donors of various genetic ancestries in quiescent or proliferative conditions and calculated the association of their expression and splicing with ~6.3 million imputed single-nucleotide polymorphism markers across the genome. RESULTS We identified 4910 expression and 4412 splicing quantitative trait loci (sQTLs) representing regions of the genome associated with transcript abundance and splicing. A total of 3660 expression quantitative trait loci (eQTLs) had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 eQTLs were SMC-specific and sex-biased, respectively. We made these results available for public query on a user-friendly website. To identify the effector transcript(s) regulated by CAD loci, we used 4 distinct colocalization approaches. We identified 84 eQTL and 164 sQTL that colocalized with CAD loci, highlighting the importance of genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. Notably, 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. One CAD locus colocalized with a sex-specific eQTL (TERF2IP), and another locus colocalized with SMC-specific eQTL (ALKBH8). The most significantly associated CAD locus, 9p21, was an sQTL for the long noncoding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. CONCLUSIONS Collectively, our results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in distinct SMC phenotypes.
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Affiliation(s)
- Rédouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Dillon Lue
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - R Noah Perry
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Yonathan Tamrat Aberra
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joon Yuhl Soh
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Tiit Örd
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Prosanta Singha
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Qianyi Yang
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Huda Gilani
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jameson Hinkle
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Gloria M Sheynkman
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Cancer Center, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Johan LM Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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19
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Karamanavi E, McVey DG, van der Laan SW, Stanczyk PJ, Morris GE, Wang Y, Yang W, Chan K, Poston RN, Luo J, Zhou X, Gong P, Jones PD, Cao J, Kostogrys RB, Webb TR, Pasterkamp G, Yu H, Xiao Q, Greer PA, Stringer EJ, Samani NJ, Ye S. The FES Gene at the 15q26 Coronary-Artery-Disease Locus Inhibits Atherosclerosis. Circ Res 2022; 131:1004-1017. [PMID: 36321446 PMCID: PMC9770135 DOI: 10.1161/circresaha.122.321146] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND Genome-wide association studies have discovered a link between genetic variants on human chromosome 15q26.1 and increased coronary artery disease (CAD) susceptibility; however, the underlying pathobiological mechanism is unclear. This genetic locus contains the FES (FES proto-oncogene, tyrosine kinase) gene encoding a cytoplasmic protein-tyrosine kinase involved in the regulation of cell behavior. We investigated the effect of the 15q26.1 variants on FES expression and whether FES plays a role in atherosclerosis. METHODS AND RESULTS Analyses of isogenic monocytic cell lines generated by CRISPR (clustered regularly interspaced short palindromic repeats)-mediated genome editing showed that monocytes with an engineered 15q26.1 CAD risk genotype had reduced FES expression. Small-interfering-RNA-mediated knockdown of FES promoted migration of monocytes and vascular smooth muscle cells. A phosphoproteomics analysis showed that FES knockdown altered phosphorylation of a number of proteins known to regulate cell migration. Single-cell RNA-sequencing revealed that in human atherosclerotic plaques, cells that expressed FES were predominately monocytes/macrophages, although several other cell types including smooth muscle cells also expressed FES. There was an association between the 15q26.1 CAD risk genotype and greater numbers of monocytes/macrophage in human atherosclerotic plaques. An animal model study demonstrated that Fes knockout increased atherosclerotic plaque size and within-plaque content of monocytes/macrophages and smooth muscle cells, in apolipoprotein E-deficient mice fed a high fat diet. CONCLUSIONS We provide substantial evidence that the CAD risk variants at the 15q26.1 locus reduce FES expression in monocytes and that FES depletion results in larger atherosclerotic plaques with more monocytes/macrophages and smooth muscle cells. This study is the first demonstration that FES plays a protective role against atherosclerosis and suggests that enhancing FES activity could be a potentially novel therapeutic approach for CAD intervention.
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Affiliation(s)
- Elisavet Karamanavi
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - David G. McVey
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Sander W. van der Laan
- Central Diagnostic Laboratory, University of Utrecht, The Netherlands (S.W.v.d.L., G.P.)
| | - Paulina J. Stanczyk
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Gavin E. Morris
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Yifan Wang
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Y.W., H.Y., S.Y.)
| | - Wei Yang
- Shantou University Medical College, China (W.Y., J.C., S.Y.)
| | - Kenneth Chan
- William Harvey Research Institute, Queen Mary University of London, United Kingdom (K.C., R.N.P., J.L., X.Z., Q.X.)
| | - Robin N. Poston
- William Harvey Research Institute, Queen Mary University of London, United Kingdom (K.C., R.N.P., J.L., X.Z., Q.X.)
| | - Jun Luo
- William Harvey Research Institute, Queen Mary University of London, United Kingdom (K.C., R.N.P., J.L., X.Z., Q.X.)
| | - Xinmiao Zhou
- William Harvey Research Institute, Queen Mary University of London, United Kingdom (K.C., R.N.P., J.L., X.Z., Q.X.)
| | - Peng Gong
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Peter D. Jones
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Junjun Cao
- Shantou University Medical College, China (W.Y., J.C., S.Y.)
| | - Renata B. Kostogrys
- Department of Human Nutrition, University of Agriculture in Kraków, Poland (R.B.K.)
| | - Tom R. Webb
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Gerard Pasterkamp
- Central Diagnostic Laboratory, University of Utrecht, The Netherlands (S.W.v.d.L., G.P.)
| | - Haojie Yu
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Y.W., H.Y., S.Y.)
| | - Qingzhong Xiao
- William Harvey Research Institute, Queen Mary University of London, United Kingdom (K.C., R.N.P., J.L., X.Z., Q.X.)
| | - Peter A. Greer
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Canada (P.A.G.)
| | - Emma J. Stringer
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
| | - Shu Ye
- Department of Cardiovascular Sciences, University of Leicester, and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (E.K., D.G.M., P.J.S., G.E.M., P.G., P.D.J., T.R.W., E.J.S., N.J.S., S.Y.)
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Y.W., H.Y., S.Y.)
- Shantou University Medical College, China (W.Y., J.C., S.Y.)
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20
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O'Donnell CJ, Bradner JE. Bridging the Gap to Translating Genome-Wide Discoveries Into Therapies to Prevent and Treat Atherosclerotic Cardiovascular Disease. Circulation 2022; 146:930-933. [PMID: 36121912 DOI: 10.1161/circulationaha.122.060998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Christopher J O'Donnell
- Novartis Institutes for BioMedical Research, Cambridge, MA (C.J.O., J.E.B.).,Cardiology Section, VA Boston Healthcare System, Harvard Medical School, MA (C.J.O.)
| | - James E Bradner
- Novartis Institutes for BioMedical Research, Cambridge, MA (C.J.O., J.E.B.)
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