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Yee EJ, Vigil I, Sun Y, Torphy RJ, Schulick RD, Zhu Y. Group XIV C-type lectins: emerging targets in tumor angiogenesis. Angiogenesis 2024; 27:173-192. [PMID: 38468017 PMCID: PMC11021320 DOI: 10.1007/s10456-024-09907-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: 10/25/2023] [Accepted: 01/23/2024] [Indexed: 03/13/2024]
Abstract
C-type lectins, distinguished by a C-type lectin binding domain (CTLD), are an evolutionarily conserved superfamily of glycoproteins that are implicated in a broad range of physiologic processes. The group XIV subfamily of CTLDs are comprised of CD93, CD248/endosialin, CLEC14a, and thrombomodulin/CD141, and have important roles in creating and maintaining blood vessels, organizing extracellular matrix, and balancing pro- and anti-coagulative processes. As such, dysregulation in the expression and downstream signaling pathways of these proteins often lead to clinically relevant pathology. Recently, group XIV CTLDs have been shown to play significant roles in cancer progression, namely tumor angiogenesis and metastatic dissemination. Interest in therapeutically targeting tumor vasculature is increasing and the search for novel angiogenic targets is ongoing. Group XIV CTLDs have emerged as key moderators of tumor angiogenesis and metastasis, thus offering substantial therapeutic promise for the clinic. Herein, we review our current knowledge of group XIV CTLDs, discuss each's role in malignancy and associated potential therapeutic avenues, briefly discuss group XIV CTLDs in the context of two other relevant lectin families, and offer future direction in further elucidating mechanisms by which these proteins function and facilitate tumor growth.
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Affiliation(s)
- Elliott J Yee
- Department of Surgery, University of Colorado Anschutz Medical Campus, 12800 E 19th Avenue, RC1-North, P18-8116, Aurora, CO, 80045, USA
| | - Isaac Vigil
- Department of Surgery, University of Colorado Anschutz Medical Campus, 12800 E 19th Avenue, RC1-North, P18-8116, Aurora, CO, 80045, USA
| | - Yi Sun
- Department of Surgery, University of Colorado Anschutz Medical Campus, 12800 E 19th Avenue, RC1-North, P18-8116, Aurora, CO, 80045, USA
| | - Robert J Torphy
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Richard D Schulick
- Department of Surgery, University of Colorado Anschutz Medical Campus, 12800 E 19th Avenue, RC1-North, P18-8116, Aurora, CO, 80045, USA
| | - Yuwen Zhu
- Department of Surgery, University of Colorado Anschutz Medical Campus, 12800 E 19th Avenue, RC1-North, P18-8116, Aurora, CO, 80045, USA.
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Wu X, Zhang H. Omics Approaches Unveiling the Biology of Human Atherosclerotic Plaques. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:482-498. [PMID: 38280419 PMCID: PMC10988765 DOI: 10.1016/j.ajpath.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/29/2024]
Abstract
Atherosclerosis is a chronic inflammatory disease of the arterial wall, characterized by the buildup of plaques with the accumulation and transformation of lipids, immune cells, vascular smooth muscle cells, and necrotic cell debris. Plaques with collagen-poor thin fibrous caps infiltrated by macrophages and lymphocytes are considered unstable because they are at the greatest risk of rupture and clinical events. However, the current histologic definition of plaque types may not fully capture the complex molecular nature of atherosclerotic plaque biology and the underlying mechanisms contributing to plaque progression, rupture, and erosion. The advances in omics technologies have changed the understanding of atherosclerosis plaque biology, offering new possibilities to improve risk prediction and discover novel therapeutic targets. Genomic studies have shed light on the genetic predisposition to atherosclerosis, and integrative genomic analyses expedite the translation of genomic discoveries. Transcriptomic, proteomic, metabolomic, and lipidomic studies have refined the understanding of the molecular signature of atherosclerotic plaques, aiding in data-driven hypothesis generation for mechanistic studies and offering new prospects for biomarker discovery. Furthermore, advancements in single-cell technologies and emerging spatial analysis techniques have unveiled the heterogeneity and plasticity of plaque cells. This review discusses key omics-based discoveries that have advanced the understanding of human atherosclerotic plaque biology, focusing on insights derived from omics profiling of human atherosclerotic vascular specimens.
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Affiliation(s)
- Xun Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York.
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Wu C, Zheng P, Ma L, Xu C, Hu L, Yang Z, Fei F, Shen Z, Zhang X, Wu Z, Cheng H, Mao W, Ke Y. Protein Tyrosine Phosphatase SHP2 in Macrophages Acts as an Antiatherosclerotic Regulator in Mice. Arterioscler Thromb Vasc Biol 2024; 44:202-217. [PMID: 37942607 DOI: 10.1161/atvbaha.123.319663] [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: 06/07/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Macrophages have versatile roles in atherosclerosis. SHP2 (Src homology 2 containing protein tyrosine phosphatase 2) has been demonstrated to play a critical role in regulating macrophage activation. However, the mechanism of SHP2 regulation of macrophage function in an atherosclerotic microenvironment remains unknown. METHODS APOE (apolipoprotein E) or LDLR (low-density lipoprotein receptor) null mice treated with SHP099 were fed a Western diet for 8 weeks, while Shp2MKO:ApoE-/- or Shp2MKO:Ldlr-/- mice and exo-AAV8-SHP2E76K/ApoE-/- mice were fed a Western diet for 12 weeks. In vitro, levels of proinflammatory factors and phagocytic function were then studied in mouse peritoneal macrophages. RNA sequencing was used to identify PPARγ (peroxisome proliferative activated receptor γ) as the key downstream molecule. A PPARγ agonist was used to rescue the phenotypes observed in SHP2-deleted mice. RESULTS Pharmacological inhibition and selective deletion in macrophages of SHP2 aggravated atherosclerosis in APOE and LDLR null mice with increased plaque macrophages and apoptotic cells. In vitro, SHP2 deficiency in APOE and LDLR null macrophages enhanced proinflammatory polarization and its efferocytosis was dramatically impaired. Conversely, the expression of gain-of-function mutation of SHP2 in mouse macrophages reduced atherosclerosis. The SHP2 agonist lovastatin repressesed macrophage inflammatory activation and enhanced efferocytosis. Mechanistically, RNA sequencing analysis identified PPARγ as a key downstream transcription factor. PPARγ was decreased in macrophages upon SHP2 deletion and inhibition. Importantly, PPARγ agonist decreased atherosclerosis in SHP2 knockout mice, restored efferocytotic defects, and reduced inflammatory activation in SHP2 deleted macrophages. PPARγ was decreased by the ubiquitin-mediated degradation upon SHP2 inhibition or deletion. Finally, we found that SHP2 was downregulated in atherosclerotic vessels. CONCLUSIONS Overall, SHP2 in macrophages was found to act as an antiatherosclerotic regulator by stabilizing PPARγ in APOE/LDLR null mice.
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Affiliation(s)
- Chenxia Wu
- Department of Cardiology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China (C.W., L.H.)
- Key Laboratory of Integrative Chinese and Western Medicine for the Diagnosis and Treatment of Circulatory Diseases of Zhejiang Province, Hangzhou, China (C.W., L.H., W.M.)
| | - Peiyao Zheng
- Department of Pathology and Pathophysiology and Department of Cardiology at Sir Run Run Shaw Hospital (P.Z., C.X., Z.Y., H.C.), Zhejiang University School of Medicine, Hangzhou, China
| | - Lan Ma
- Department of Cardiology, Affiliated Hospital of Nantong University, China (L.M.)
| | - Chen Xu
- Department of Pathology and Pathophysiology and Department of Cardiology at Sir Run Run Shaw Hospital (P.Z., C.X., Z.Y., H.C.), Zhejiang University School of Medicine, Hangzhou, China
| | - Luoxia Hu
- Department of Cardiology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China (C.W., L.H.)
- Key Laboratory of Integrative Chinese and Western Medicine for the Diagnosis and Treatment of Circulatory Diseases of Zhejiang Province, Hangzhou, China (C.W., L.H., W.M.)
| | - Zhiyi Yang
- Department of Pathology and Pathophysiology and Department of Cardiology at Sir Run Run Shaw Hospital (P.Z., C.X., Z.Y., H.C.), Zhejiang University School of Medicine, Hangzhou, China
| | - Fan Fei
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China (F.F.)
| | - Zhuxia Shen
- Department of Cardiology, Jing'an District Centre Hospital of Shanghai, Fudan University, China (Z.S.)
| | - Xue Zhang
- Department of Pathology and Pathophysiology and Department of Respiratory Medicine at Sir Run Run Shaw Hospital (X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Ziheng Wu
- Department of Vascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China (Z.W.)
| | - Hongqiang Cheng
- Department of Pathology and Pathophysiology and Department of Cardiology at Sir Run Run Shaw Hospital (P.Z., C.X., Z.Y., H.C.), Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Mao
- Department of Pathology and Pathophysiology and Department of Cardiology at Sir Run Run Shaw Hospital (P.Z., C.X., Z.Y., H.C.), Zhejiang University School of Medicine, Hangzhou, China
- Department of Cardiology, Affiliated Zhejiang Hospital (W.M.), Zhejiang University School of Medicine, Hangzhou, China
| | - Yuehai Ke
- Department of Pathology and Pathophysiology and Department of Respiratory Medicine at Sir Run Run Shaw Hospital (X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
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Cheng J, Cheng M, Lusis AJ, Yang X. Gene Regulatory Networks in Coronary Artery Disease. Curr Atheroscler Rep 2023; 25:1013-1023. [PMID: 38008808 DOI: 10.1007/s11883-023-01170-7] [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] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
PURPOSE OF REVIEW Coronary artery disease is a complex disorder and the leading cause of mortality worldwide. As technologies for the generation of high-throughput multiomics data have advanced, gene regulatory network modeling has become an increasingly powerful tool in understanding coronary artery disease. This review summarizes recent and novel gene regulatory network tools for bulk tissue and single cell data, existing databases for network construction, and applications of gene regulatory networks in coronary artery disease. RECENT FINDINGS New gene regulatory network tools can integrate multiomics data to elucidate complex disease mechanisms at unprecedented cellular and spatial resolutions. At the same time, updates to coronary artery disease expression data in existing databases have enabled researchers to build gene regulatory networks to study novel disease mechanisms. Gene regulatory networks have proven extremely useful in understanding CAD heritability beyond what is explained by GWAS loci and in identifying mechanisms and key driver genes underlying disease onset and progression. Gene regulatory networks can holistically and comprehensively address the complex nature of coronary artery disease. In this review, we discuss key algorithmic approaches to construct gene regulatory networks and highlight state-of-the-art methods that model specific modes of gene regulation. We also explore recent applications of these tools in coronary artery disease patient data repositories to understand disease heritability and shared and distinct disease mechanisms and key driver genes across tissues, between sexes, and between species.
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Grants
- DK120342, HL148577, and HL147883 (AJL). NS111378, NS117148, HL147883 (XY) NIH HHS
- DK120342, HL148577, and HL147883 (AJL). NS111378, NS117148, HL147883 (XY) NIH HHS
- DK120342, HL148577, and HL147883 (AJL). NS111378, NS117148, HL147883 (XY) NIH HHS
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Affiliation(s)
- Jenny Cheng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Michael Cheng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Aldons J Lusis
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, 650 Charles E Young Drive South, Los Angeles, CA, 90095, USA.
- Departments of Human Genetics & Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
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Zhang G, Cui X, Qin Z, Wang Z, Lu Y, Xu Y, Xu S, Tang L, Zhang L, Liu G, Wang X, Zhang J, Tang J. Atherosclerotic plaque vulnerability quantification system for clinical and biological interpretability. iScience 2023; 26:107587. [PMID: 37664595 PMCID: PMC10470306 DOI: 10.1016/j.isci.2023.107587] [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: 09/30/2022] [Revised: 05/02/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Acute myocardial infarction dominates coronary artery disease mortality. Identifying bio-signatures for plaque destabilization and rupture is important for preventing the transition from coronary stability to instability and the occurrence of thrombosis events. This computational systems biology study enrolled 2,235 samples from 22 independent bulks cohorts and 14 samples from two single-cell cohorts. A machine-learning integrative program containing nine learners was developed to generate a warning classifier linked to atherosclerotic plaque vulnerability signature (APVS). The classifier displays the reliable performance and robustness for distinguishing ST-elevation myocardial infarction from chronic coronary syndrome at presentation, and revealed higher accuracy to 33 pathogenic biomarkers. We also developed an APVS-based quantification system (APVSLevel) for comprehensively quantifying atherosclerotic plaque vulnerability, empowering early-warning capabilities, and accurate assessment of atherosclerosis severity. It unraveled the multidimensional dysregulated mechanisms at high resolution. This study provides a potential tool for macro-level differential diagnosis and evaluation of subtle genetic pathological changes in atherosclerosis.
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Affiliation(s)
- Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Xiaolin Cui
- School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Zhen Qin
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Zeyu Wang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Yongzheng Lu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Yanyan Xu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Shuai Xu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Laiyi Tang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Li Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Gangqiong Liu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Xiaofang Wang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Jinying Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
| | - Junnan Tang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, Henan 450052, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, Henan 450052, China
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Jurrjens AW, Seldin MM, Giles C, Meikle PJ, Drew BG, Calkin AC. The potential of integrating human and mouse discovery platforms to advance our understanding of cardiometabolic diseases. eLife 2023; 12:e86139. [PMID: 37000167 PMCID: PMC10065800 DOI: 10.7554/elife.86139] [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: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Cardiometabolic diseases encompass a range of interrelated conditions that arise from underlying metabolic perturbations precipitated by genetic, environmental, and lifestyle factors. While obesity, dyslipidaemia, smoking, and insulin resistance are major risk factors for cardiometabolic diseases, individuals still present in the absence of such traditional risk factors, making it difficult to determine those at greatest risk of disease. Thus, it is crucial to elucidate the genetic, environmental, and molecular underpinnings to better understand, diagnose, and treat cardiometabolic diseases. Much of this information can be garnered using systems genetics, which takes population-based approaches to investigate how genetic variance contributes to complex traits. Despite the important advances made by human genome-wide association studies (GWAS) in this space, corroboration of these findings has been hampered by limitations including the inability to control environmental influence, limited access to pertinent metabolic tissues, and often, poor classification of diseases or phenotypes. A complementary approach to human GWAS is the utilisation of model systems such as genetically diverse mouse panels to study natural genetic and phenotypic variation in a controlled environment. Here, we review mouse genetic reference panels and the opportunities they provide for the study of cardiometabolic diseases and related traits. We discuss how the post-GWAS era has prompted a shift in focus from discovery of novel genetic variants to understanding gene function. Finally, we highlight key advantages and challenges of integrating complementary genetic and multi-omics data from human and mouse populations to advance biological discovery.
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Affiliation(s)
- Aaron W Jurrjens
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, United States
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Brian G Drew
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - Anna C Calkin
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
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Identification of Cardiovascular Disease-Related Genes Based on the Co-Expression Network Analysis of Genome-Wide Blood Transcriptome. Cells 2022; 11:cells11182867. [PMID: 36139449 PMCID: PMC9496853 DOI: 10.3390/cells11182867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 09/10/2022] [Indexed: 12/02/2022] Open
Abstract
Inference of co-expression network and identification of disease-related modules and gene sets can help us understand disease-related molecular pathophysiology. We aimed to identify a cardiovascular disease (CVD)-related transcriptomic signature, specifically, in peripheral blood tissue, based on differential expression (DE) and differential co-expression (DcoE) analyses. Publicly available blood sample datasets for coronary artery disease (CAD) and acute coronary syndrome (ACS) statuses were integrated to establish a co-expression network. A weighted gene co-expression network analysis was used to construct modules that include genes with highly correlated expression values. The DE criterion is a linear regression with module eigengenes for module-specific genes calculated from principal component analysis and disease status as the dependent and independent variables, respectively. The DcoE criterion is a paired t-test for intramodular connectivity between disease and matched control statuses. A total of 21 and 23 modules were established from CAD status- and ACS-related datasets, respectively, of which six modules per disease status (i.e., obstructive CAD and ACS) were selected based on the DE and DcoE criteria. For each module, gene–gene interactions with extremely high correlation coefficients were individually selected under the two conditions. Genes displaying a significant change in the number of edges (gene–gene interaction) were selected. A total of 6, 10, and 7 genes in each of the three modules were identified as potential CAD status-related genes, and 14 and 8 genes in each of the two modules were selected as ACS-related genes. Our study identified gene sets and genes that were dysregulated in CVD blood samples. These findings may contribute to the understanding of CVD pathophysiology.
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Effects of ACTH-Induced Long-Term Hypercortisolism on the Transcriptome of Canine Visceral Adipose Tissue. Vet Sci 2022; 9:vetsci9060250. [PMID: 35737302 PMCID: PMC9228614 DOI: 10.3390/vetsci9060250] [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: 03/16/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
Cushing’s syndrome, or hypercortisolism (HC), a common endocrinopathy in adult dogs, is caused by chronic hypercortisolemia. Among different metabolic disorders, this syndrome is associated with enhanced subcutaneous lipolysis and visceral adiposity. However, effects of HC in adipose tissue, especially regarding visceral adipose tissue (VAT), are still poorly understood. Herein, the transcriptomic effects of chronic HC on VAT of dogs were evaluated. For this, subcutaneously implanted ACTH-releasing pumps were used, followed by deep RNA sequencing of the canine VAT. Prolonged HC seems to affect a plethora of regulatory mechanisms in VAT of treated dogs, with 1190 differentially expressed genes (DEGs, p and FDR < 0.01) being found. The 691 downregulated DEGs were mostly associated with functional terms like cell adhesion and migration, intracellular signaling, immune response, extracellular matrix and angiogenesis. Treatment also appeared to modulate local glucocorticoid and insulin signaling and hormonal sensitivity, and several factors, e.g., TIMP4, FGF1, CCR2, CXCR4 and HSD11B1/2, were identified as possible important players in the glucocorticoid-related expansion of VAT. Modulation of their function during chronic HC might present interesting targets for further clinical studies. Similarities in the effects of chronic HC on VAT of dogs and humans are highlighted.
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Sonawane AR, Aikawa E, Aikawa M. Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:873582. [PMID: 35665246 PMCID: PMC9160390 DOI: 10.3389/fcvm.2022.873582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/19/2022] [Indexed: 01/18/2023] Open
Abstract
Cardiovascular diseases (CVD) are diverse disorders affecting the heart and vasculature in millions of people worldwide. Like other fields, CVD research has benefitted from the deluge of multiomics biomedical data. Current CVD research focuses on disease etiologies and mechanisms, identifying disease biomarkers, developing appropriate therapies and drugs, and stratifying patients into correct disease endotypes. Systems biology offers an alternative to traditional reductionist approaches and provides impetus for a comprehensive outlook toward diseases. As a focus area, network medicine specifically aids the translational aspect of in silico research. This review discusses the approach of network medicine and its application to CVD research.
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Affiliation(s)
- Abhijeet Rajendra Sonawane
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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10
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El Hadi C, Ayoub G, Bachir Y, Haykal M, Jalkh N, Kourie HR. Polygenic and Network-Based Studies in Risk Identification and Demystification of cancer. Expert Rev Mol Diagn 2022; 22:427-438. [PMID: 35400274 DOI: 10.1080/14737159.2022.2065195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Diseases were initially thought to be the consequence of a single gene mutation. Advances in DNA sequencing tools and our understanding of gene behavior have revealed that complex diseases, such as cancer, are the product of genes cooperating with each other and with their environment in orchestrated communication networks. Seeing that the function of individual genes is still used to analyze cancer, the shift to using functionally interacting groups of genes as a new unit of study holds promise for demystifying cancer. AREAS COVERED The literature search focused on three types of cancer, namely breast, lung, and prostate, but arguments from other cancers were also included. The aim was to prove that multigene analyses can accurately predict and prognosticate cancer risk, subtype cancer for more personalized and effective treatments, and discover anti-cancer therapies. Computational intelligence is being harnessed to analyze this type of data and is proving indispensable to scientific progress. EXPERT OPINION In the future, comprehensive profiling of all kinds of patient data (e.g., serum molecules, environmental exposures) can be used to build universal networks that should help us elucidate the molecular mechanisms underlying diseases and provide appropriate preventive measures, ensuring lifelong health and longevity.
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Affiliation(s)
| | - George Ayoub
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Yara Bachir
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Michèle Haykal
- Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Technology and Health division, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Department of Hematology-Oncology, Hotel Dieu de France University Hospital, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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Salgado Pardo JI, Delgado Bermejo JV, González Ariza A, León Jurado JM, Marín Navas C, Iglesias Pastrana C, Martínez Martínez MDA, Navas González FJ. Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats ( Capra hircus). Animals (Basel) 2022; 12:ani12080988. [PMID: 35454235 PMCID: PMC9026325 DOI: 10.3390/ani12080988] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary During the present decade, highly selected caprine farming has increased in popularity due to the hardiness and adaptability inherent to goats. Recent advances in genetics have enabled the improvement in goat selection efficiency. The present review explores how genetic technologies have been applied to the goat-farming sector in the last century. The main candidate genes related to economically relevant traits are reported. The major source of income in goat farming derives from the sale of milk and meat. Consequently, yield and quality must be specially considered. Meat-related traits were evaluated considering three functional groups (weight gain, carcass quality and fat profile). Milk traits were assessed in three additional functional groups (milk production, protein and fat content). Abstract Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in genomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability.
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Affiliation(s)
- Jose Ignacio Salgado Pardo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - José Manuel León Jurado
- Agropecuary Provincial Center of Córdoba, Provincial Council of Córdoba, 14014 Córdoba, Spain;
| | - Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Carlos Iglesias Pastrana
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - María del Amparo Martínez Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
- Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, 14004 Córdoba, Spain
- Correspondence: ; Tel.: +34-63-853-5046 (ext. 621262)
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Liu H, Xiang C, Wang Z, Song Y. Identification of Potential Ferroptosis-Related Biomarkers and Immune Infiltration in Human Coronary Artery Atherosclerosis. Int J Gen Med 2022; 15:2979-2990. [PMID: 35308568 PMCID: PMC8932925 DOI: 10.2147/ijgm.s346482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Ferroptosis is a specific subtype of programmed cell death, which plays an essential role in the immune-associated disease, atherosclerosis (AS). The purpose of this study was to identify potential ferroptosis-related gene biomarkers and its association with immune infiltration characteristics in atherosclerosis with bioinformatics methods. Methods Differentially expressed genes (DEGs) between AS and control groups were screened from GSE40231, analyzed for functional enrichment and then intersected with ferroptosis-related genes. Then, a random forest model was constructed based on these differentially expressed ferroptosis-related genes (DE-FRGs) and validated with dataset GSE132651. The performance of the models was evaluated with the area under receiver operating characteristic curves (AUC). Finally, we analyzed the correlation between DE-FRGs above and the characteristics of immune infiltration via CIBERSORT method. Results Six DE-FRGs (IL6, ANGPTL7, CDKN1A, AKR1C3, NOX4 and VLDLR) were detected based on dataset of GSE40231. Furthermore, a random forest model was constructed based on them with a compelling diagnostic performance of AUC = 0.8974 in the validation dataset GSE132651. In addition, the proportion of follicular helper T (Tfh) cells was significantly higher in AS group (P < 0.001). And we found significant correlation relationship between Tfh and expression level of ANGPTL7 (R = 0.35, P < 0.01), CDKN1A (R = 0.4, P < 0.0001), AKR1C3 (R = 0.64, P < 0.0001), NOX4 (R = 0.32, P < 0.01) and VLDLR (R = −0.43, P < 0.0001). Conclusion This study identified 6 DE-FRGs and validated a predicted model for the early prediction of AS, which also proved the close relationship between ferroptosis and immunity in the pathogenesis of AS.
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Affiliation(s)
- Hui Liu
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Chunhua Xiang
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Zhaohui Wang
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Yi Song
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
- Correspondence: Yi Song, Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China, Tel +86-15629054511, Email
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Slenders L, Tessels DE, van der Laan SW, Pasterkamp G, Mokry M. The Applications of Single-Cell RNA Sequencing in Atherosclerotic Disease. Front Cardiovasc Med 2022; 9:826103. [PMID: 35211529 PMCID: PMC8860895 DOI: 10.3389/fcvm.2022.826103] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 02/05/2023] Open
Abstract
Atherosclerosis still is the primary cause of death worldwide. Our characterization of the atherosclerotic lesion is mainly rooted in definitions based on pathological descriptions. We often speak in absolutes regarding plaque phenotypes: vulnerable vs. stable plaques or plaque rupture vs. plaque erosion. By focusing on these concepts, we may have oversimplified the atherosclerotic disease and its mechanisms. The widely used definitions of pathology-based plaque phenotypes can be fine-tuned with observations made with various -omics techniques. Recent advancements in single-cell transcriptomics provide the opportunity to characterize the cellular composition of the atherosclerotic plaque. This additional layer of information facilitates the in-depth characterization of the atherosclerotic plaque. In this review, we discuss the impact that single-cell transcriptomics may exert on our current understanding of atherosclerosis.
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Affiliation(s)
- Lotte Slenders
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, Netherlands
| | - Daniëlle E Tessels
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, Netherlands
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, Netherlands
| | - Michal Mokry
- Central Diagnostics Laboratory, University Medical Center Utrecht, University Utrecht, Utrecht, Netherlands.,Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University Utrecht, Utrecht, Netherlands
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Abstract
During the past decade, genome-wide association studies (GWAS) have transformed our understanding of many heritable traits. Three recent large-scale GWAS meta-analyses now further markedly expand the knowledge on coronary artery disease (CAD) genetics in doubling the number of loci with genome-wide significant signals. Here, we review the unprecedented discoveries of CAD GWAS on low-frequency variants, underrepresented populations, sex differences and integrated polygenic risk. We present the milestones of CAD GWAS and post-GWAS studies from 2007 to 2021, and the trend in identification of variants with smaller odds ratio by year due to the increasing sample size. We compile the 321 CAD loci discovered thus far and classify candidate genes as well as distinct functional pathways on the road to indepth biological investigation and identification of novel treatment targets. We draw attention to systems genetics in integrating these loci into gene regulatory networks within and across tissues. We review the traits, biomarkers and diseases scrutinized by Mendelian randomization studies for CAD. Finally, we discuss the potentials and concerns of polygenic scores in predicting CAD risk in patient care as well as future directions of GWAS and post-GWAS studies in the field of precision medicine.
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Affiliation(s)
- Zhifen Chen
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany.,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany.,Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
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15
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Jeong K, Murphy JM, Kim JH, Campbell PM, Park H, Rodriguez Y, Choi C, Kim JS, Park S, Kim HJ, Scammell JG, Weber DS, Honkanen RE, Schlaepfer DD, Ahn EYE, Lim STS. FAK Activation Promotes SMC Dedifferentiation via Increased DNA Methylation in Contractile Genes. Circ Res 2021; 129:e215-e233. [PMID: 34702049 DOI: 10.1161/circresaha.121.319066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rationale: Vascular smooth muscle cells (SMCs) exhibit remarkable plasticity and can undergo dedifferentiation upon pathological stimuli associated with disease and interventions. Objective: Although epigenetic changes are critical in SMC phenotype switching, a fundamental regulator that governs the epigenetic machineries regulating the fate of SMC phenotype has not been elucidated. Methods and Results: Using SMCs, mouse models, and human atherosclerosis specimens, we found that focal adhesion kinase (FAK) activation elicits SMC dedifferentiation by stabilizing DNA methyltransferase 3A (DNMT3A). FAK in SMCs is activated in the cytoplasm upon serum stimulation in vitro or vessel injury and active FAK prevents DNMT3A from nuclear FAK-mediated degradation. However, pharmacological or genetic FAK catalytic inhibition forced FAK nuclear localization, which reduced DNMT3A protein via enhanced ubiquitination and proteasomal degradation. Reduced DNMT3A protein led to DNA hypomethylation in contractile gene promoters, which increased SMC contractile protein expression. RNA sequencing identified SMC contractile genes as a foremost upregulated group by FAK inhibition from injured femoral artery samples compared to vehicle group. DNMT3A knockdown in injured arteries reduced DNA methylation and enhanced contractile gene expression supports the notion that nuclear FAK-mediated DNMT3A degradation via E3 ligase TRAF6 drives differentiation of SMCs. Furthermore, we observed that SMCs of human atherosclerotic lesions exhibited decreased nuclear FAK, which was associated with increased DNMT3A levels and decreased contractile gene expression. Conclusions: This study reveals that nuclear FAK induced by FAK catalytic inhibition specifically suppresses DNMT3A expression in injured vessels resulting in maintaining SMC differentiation by promoting the contractile gene expression. Thus, FAK inhibitors may provide a new treatment option to block SMC phenotypic switching during vascular remodeling and atherosclerosis.
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Affiliation(s)
- Kyuho Jeong
- Biochemistry and Molecular Biology, University of South Alabama College of Medicine, UNITED STATES
| | - James M Murphy
- Biochemistry and Molecular Biology, University of South Alabama College of Medicine, UNITED STATES
| | - Jung-Hyun Kim
- Biochemistry and Molecular Biology, University of South Alabama College of Medicine, UNITED STATES
| | | | - Hyeonsoo Park
- Biochemistry and Molecular Biology, University of South Alabama College of Medicine, KOREA, REPUBLIC OF
| | - Yelitza Rodriguez
- Biochemistry and Molecular Biology, University of South Alabama College of Medicine, UNITED STATES
| | - Chungsik Choi
- Physiology, University of South Alabama College of Medicine, UNITED STATES
| | - Jun-Sub Kim
- Biotechnology, Korea National University of Transportation, KOREA, REPUBLIC OF
| | - Sangwon Park
- Pharmacology, Gyeongsang National University, KOREA, REPUBLIC OF
| | - Hyun Joon Kim
- Anatomy and Convergence Medical Sciences, Gyeongsang National University
| | - Jonathan G Scammell
- Comparative Medicine, University of South Alabama College of Medicine, UNITED STATES
| | - David S Weber
- Physiology and Cell Biology, University of South Alabama College of Medicine, UNITED STATES
| | - Richard E Honkanen
- Biochemistry and Molecualr Biology, University of South Alabama College of Medicine, UNITED STATES
| | - David D Schlaepfer
- Obstetrics, Gynecology, and Reproductive Medicine, University of California, San Diego Moores Cancer Center, UNITED STATES
| | | | - Ssang-Taek Steve Lim
- Biochemistry and Molecular Biology, University of South Alabama College of Medicine, UNITED STATES
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Lee T, Lee H. Identification of Disease-Related Genes That Are Common between Alzheimer's and Cardiovascular Disease Using Blood Genome-Wide Transcriptome Analysis. Biomedicines 2021; 9:biomedicines9111525. [PMID: 34829754 PMCID: PMC8614900 DOI: 10.3390/biomedicines9111525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/09/2023] Open
Abstract
Accumulating evidence has suggested a shared pathophysiology between Alzheimer’s disease (AD) and cardiovascular disease (CVD). Based on genome-wide transcriptomes, specifically those of blood samples, we identify the shared disease-related signatures between AD and CVD. In addition to gene expressions in blood, the following prior knowledge were utilized to identify several candidate disease-related gene (DRG) sets: protein–protein interactions, transcription factors, disease–gene relationship databases, and single nucleotide polymorphisms. We selected the respective DRG sets for AD and CVD that show a high accuracy for disease prediction in bulk and single-cell gene expression datasets. Then, gene regulatory networks (GRNs) were constructed from each of the AD and CVD DRG sets to identify the upstream regulating genes. Using the GRNs, we identified two common upstream genes (GPBP1 and SETDB2) between the AD and CVD GRNs. In summary, this study has identified the potential AD- and CVD-related genes and common hub genes between these sets, which may help to elucidate the shared mechanisms between these two diseases.
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Affiliation(s)
- Taesic Lee
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
- Department of Family Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Korea
| | - Hyunju Lee
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Correspondence: ; Tel.: +82-62-715-2213
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Márquez AB, van der Vorst EPC, Maas SL. Key Chemokine Pathways in Atherosclerosis and Their Therapeutic Potential. J Clin Med 2021; 10:3825. [PMID: 34501271 PMCID: PMC8432216 DOI: 10.3390/jcm10173825] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022] Open
Abstract
The search to improve therapies to prevent or treat cardiovascular diseases (CVDs) rages on, as CVDs remain a leading cause of death worldwide. Here, the main cause of CVDs, atherosclerosis, and its prevention, take center stage. Chemokines and their receptors have long been known to play an important role in the pathophysiological development of atherosclerosis. Their role extends from the initiation to the progression, and even the potential regression of atherosclerotic lesions. These important regulators in atherosclerosis are therefore an obvious target in the development of therapeutic strategies. A plethora of preclinical studies have assessed various possibilities for targeting chemokine signaling via various approaches, including competitive ligands and microRNAs, which have shown promising results in ameliorating atherosclerosis. Developments in the field also include detailed imaging with tracers that target specific chemokine receptors. Lastly, clinical trials revealed the potential of various therapies but still require further investigation before commencing clinical use. Although there is still a lot to be learned and investigated, it is clear that chemokines and their receptors present attractive yet extremely complex therapeutic targets. Therefore, this review will serve to provide a general overview of the connection between various chemokines and their receptors with atherosclerosis. The different developments, including mouse models and clinical trials that tackle this complex interplay will also be explored.
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Affiliation(s)
- Andrea Bonnin Márquez
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, 52074 Aachen, Germany;
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52074 Aachen, Germany
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6229 ER Maastricht, The Netherlands
| | - Emiel P. C. van der Vorst
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, 52074 Aachen, Germany;
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52074 Aachen, Germany
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6229 ER Maastricht, The Netherlands
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80336 Munich, Germany
| | - Sanne L. Maas
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, 52074 Aachen, Germany;
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52074 Aachen, Germany
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Qian C, Jing Y, Xia M, Ye Q. Comprehensive analysis of dysregulated genes associated with atherosclerotic plaque destabilization. Exp Biol Med (Maywood) 2021; 246:2487-2494. [PMID: 34308657 DOI: 10.1177/15353702211033247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Atherosclerotic plaque destabilization is a dominating cause of acute cardiovascular events such as myocardial infarction and stroke. This study aims to identify genetic biomarkers related to atherosclerotic plaque destabilization using bioinformatics. Three transcriptome datasets of human carotid atherosclerotic plaque samples were downloaded from ArrayExpress and Gene Expression Omnibus databases, including E-MATB-2055, E-TABM-190, and GSE120521. With Robust Rank Aggregation analysis, we documented 46 differentially expressed genes between stable and unstable/ruptured plaques. Functional enrichment analysis using DAVID tool demonstrated that these genes were mainly related to biological functions such as extracellular matrix disassembly, collagen catabolic process, response to mechanical stimulus, and PPAR signaling pathway. A protein-protein interaction network for the differentially expressed genes was constructed, and eight pivotal genes (ITGAM, MMP9, PLAUR, CCR1, CD163, CD36, ADAM8, and IL1RN) were obtained from the network with a connective degree > 5. The expression patterns of these hub differentially expressed genes could be verified in atherosclerotic plaque samples with intraplaque hemorrhage. Using gene set variation analysis, the eight genes were integrated to generate an atherosclerotic plaque destabilization score, which showed a high performance in not only discriminating individuals with myocardial infarction from those with stable coronary illness, but also in predicting future acute cardiovascular events in atherosclerotic patients. In conclusion, the findings of this study will enhance our knowledge on the pathological mechanisms involved in atherosclerotic plaque destabilization, and provide potential gene biomarkers for risk stratification of patients with atherosclerotic cardiovascular disease.
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Affiliation(s)
- Cheng Qian
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Yuling Jing
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Meng Xia
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Qiang Ye
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
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Targeting the chemokine network in atherosclerosis. Atherosclerosis 2021; 330:95-106. [PMID: 34247863 DOI: 10.1016/j.atherosclerosis.2021.06.912] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/07/2021] [Accepted: 06/24/2021] [Indexed: 01/31/2023]
Abstract
Chemokines and their receptors represent a potential target for immunotherapy in chronic inflammation. They comprise a large family of cytokines with chemotactic activity, and their cognate receptors are expressed on all cells of the body. This network dictates leukocyte recruitment and activation, angiogenesis, cell proliferation and maturation. Dysregulation of chemokine and chemokine receptor expression as well as function participates in many pathologies including cancer, autoimmune diseases and chronic inflammation. In atherosclerosis, a lipid-driven chronic inflammation of middle-sized and large arteries, chemokines and their receptors participates in almost all stages of the disease from initiation of fatty streaks to mature atherosclerotic plaque formation. Atherosclerosis and its complications are the main driver of mortality and morbidity in cardiovascular diseases (CVD). Hence, exploring new fields of therapeutic targeting of atherosclerosis is of key importance. This review gives an overview of the recent advances on the role of key chemokines and chemokine receptors in atherosclerosis, addresses chemokine-based biomarkers at biochemical, imaging and genetic level in human studies, and highlights the clinial trials targeting atherosclerosis.
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20
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Stein S, Weber J, Nusser-Stein S, Pahla J, Zhang HE, Mohammed SA, Oppi S, Gaul DS, Paneni F, Tailleux A, Staels B, von Meyenn F, Ruschitzka F, Gorrell MD, Lüscher TF, Matter CM. Deletion of fibroblast activation protein provides atheroprotection. Cardiovasc Res 2021; 117:1060-1069. [PMID: 32402085 DOI: 10.1093/cvr/cvaa142] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/30/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
AIMS Fibroblast activation protein (FAP) is upregulated at sites of tissue remodelling including chronic arthritis, solid tumours, and fibrotic hearts. It has also been associated with human coronary atherosclerotic plaques. Yet, the causal role of FAP in atherosclerosis remains unknown. To investigate the cause-effect relationship of endogenous FAP in atherogenesis, we assessed the effects of constitutive Fap deletion on plaque formation in atherosclerosis-prone apolipoprotein E (Apoe) or low-density lipoprotein receptor (Ldlr) knockout mice. METHODS AND RESULTS Using en face analyses of thoraco-abdominal aortae and aortic sinus cross-sections, we demonstrate that Fap deficiency decreased plaque formation in two atherosclerotic mouse models (-46% in Apoe and -34% in Ldlr knockout mice). As a surrogate of plaque vulnerability fibrous cap thickness was used; it was increased in Fap-deficient mice, whereas Sirius red staining demonstrated that total collagen content remained unchanged. Using polarized light, atherosclerotic lesions from Fap-deficient mice displayed increased FAP targets in terms of enhanced collagen birefringence in plaques and increased pre-COL3A1 expression in aortic lysates. Analyses of the Stockholm Atherosclerosis Gene Expression data revealed that FAP expression was increased in human atherosclerotic compared to non-atherosclerotic arteries. CONCLUSIONS Our data provide causal evidence that constitutive Fap deletion decreases progression of experimental atherosclerosis and increases features of plaque stability with decreased collagen breakdown. Thus, inhibition of FAP expression or activity may not only represent a promising therapeutic target in atherosclerosis but appears safe at the experimental level for FAP-targeted cancer therapies.
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MESH Headings
- Animals
- Aorta/enzymology
- Aorta/pathology
- Aortic Diseases/enzymology
- Aortic Diseases/genetics
- Aortic Diseases/pathology
- Aortic Diseases/prevention & control
- Atherosclerosis/enzymology
- Atherosclerosis/genetics
- Atherosclerosis/pathology
- Atherosclerosis/prevention & control
- Case-Control Studies
- Collagen/genetics
- Collagen/metabolism
- Disease Models, Animal
- Endopeptidases/deficiency
- Endopeptidases/genetics
- Fibrosis
- Gene Deletion
- Humans
- Lipids/blood
- Male
- Membrane Proteins/deficiency
- Membrane Proteins/genetics
- Mice, Inbred C57BL
- Mice, Knockout, ApoE
- Muscle, Smooth, Vascular/enzymology
- Muscle, Smooth, Vascular/pathology
- Plaque, Atherosclerotic
- Proteome
- Receptors, LDL/deficiency
- Receptors, LDL/genetics
- Transcriptome
- Vascular Remodeling
- Mice
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Affiliation(s)
- Sokrates Stein
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland
| | - Julien Weber
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Stefanie Nusser-Stein
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Jürgen Pahla
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Hui E Zhang
- Liver Enzymes in Metabolism and Inflammation Program, Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, NSW 2050, Liver Enzymes in Metabolism and Inflammation Program, Centenary Institute, Australia
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Sara Oppi
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Daniel S Gaul
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland
- Department of Research and Education, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland
| | - Anne Tailleux
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, Lille, 42 Rue Paul Duez, 59000 Lille, France
| | - Bart Staels
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, Lille, 42 Rue Paul Duez, 59000 Lille, France
| | - Ferdinand von Meyenn
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Schorenstrasse 16 CH-8603 Schwerzenbach, Switzerland
| | - Frank Ruschitzka
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland
| | - Mark D Gorrell
- Liver Enzymes in Metabolism and Inflammation Program, Centenary Institute, The University of Sydney Faculty of Medicine and Health, Sydney, NSW 2050, Liver Enzymes in Metabolism and Inflammation Program, Centenary Institute, Australia
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
- Cardiology, Royal Brompton & Harefield Hospital Trust, Imperial College London, 77 Wimpole Street, London SW3 6NP, UK
| | - Christian M Matter
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, CH-8952 Schlieren, Switzerland
- Department of Cardiology, University Heart Center Zurich, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland
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21
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Hartman RJG, Owsiany K, Ma L, Koplev S, Hao K, Slenders L, Civelek M, Mokry M, Kovacic JC, Pasterkamp G, Owens G, Björkegren JLM, den Ruijter HM. Sex-Stratified Gene Regulatory Networks Reveal Female Key Driver Genes of Atherosclerosis Involved in Smooth Muscle Cell Phenotype Switching. Circulation 2021; 143:713-726. [PMID: 33499648 PMCID: PMC7930467 DOI: 10.1161/circulationaha.120.051231] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Although sex differences in coronary artery disease are widely accepted with women developing more stable atherosclerosis than men, the underlying pathobiology of such differences remains largely unknown. In coronary artery disease, recent integrative systems biological studies have inferred gene regulatory networks (GRNs). Within these GRNs, key driver genes have shown great promise but have thus far been unidentified in women. METHODS We generated sex-specific GRNs of the atherosclerotic arterial wall in 160 women and age-matched men in the STARNET study (Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task). We integrated the female GRNs with single-cell RNA-sequencing data of the human atherosclerotic plaque and single-cell RNA sequencing of advanced atherosclerotic lesions from wild type and Klf4 knockout atherosclerotic smooth muscle cell (SMC) lineage-tracing mice. RESULTS By comparing sex-specific GRNs, we observed clear sex differences in network activity within the atherosclerotic tissues. Genes more active in women were associated with mesenchymal cells and endothelial cells, whereas genes more active in men were associated with the immune system. We determined that key drivers of GRNs active in female coronary artery disease were predominantly found in (SMCs by single-cell sequencing of the human atherosclerotic plaques, and higher expressed in female plaque SMCs, as well. To study the functions of these female SMC key drivers in atherosclerosis, we examined single-cell RNA sequencing of advanced atherosclerotic lesions from wild type and Klf4 knockout atherosclerotic SMC lineage-tracing mice. The female key drivers were found to be expressed by phenotypically modulated SMCs and affected by Klf4, suggesting that sex differences in atherosclerosis involve phenotypic switching of plaque SMCs. CONCLUSIONS Our systems approach provides novel insights into molecular mechanisms that underlie sex differences in atherosclerosis. To discover sex-specific therapeutic targets for atherosclerosis, an increased emphasis on sex-stratified approaches in the analysis of multi-omics data sets is warranted.
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Affiliation(s)
- Robin J G Hartman
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (R.J.G.H., M.M., H.M.d.R.)
| | - Katie Owsiany
- Robert M. Berne Cardiovascular Research Center (K.O., G.O.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Department of Biochemistry and Molecular Genetics (K.O.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Lijiang Ma
- University of Virginia-School of Medicine, Charlottesville. Department of Genetics and Genomic Sciences (L.M., S.K., K.H., J.L.M.B.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Simon Koplev
- University of Virginia-School of Medicine, Charlottesville. Department of Genetics and Genomic Sciences (L.M., S.K., K.H., J.L.M.B.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Ke Hao
- University of Virginia-School of Medicine, Charlottesville. Department of Genetics and Genomic Sciences (L.M., S.K., K.H., J.L.M.B.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Icahn Institute of Genomics and Multiscale Biology (K.H., J.L.M.B.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Lotte Slenders
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, The Netherlands (L.S., M.M., G.P.)
| | - Mete Civelek
- Center for Public Health Genomics, Department of Biomedical Engineering (M.C.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Michal Mokry
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (R.J.G.H., M.M., H.M.d.R.).,Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, The Netherlands (L.S., M.M., G.P.)
| | - Jason C Kovacic
- Icahn School of Medicine at Mount Sinai (J.C.K.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,St Vincent's Clinical School, University of NSW (J.C.K.)
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht University, The Netherlands (L.S., M.M., G.P.)
| | - Gary Owens
- Robert M. Berne Cardiovascular Research Center (K.O., G.O.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Johan L M Björkegren
- University of Virginia-School of Medicine, Charlottesville. Department of Genetics and Genomic Sciences (L.M., S.K., K.H., J.L.M.B.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Icahn Institute of Genomics and Multiscale Biology (K.H., J.L.M.B.), New York. Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden (J.L.M.B.)
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (R.J.G.H., M.M., H.M.d.R.)
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22
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Shared Blood Transcriptomic Signatures between Alzheimer's Disease and Diabetes Mellitus. Biomedicines 2021; 9:biomedicines9010034. [PMID: 33406707 PMCID: PMC7823888 DOI: 10.3390/biomedicines9010034] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/29/2022] Open
Abstract
Alzheimer’s disease (AD) and diabetes mellitus (DM) are known to have a shared molecular mechanism. We aimed to identify shared blood transcriptomic signatures between AD and DM. Blood expression datasets for each disease were combined and a co-expression network was used to construct modules consisting of genes with similar expression patterns. For each module, a gene regulatory network based on gene expression and protein-protein interactions was established to identify hub genes. We selected one module, where COPS4, PSMA6, GTF2B, GTF2F2, and SSB were identified as dysregulated transcription factors that were common between AD and DM. These five genes were also differentially co-expressed in disease-related tissues, such as the brain in AD and the pancreas in DM. Our study identified gene modules that were dysregulated in both AD and DM blood samples, which may contribute to reveal common pathophysiology between two diseases.
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23
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Gaikwad AS, Hu J, Chapple DG, O'Bryan MK. The functions of CAP superfamily proteins in mammalian fertility and disease. Hum Reprod Update 2020; 26:689-723. [PMID: 32378701 DOI: 10.1093/humupd/dmaa016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/11/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Members of the cysteine-rich secretory proteins (CRISPS), antigen 5 (Ag5) and pathogenesis-related 1 (Pr-1) (CAP) superfamily of proteins are found across the bacterial, fungal, plant and animal kingdoms. Although many CAP superfamily proteins remain poorly characterized, over the past decade evidence has accumulated, which provides insights into the functional roles of these proteins in various processes, including fertilization, immune defence and subversion, pathogen virulence, venom toxicology and cancer biology. OBJECTIVE AND RATIONALE The aim of this article is to summarize the current state of knowledge on CAP superfamily proteins in mammalian fertility, organismal homeostasis and disease pathogenesis. SEARCH METHODS The scientific literature search was undertaken via PubMed database on all articles published prior to November 2019. Search terms were based on following keywords: 'CAP superfamily', 'CRISP', 'Cysteine-rich secretory proteins', 'Antigen 5', 'Pathogenesis-related 1', 'male fertility', 'CAP and CTL domain containing', 'CRISPLD1', 'CRISPLD2', 'bacterial SCP', 'ion channel regulator', 'CatSper', 'PI15', 'PI16', 'CLEC', 'PRY proteins', 'ASP proteins', 'spermatogenesis', 'epididymal maturation', 'capacitation' and 'snake CRISP'. In addition to that, reference lists of primary and review article were reviewed for additional relevant publications. OUTCOMES In this review, we discuss the breadth of knowledge on CAP superfamily proteins with regards to their protein structure, biological functions and emerging significance in reproduction, health and disease. We discuss the evolution of CAP superfamily proteins from their otherwise unembellished prokaryotic predecessors into the multi-domain and neofunctionalized members found in eukaryotic organisms today. At least in part because of the rapid evolution of these proteins, many inconsistencies in nomenclature exist within the literature. As such, and in part through the use of a maximum likelihood phylogenetic analysis of the vertebrate CRISP subfamily, we have attempted to clarify this confusion, thus allowing for a comparison of orthologous protein function between species. This framework also allows the prediction of functional relevance between species based on sequence and structural conservation. WIDER IMPLICATIONS This review generates a picture of critical roles for CAP proteins in ion channel regulation, sterol and lipid binding and protease inhibition, and as ligands involved in the induction of multiple cellular processes.
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Affiliation(s)
- Avinash S Gaikwad
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Jinghua Hu
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Moira K O'Bryan
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
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24
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Qian C, Xia M, Yang X, Chen P, Ye Q. Long Noncoding RNAs in the Progression of Atherosclerosis: An Integrated Analysis Based on Competing Endogenous RNA Theory. DNA Cell Biol 2020; 40:283-292. [PMID: 33332208 DOI: 10.1089/dna.2020.6106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been increasingly accepted to function importantly in human diseases by serving as competing endogenous RNAs (ceRNAs). To date, the ceRNA mechanisms of lncRNAs in the progression of atherosclerosis (AS) remain largely unclear. On the basis of ceRNA theory, we implemented a multistep computational analysis to construct an lncRNA-mRNA network for AS progression (ASpLMN). The probe reannotation method and microRNA-target interactions from databases were systematically integrated. Three lncRNAs (GS1-358P8.4, OIP5-AS1, and TUG1) with central topological features in the ASpLMN were firstly identified. By using subnetwork analysis, we then obtained two highly clustered modules and one dysregulated module from the ASpLMN network. These modules, sharing three lncRNAs (GS1-358P8.4, OIP5-AS1, and RP11-690D19.3), were significantly enriched in biological pathways such as regulation of actin cytoskeleton, tryptophan metabolism, lysosome, and arginine and proline metabolism. In addition, random walking in the ASpLMN network indicated that lncRNA RP1-39G22.7 and MBNL1-AS1 may also play an essential role in the pathology of AS progression. The identified six lncRNAs from the aforementioned steps could distinguish advanced- from early-staged AS, with a strong diagnostic power for AS occurrence. In conclusion, the results of this study will improve our understanding about the ceRNA-mediated regulatory mechanisms in AS progression, and provide novel lncRNAs as biomarkers or therapeutic targets for acute cardiovascular events.
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Affiliation(s)
- Cheng Qian
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Meng Xia
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Xueying Yang
- Department of Medical Records, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei Province, China
| | - Pengfei Chen
- Department of Gastroenterology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei Province, China
| | - Qiang Ye
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
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Xue Y, Guo Y, Luo S, Zhou W, Xiang J, Zhu Y, Xiang Z, Shen J. Aberrantly Methylated-Differentially Expressed Genes Identify Novel Atherosclerosis Risk Subtypes. Front Genet 2020; 11:569572. [PMID: 33381146 PMCID: PMC7767999 DOI: 10.3389/fgene.2020.569572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence has indicated that modulation of epigenetic mechanisms, especially methylation and long-non-coding RNA (lncRNA) regulation, plays a pivotal role in the process of atherosclerosis; however, few studies focused on revealing the epigenetic-related subgroups during atherosclerotic progression using unsupervised clustering analysis. Hence, we aimed to identify the epigenetics-related differentially expressed genes associated with atherosclerosis subtypes and characterize their clinical utility in atherosclerosis. Eighty samples with expression data (GSE40231) and 49 samples with methylation data (GSE46394) from a large artery plaque were downloaded from the GEO database, and aberrantly methylated-differentially expressed (AMDE) genes were identified based on the relationship between methylation and expression. Furthermore, we conducted weighted correlation network analysis (WGCNA) and co-expression analysis to identify the core AMDE genes strongly involved in atherosclerosis. K-means clustering was used to characterize two subtypes of atherosclerosis in GSE40231, and then 29 samples were recognized as validation dataset (GSE28829). In a blood sample cohort (GSE90074), chi-square test and logistic analysis were performed to explore the clinical implication of the K-means clusters. Furthermore, significance analysis of microarrays and prediction analysis of microarrays (PAM) were applied to identify the signature AMDE genes. Moreover, the classification performance of signature AMDE gene-based classifier from PAM was validated in another blood sample cohort (GSE34822). A total of 1,569 AMDE mRNAs and eight AMDE long non-coding RNAs (lncRNAs) were identified by differential analysis. Through the WGCNA and co-expression analysis, 32 AMDE mRNAs and seven AMDE lncRNAs were identified as the core genes involved in atherosclerosis development. Functional analysis revealed that AMDE genes were strongly related to inflammation and axon guidance. In the clinical analysis, the atherosclerotic subtypes were associated with the severity of coronary artery disease and risk of adverse events. Eight genes, including PARP15, SERGEF, PDGFD, MRPL45, UBR1, STAU1, WIZ, and LSM4, were selected as the signature AMDE genes that most significantly differentiated between atherosclerotic subtypes. Ultimately, the area under the curve of signature AMDE gene-based classifier for atherosclerotic subtypes was 0.858 and 0.812 in GSE90074 and GSE34822, respectively. This study identified the AMDE genes (lncRNAs and mRNAs) that could be implemented in clinical clustering to recognize high-risk atherosclerotic patients.
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Affiliation(s)
- Yuzhou Xue
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongzheng Guo
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Suxin Luo
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Zhou
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Xiang
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuansong Zhu
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhenxian Xiang
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian Shen
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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26
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Dibus M, Brábek J, Rösel D. A Screen for PKN3 Substrates Reveals an Activating Phosphorylation of ARHGAP18. Int J Mol Sci 2020; 21:ijms21207769. [PMID: 33092266 PMCID: PMC7594087 DOI: 10.3390/ijms21207769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022] Open
Abstract
Protein kinase N3 (PKN3) is a serine/threonine kinase implicated in tumor progression of multiple cancer types, however, its substrates and effector proteins still remain largely understudied. In the present work we aimed to identify novel PKN3 substrates in a phosphoproteomic screen using analog sensitive PKN3. Among the identified putative substrates we selected ARHGAP18, a protein from RhoGAP family, for validation of the screen and further study. We confirmed that PKN3 can phosphorylate ARHGAP18 in vitro and we also characterized the interaction of the two proteins, which is mediated via the N-terminal part of ARHGAP18. We present strong evidence that PKN3-ARHGAP18 interaction is increased upon ARHGAP18 phosphorylation and that the phosphorylation of ARHGAP18 by PKN3 enhances its GAP domain activity and contributes to negative regulation of active RhoA. Taken together, we identified new set of potential PKN3 substrates and revealed a new negative feedback regulatory mechanism of Rho signaling mediated by PKN3-induced ARHGAP18 activation.
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Affiliation(s)
- Michal Dibus
- Department of Cell Biology, Charles University, Viničná 7, 12800 Prague, Czech Republic; (M.D.); (J.B.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242 Vestec u Prahy, Czech Republic
| | - Jan Brábek
- Department of Cell Biology, Charles University, Viničná 7, 12800 Prague, Czech Republic; (M.D.); (J.B.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242 Vestec u Prahy, Czech Republic
| | - Daniel Rösel
- Department of Cell Biology, Charles University, Viničná 7, 12800 Prague, Czech Republic; (M.D.); (J.B.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242 Vestec u Prahy, Czech Republic
- Correspondence:
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27
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Adipose tissue in health and disease through the lens of its building blocks. Sci Rep 2020; 10:10433. [PMID: 32591560 PMCID: PMC7319996 DOI: 10.1038/s41598-020-67177-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/21/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding adipose tissue cellular heterogeneity and homeostasis is essential to comprehend the cell type dynamics in metabolic diseases. Cellular subpopulations in the adipose tissue have been related to disease development, but efforts towards characterizing the adipose tissue cell type composition are limited. Here, we identify the cell type composition of the adipose tissue by using gene expression deconvolution of large amounts of publicly available transcriptomics level data. The proposed approach allows to present a comprehensive study of adipose tissue cell type composition, determining the relative amounts of 21 different cell types in 1282 adipose tissue samples detailing differences across four adipose tissue depots, between genders, across ranges of BMI and in different stages of type-2 diabetes. We compare our results to previous marker-based studies by conducting a literature review of adipose tissue cell type composition and propose candidate cellular markers to distinguish different cell types within the adipose tissue. This analysis reveals gender-specific differences in CD4+ and CD8+ T cell subsets; identifies adipose tissue as rich source of multipotent stem/stromal cells; and highlights a strongly increased immune cell content in epicardial and pericardial adipose tissue compared to subcutaneous and omental depots. Overall, this systematic analysis provides comprehensive insights into adipose tissue cell-type heterogeneity in health and disease.
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28
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Zeng L, Talukdar HA, Koplev S, Giannarelli C, Ivert T, Gan LM, Ruusalepp A, Schadt EE, Kovacic JC, Lusis AJ, Michoel T, Schunkert H, Björkegren JLM. Contribution of Gene Regulatory Networks to Heritability of Coronary Artery Disease. J Am Coll Cardiol 2020; 73:2946-2957. [PMID: 31196451 DOI: 10.1016/j.jacc.2019.03.520] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/27/2019] [Accepted: 03/16/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Genetic variants currently known to affect coronary artery disease (CAD) risk explain less than one-quarter of disease heritability. The heritability contribution of gene regulatory networks (GRNs) in CAD, which are modulated by both genetic and environmental factors, is unknown. OBJECTIVES This study sought to determine the heritability contributions of single nucleotide polymorphisms affecting gene expression (eSNPs) in GRNs causally linked to CAD. METHODS Seven vascular and metabolic tissues collected in 2 independent genetics-of-gene-expression studies of patients with CAD were used to identify eSNPs and to infer coexpression networks. To construct GRNs with causal relations to CAD, the prior information of eSNPs in the coexpression networks was used in a Bayesian algorithm. Narrow-sense CAD heritability conferred by the GRNs was calculated from individual-level genotype data from 9 European genome-wide association studies (GWAS) (13,612 cases, 13,758 control cases). RESULTS The authors identified and replicated 28 independent GRNs active in CAD. The genetic variation in these networks contributed to 10.0% of CAD heritability beyond the 22% attributable to risk loci identified by GWAS. GRNs in the atherosclerotic arterial wall (n = 7) and subcutaneous or visceral abdominal fat (n = 9) were most strongly implicated, jointly explaining 8.2% of CAD heritability. In all, these 28 GRNs (each contributing to >0.2% of CAD heritability) comprised 24 to 841 genes, whereof 1 to 28 genes had strong regulatory effects (key disease drivers) and harbored many relevant functions previously associated with CAD. The gene activity in these 28 GRNs also displayed strong associations with genetic and phenotypic cardiometabolic disease variations both in humans and mice, indicative of their pivotal roles as mediators of gene-environmental interactions in CAD. CONCLUSIONS GRNs capture a major portion of genetic variance and contribute to heritability beyond that of genetic loci currently known to affect CAD risk. These networks provide a framework to identify novel risk genes/pathways and study molecular interactions within and across disease-relevant tissues leading to CAD.
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Affiliation(s)
- Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Husain A Talukdar
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Simon Koplev
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chiara Giannarelli
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Torbjörn Ivert
- Department of Thoracic Surgery, Karolinska University Hospital and Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Li-Ming Gan
- Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia; Clinical Gene Networks AB, Stockholm, Sweden
| | - Eric E Schadt
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jason C Kovacic
- Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aldons J Lusis
- Departments of Medicine, Cardiology, Human Genetics, Microbiology, Immunology & Molecular Genetics, University of California-Los Angeles, Los Angeles, California
| | - Tom Michoel
- Clinical Gene Networks AB, Stockholm, Sweden; Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany.
| | - Johan L M Björkegren
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany; Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden; Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Clinical Gene Networks AB, Stockholm, Sweden.
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29
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Huang J, Cai C, Zheng T, Wu X, Wang D, Zhang K, Xu B, Yan R, Gong H, Zhang J, Shi Y, Xu Z, Zhang X, Zhang X, Shang T, Zhou J, Guo X, Zeng C, Lai EY, Xiao C, Chen J, Wan S, Liu WH, Ke Y, Cheng H. Endothelial Scaffolding Protein ENH (Enigma Homolog Protein) Promotes PHLPP2 (Pleckstrin Homology Domain and Leucine-Rich Repeat Protein Phosphatase 2)-Mediated Dephosphorylation of AKT1 and eNOS (Endothelial NO Synthase) Promoting Vascular Remodeling. Arterioscler Thromb Vasc Biol 2020; 40:1705-1721. [PMID: 32268790 DOI: 10.1161/atvbaha.120.314172] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE A decrease in nitric oxide, leading to vascular smooth muscle cell proliferation, is a common pathological feature of vascular proliferative diseases. Nitric oxide synthesis by eNOS (endothelial nitric oxide synthase) is precisely regulated by protein kinases including AKT1. ENH (enigma homolog protein) is a scaffolding protein for multiple protein kinases, but whether it regulates eNOS activation and vascular remodeling remains unknown. Approach and Results: ENH was upregulated in injured mouse arteries and human atherosclerotic plaques and was associated with coronary artery disease. Neointima formation in carotid arteries, induced by ligation or wire injury, was greatly decreased in endothelium-specific ENH-knockout mice. Vascular ligation reduced AKT and eNOS phosphorylation and nitric oxide production in the endothelium of control but not ENH-knockout mice. ENH was found to interact with AKT1 and its phosphatase PHLPP2 (pleckstrin homology domain and leucine-rich repeat protein phosphatase 2). AKT and eNOS activation were prolonged in VEGF (vascular endothelial growth factor)-induced ENH- or PHLPP2-deficient endothelial cells. Inhibitors of either AKT or eNOS effectively restored ligation-induced neointima formation in ENH-knockout mice. Moreover, endothelium-specific PHLPP2-knockout mice displayed reduced ligation-induced neointima formation. Finally, PHLPP2 was increased in the endothelia of human atherosclerotic plaques and blood cells from patients with coronary artery disease. CONCLUSIONS ENH forms a complex with AKT1 and its phosphatase PHLPP2 to negatively regulate AKT1 activation in the artery endothelium. AKT1 deactivation, a decrease in nitric oxide generation, and subsequent neointima formation induced by vascular injury are mediated by ENH and PHLPP2. ENH and PHLPP2 are thus new proatherosclerotic factors that could be therapeutically targeted.
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Affiliation(s)
- Jiaqi Huang
- From the Department of Pathology and Pathophysiology and Department of Cardiology, Sir Run Run Shaw Hospital (J.H., K.Z., H.C.), Zhejiang University School of Medicine, Hangzhou, China
| | - Changhong Cai
- Department of Cardiology, Lishui Hospital, Zhejiang University School of Medicine, China. (C.C., C.Z.)
| | - Tianyu Zheng
- Department of Pathology and Pathophysiology (T.Z., X. Wu, R.Y., Y.S., Z.X., X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyan Wu
- Department of Pathology and Pathophysiology (T.Z., X. Wu, R.Y., Y.S., Z.X., X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Dongfei Wang
- Department of Cardiovascular Science, The First Affiliated Hospital of Zhejiang University (D.W., X.G.), Zhejiang University School of Medicine, Hangzhou, China
| | - Kaijie Zhang
- From the Department of Pathology and Pathophysiology and Department of Cardiology, Sir Run Run Shaw Hospital (J.H., K.Z., H.C.), Zhejiang University School of Medicine, Hangzhou, China
| | - Bocheng Xu
- Institute of Feed Science, College of Animal Sciences, Zhejiang University, Hangzhou, China (B.X.)
| | - Ruochen Yan
- Department of Pathology and Pathophysiology (T.Z., X. Wu, R.Y., Y.S., Z.X., X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Gong
- Key Laboratory for Translational Medicine, First Affiliated Hospital, Huzhou University, China (H.G.)
| | - Jie Zhang
- Department of Urology, Sir Run Run Shaw Hospital (J. Zhang), Zhejiang University School of Medicine, Hangzhou, China
| | - Yueli Shi
- Department of Pathology and Pathophysiology (T.Z., X. Wu, R.Y., Y.S., Z.X., X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Zhiyong Xu
- Department of Pathology and Pathophysiology (T.Z., X. Wu, R.Y., Y.S., Z.X., X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Xue Zhang
- Department of Pathology and Pathophysiology (T.Z., X. Wu, R.Y., Y.S., Z.X., X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Xuemin Zhang
- Department of Vascular Surgery, Peking University People's Hospital, Peking University Health Science Center, Peking University, Beijing, China (X. Zhang)
| | - Tao Shang
- Department of Vascular Surgery, The First Affiliated Hospital (T.S.)
| | - Jianhong Zhou
- Department of Gynecology, School of Medicine, Zhejiang University, Hangzhou, China (J. Zhou)
| | - Xiaogang Guo
- Department of Cardiovascular Science, The First Affiliated Hospital of Zhejiang University (D.W., X.G.), Zhejiang University School of Medicine, Hangzhou, China
| | - Chunlai Zeng
- Department of Cardiology, Lishui Hospital, Zhejiang University School of Medicine, China. (C.C., C.Z.)
| | - En Yin Lai
- Department of Physiology, School of Basic Medical Sciences (E.Y.L.), Zhejiang University School of Medicine, Hangzhou, China
| | - Changchun Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, China (C.X., W.-H.L.).,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA (C.X.)
| | - Ju Chen
- Department of Medicine and Cardiology, University of California San Diego, La Jolla (J.C.)
| | - Shu Wan
- Brain Center of Zhejiang Hospital, Hangzhou, China (S.W.)
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, China (C.X., W.-H.L.)
| | - Yuehai Ke
- Department of Pathology and Pathophysiology (T.Z., X. Wu, R.Y., Y.S., Z.X., X.Z., Y.K.), Zhejiang University School of Medicine, Hangzhou, China
| | - Hongqiang Cheng
- From the Department of Pathology and Pathophysiology and Department of Cardiology, Sir Run Run Shaw Hospital (J.H., K.Z., H.C.), Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Hangzhou, China (H.C.)
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30
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Fathzadeh M, Li J, Rao A, Cook N, Chennamsetty I, Seldin M, Zhou X, Sangwung P, Gloudemans MJ, Keller M, Attie A, Yang J, Wabitsch M, Carcamo-Orive I, Tada Y, Lusis AJ, Shin MK, Molony CM, McLaughlin T, Reaven G, Montgomery SB, Reilly D, Quertermous T, Ingelsson E, Knowles JW. FAM13A affects body fat distribution and adipocyte function. Nat Commun 2020; 11:1465. [PMID: 32193374 PMCID: PMC7081215 DOI: 10.1038/s41467-020-15291-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/20/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic variation in the FAM13A (Family with Sequence Similarity 13 Member A) locus has been associated with several glycemic and metabolic traits in genome-wide association studies (GWAS). Here, we demonstrate that in humans, FAM13A alleles are associated with increased FAM13A expression in subcutaneous adipose tissue (SAT) and an insulin resistance-related phenotype (e.g. higher waist-to-hip ratio and fasting insulin levels, but lower body fat). In human adipocyte models, knockdown of FAM13A in preadipocytes accelerates adipocyte differentiation. In mice, Fam13a knockout (KO) have a lower visceral to subcutaneous fat (VAT/SAT) ratio after high-fat diet challenge, in comparison to their wild-type counterparts. Subcutaneous adipocytes in KO mice show a size distribution shift toward an increased number of smaller adipocytes, along with an improved adipogenic potential. Our results indicate that GWAS-associated variants within the FAM13A locus alter adipose FAM13A expression, which in turn, regulates adipocyte differentiation and contribute to changes in body fat distribution.
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Affiliation(s)
- Mohsen Fathzadeh
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Jiehan Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Abhiram Rao
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Bioengineering Department, School of Engineering and Medicine, Stanford, CA, USA
| | - Naomi Cook
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Indumathi Chennamsetty
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Marcus Seldin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xiang Zhou
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Panjamaporn Sangwung
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | | | - Mark Keller
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Allan Attie
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Jing Yang
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Martin Wabitsch
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, University of Ulm, Ulm, Germany
| | - Ivan Carcamo-Orive
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Yuko Tada
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Myung Kyun Shin
- Genetics and Pharmacogenomics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Cliona M Molony
- Genetics and Pharmacogenomics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Tracey McLaughlin
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald Reaven
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, California, CA, USA
- Department of Medicine, Division of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, California, CA, USA
| | - Dermot Reilly
- Genetics and Pharmacogenomics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA.
| | - Joshua W Knowles
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA.
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31
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Oppi S, Nusser-Stein S, Blyszczuk P, Wang X, Jomard A, Marzolla V, Yang K, Velagapudi S, Ward LJ, Yuan XM, Geiger MA, Guillaumon AT, Othman A, Hornemann T, Rancic Z, Ryu D, Oosterveer MH, Osto E, Lüscher TF, Stein S. Macrophage NCOR1 protects from atherosclerosis by repressing a pro-atherogenic PPARγ signature. Eur Heart J 2020; 41:995-1005. [PMID: 31529020 DOI: 10.1093/eurheartj/ehz667] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/28/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022] Open
Abstract
AIMS Nuclear receptors and their cofactors regulate key pathophysiological processes in atherosclerosis development. The transcriptional activity of these nuclear receptors is controlled by the nuclear receptor corepressors (NCOR), scaffolding proteins that form the basis of large corepressor complexes. Studies with primary macrophages demonstrated that the deletion of Ncor1 increases the expression of atherosclerotic molecules. However, the role of nuclear receptor corepressors in atherogenesis is unknown. METHODS AND RESULTS We generated myeloid cell-specific Ncor1 knockout mice and crossbred them with low-density lipoprotein receptor (Ldlr) knockouts to study the role of macrophage NCOR1 in atherosclerosis. We demonstrate that myeloid cell-specific deletion of nuclear receptor corepressor 1 (NCOR1) aggravates atherosclerosis development in mice. Macrophage Ncor1-deficiency leads to increased foam cell formation, enhanced expression of pro-inflammatory cytokines, and atherosclerotic lesions characterized by larger necrotic cores and thinner fibrous caps. The immunometabolic effects of NCOR1 are mediated via suppression of peroxisome proliferator-activated receptor gamma (PPARγ) target genes in mouse and human macrophages, which lead to an enhanced expression of the CD36 scavenger receptor and subsequent increase in oxidized low-density lipoprotein uptake in the absence of NCOR1. Interestingly, in human atherosclerotic plaques, the expression of NCOR1 is reduced whereas the PPARγ signature is increased, and this signature is more pronounced in ruptured compared with non-ruptured carotid plaques. CONCLUSIONS Our findings show that macrophage NCOR1 blocks the pro-atherogenic functions of PPARγ in atherosclerosis and suggest that stabilizing the NCOR1-PPARγ binding could be a promising strategy to block the pro-atherogenic functions of plaque macrophages and lesion progression in atherosclerotic patients.
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Affiliation(s)
- Sara Oppi
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
| | - Stefanie Nusser-Stein
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
| | - Przemyslaw Blyszczuk
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, 8091 Zurich, Switzerland
- Department of Clinical Immunology, Jagiellonian University Medical College, 31-008 Cracow, Poland
| | - Xu Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Anne Jomard
- Laboratory of Translational Nutrition Biology, Institute of Food, Nutrition and Health, ETH Zurich, 8603 Schwerzenbach, Switzerland
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Vincenzo Marzolla
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
- Laboratory of Cardiovascular Endocrinology, IRCCS San Raffaele Pisana, 00163 Rome, Italy
| | - Kangmin Yang
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
| | - Srividya Velagapudi
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
| | - Liam J Ward
- Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Xi-Ming Yuan
- Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Martin A Geiger
- Vascular Diseases Discipline, Clinics Hospital of the University of Campinas, 13083-970 Campinas, Brazil
| | - Ana T Guillaumon
- Vascular Diseases Discipline, Clinics Hospital of the University of Campinas, 13083-970 Campinas, Brazil
| | - Alaa Othman
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Zoran Rancic
- Clinic for Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, 16419 Suwon, Republic of Korea
| | - Maaike H Oosterveer
- Department of Pediatrics, Center for Liver Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Elena Osto
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
- Laboratory of Translational Nutrition Biology, Institute of Food, Nutrition and Health, ETH Zurich, 8603 Schwerzenbach, Switzerland
- Institute for Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
- Department of Cardiology, Royal Brompton & Harefield Hospital Trust, London, SW3 6NP, UK
- Imperial College London, London, SW7 2AZ, UK
| | - Sokrates Stein
- Center for Molecular Cardiology, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland
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32
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Erola P, Björkegren JLM, Michoel T. Model-based clustering of multi-tissue gene expression data. Bioinformatics 2020; 36:1807-1813. [PMID: 31688915 PMCID: PMC7162352 DOI: 10.1093/bioinformatics/btz805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 09/05/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Recently, it has become feasible to generate large-scale, multi-tissue gene expression data, where expression profiles are obtained from multiple tissues or organs sampled from dozens to hundreds of individuals. When traditional clustering methods are applied to this type of data, important information is lost, because they either require all tissues to be analyzed independently, ignoring dependencies and similarities between tissues, or to merge tissues in a single, monolithic dataset, ignoring individual characteristics of tissues. RESULTS We developed a Bayesian model-based multi-tissue clustering algorithm, revamp, which can incorporate prior information on physiological tissue similarity, and which results in a set of clusters, each consisting of a core set of genes conserved across tissues as well as differential sets of genes specific to one or more subsets of tissues. Using data from seven vascular and metabolic tissues from over 100 individuals in the STockholm Atherosclerosis Gene Expression (STAGE) study, we demonstrate that multi-tissue clusters inferred by revamp are more enriched for tissue-dependent protein-protein interactions compared to alternative approaches. We further demonstrate that revamp results in easily interpretable multi-tissue gene expression associations to key coronary artery disease processes and clinical phenotypes in the STAGE individuals. AVAILABILITY AND IMPLEMENTATION Revamp is implemented in the Lemon-Tree software, available at https://github.com/eb00/lemon-tree. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pau Erola
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Midlothian EH25 9RG, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Integrated Cardio Metabolic Centre (ICMC), Karolinska Institutet, Huddinge 141 57, Sweden
| | - Tom Michoel
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Midlothian EH25 9RG, UK
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen N-5020, Norway
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33
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Rykaczewska U, Suur BE, Röhl S, Razuvaev A, Lengquist M, Sabater-Lleal M, van der Laan SW, Miller CL, Wirka RC, Kronqvist M, Gonzalez Diez M, Vesterlund M, Gillgren P, Odeberg J, Lindeman JH, Veglia F, Humphries SE, de Faire U, Baldassarre D, Tremoli E, Lehtiö J, Hansson GK, Paulsson-Berne G, Pasterkamp G, Quertermous T, Hamsten A, Eriksson P, Hedin U, Matic L. PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling. Circ Res 2020; 126:571-585. [PMID: 31893970 DOI: 10.1161/circresaha.119.316063] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RATIONALE PCSKs (Proprotein convertase subtilisins/kexins) are a protease family with unknown functions in vasculature. Previously, we demonstrated PCSK6 upregulation in human atherosclerotic plaques associated with smooth muscle cells (SMCs), inflammation, extracellular matrix remodeling, and mitogens. OBJECTIVE Here, we applied a systems biology approach to gain deeper insights into the PCSK6 role in normal and diseased vessel wall. METHODS AND RESULTS Genetic analyses revealed association of intronic PCSK6 variant rs1531817 with maximum internal carotid intima-media thickness progression in high-cardiovascular risk subjects. This variant was linked with PCSK6 mRNA expression in healthy aortas and plaques but also with overall plaque SMA+ cell content and pericyte fraction. Increased PCSK6 expression was found in several independent human cohorts comparing atherosclerotic lesions versus healthy arteries, using transcriptomic and proteomic datasets. By immunohistochemistry, PCSK6 was localized to fibrous cap SMA+ cells and neovessels in plaques. In human, rat, and mouse intimal hyperplasia, PCSK6 was expressed by proliferating SMA+ cells and upregulated after 5 days in rat carotid balloon injury model, with positive correlation to PDGFB (platelet-derived growth factor subunit B) and MMP (matrix metalloprotease) 2/MMP14. Here, PCSK6 was shown to colocalize and cointeract with MMP2/MMP14 by in situ proximity ligation assay. Microarrays of carotid arteries from Pcsk6-/- versus control mice revealed suppression of contractile SMC markers, extracellular matrix remodeling enzymes, and cytokines/receptors. Pcsk6-/- mice showed reduced intimal hyperplasia response upon carotid ligation in vivo, accompanied by decreased MMP14 activation and impaired SMC outgrowth from aortic rings ex vivo. PCSK6 silencing in human SMCs in vitro leads to downregulation of contractile markers and increase in MMP2 expression. Conversely, PCSK6 overexpression increased PDGFBB (platelet-derived growth factor BB)-induced cell proliferation and particularly migration. CONCLUSIONS PCSK6 is a novel protease that induces SMC migration in response to PDGFB, mechanistically via modulation of contractile markers and MMP14 activation. This study establishes PCSK6 as a key regulator of SMC function in vascular remodeling. Visual Overview: An online visual overview is available for this article.
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Affiliation(s)
- Urszula Rykaczewska
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Bianca E Suur
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Samuel Röhl
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Anton Razuvaev
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Mariette Lengquist
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Maria Sabater-Lleal
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.).,Unit of Genomics of Complex Diseases, Institut de Recerca Hospital de Sant Pau (IIB-Sant Pau), Barcelona, Spain (M.S.-L.)
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, The Netherlands (S.v.d.L.)
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville (C.L.M.).,Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (C.L.M., R.C.W., T.Q.)
| | - Robert C Wirka
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (C.L.M., R.C.W., T.Q.)
| | - Malin Kronqvist
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Maria Gonzalez Diez
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Mattias Vesterlund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Sweden (M.V., J.L.)
| | - Peter Gillgren
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, and Department of Vascular Surgery, Södersjukhuset, Stockholm, Sweden (P.G.)
| | - Jacob Odeberg
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.).,Science for Life Laboratory, Department of Proteomics, School of Chemistry Biotechnology and Health (CBH), KTH, Stockholm, Sweden (J.O.)
| | - Jan H Lindeman
- Department of Vascular Surgery, Leiden University Medical Center, The Netherlands (J.H.N.L.)
| | - Fabrizio Veglia
- Centro Cardiologico Monzino, IRCCS, Milan, Italy (F.V., D.B., E.T.)
| | - Steve E Humphries
- Cardiovascular Genetics, Institute Cardiovascular Science, University College of London, Department of Medicine, Rayne Building, United Kingdom (S.E.H.)
| | - Ulf de Faire
- Division of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Sweden (H.d.F.)
| | - Damiano Baldassarre
- Centro Cardiologico Monzino, IRCCS, Milan, Italy (F.V., D.B., E.T.).,Department of Medical Biotechnology and Translational Medicine, Università di Milano, Milan, Italy (D.B.)
| | - Elena Tremoli
- Centro Cardiologico Monzino, IRCCS, Milan, Italy (F.V., D.B., E.T.)
| | | | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Sweden (M.V., J.L.)
| | - Göran K Hansson
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Gabrielle Paulsson-Berne
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Gerard Pasterkamp
- Laboratory of Experimental Cardiology, Division Heart & Lungs, University Medical Center Utrecht, The Netherlands (G.P.)
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA (C.L.M., R.C.W., T.Q.)
| | - Anders Hamsten
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Per Eriksson
- Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (M.S.-L., M.G.D., G.P.-B., G.K.H., A.H., P.E., J.O.)
| | - Ulf Hedin
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
| | - Ljubica Matic
- From the Department of Molecular Medicine and Surgery, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden (U.R., B.E.S., S.R., A.R., M.L., M.K., U.H., L.M.)
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van der Laan SW, Siemelink MA, Haitjema S, Foroughi Asl H, Perisic L, Mokry M, van Setten J, Malik R, Dichgans M, Worrall BB, Samani NJ, Schunkert H, Erdmann J, Hedin U, Paulsson-Berne G, Björkegrenn JLM, de Borst GJ, Asselbergs FW, den Ruijter FW, de Bakker PIW, Pasterkamp G. Genetic Susceptibility Loci for Cardiovascular Disease and Their Impact on Atherosclerotic Plaques. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002115. [PMID: 30354329 PMCID: PMC7664607 DOI: 10.1161/circgen.118.002115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Supplemental Digital Content is available in the text. Background: Atherosclerosis is a chronic inflammatory disease in part caused by lipid uptake in the vascular wall, but the exact underlying mechanisms leading to acute myocardial infarction and stroke remain poorly understood. Large consortia identified genetic susceptibility loci that associate with large artery ischemic stroke and coronary artery disease. However, deciphering their underlying mechanisms are challenging. Histological studies identified destabilizing characteristics in human atherosclerotic plaques that associate with clinical outcome. To what extent established susceptibility loci for large artery ischemic stroke and coronary artery disease relate to plaque characteristics is thus far unknown but may point to novel mechanisms. Methods: We studied the associations of 61 established cardiovascular risk loci with 7 histological plaque characteristics assessed in 1443 carotid plaque specimens from the Athero-Express Biobank Study. We also assessed if the genotyped cardiovascular risk loci impact the tissue-specific gene expression in 2 independent biobanks, Biobank of Karolinska Endarterectomy and Stockholm Atherosclerosis Gene Expression. Results: A total of 21 established risk variants (out of 61) nominally associated to a plaque characteristic. One variant (rs12539895, risk allele A) at 7q22 associated to a reduction of intraplaque fat, P=5.09×10−6 after correction for multiple testing. We further characterized this 7q22 Locus and show tissue-specific effects of rs12539895 on HBP1 expression in plaques and COG5 expression in whole blood and provide data from public resources showing an association with decreased LDL (low-density lipoprotein) and increase HDL (high-density lipoprotein) in the blood. Conclusions: Our study supports the view that cardiovascular susceptibility loci may exert their effect by influencing the atherosclerotic plaque characteristics.
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Affiliation(s)
- Sander W van der Laan
- Laboratory of Experimental Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University Utrecht, The Netherlands (S.W.v.d.L., M.A.S., S.H., H.M.d.R., G.P.)
| | - Marten A Siemelink
- Laboratory of Experimental Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University Utrecht, The Netherlands (S.W.v.d.L., M.A.S., S.H., H.M.d.R., G.P.).,Department of Clinical Genetics, University Medical Center Utrecht, University Utrecht, The Netherlands (M.A.S.)
| | - Saskia Haitjema
- Laboratory of Experimental Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University Utrecht, The Netherlands (S.W.v.d.L., M.A.S., S.H., H.M.d.R., G.P.)
| | - Hassan Foroughi Asl
- Cardiovascular Genomics Group, Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden (H.F.A.)
| | - Ljubica Perisic
- Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden (L.P., U.H.)
| | - Michal Mokry
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, University Utrecht, The Netherlands (M.M.).,Regenerative Medicine Center Utrecht, University Medical Center Utrecht, University Utrecht, The Netherlands (M.M.)
| | - Jessica van Setten
- Department of Cardiology, Division of Heart & Lungs, University Medical Center Utrecht, University Utrecht, The Netherlands (F.W.A., J.v.S.)
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany (R.M., M.D.)
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany (R.M., M.D.).,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany (M.D.)
| | - Bradford B Worrall
- Departments of Neurology and Public Health Sciences, University of Virginia, Charlottesville (B.B.W.)
| | | | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester (N.J.S.).,NIHR Leicester Biomedical Research Unit Centre, BHF Cardiovascular Research Centre, Glenfield Hospital, Leicester, United Kingdom (N.J.S.)
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik an der TU München, Munich Heart Alliance (DZHK), Germany (H.S., J.E.)
| | - Jeanette Erdmann
- Deutsches Herzzentrum München, Klinik an der TU München, Munich Heart Alliance (DZHK), Germany (H.S., J.E.)
| | - Ulf Hedin
- Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden (L.P., U.H.)
| | - Gabrielle Paulsson-Berne
- Unit of Cardiovascular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden (G.P.-B.)
| | - Johan L M Björkegrenn
- CMM, Karolinska Institutet, Stockholm, Sweden. Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York (J.L.M.B.).,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden (J.L.M.B.).,Clinical Gene Networks AB, Stockholm,Sweden (J.L.M.B.)
| | - Gert J de Borst
- Division of Surgical Specialties, Department of Surgery, University Medical Center Utrecht, University Utrecht, The Netherlands (G.J.d.B.)
| | - Folkert W Asselbergs
- Department of Cardiology, Division of Heart & Lungs, University Medical Center Utrecht, University Utrecht, The Netherlands (F.W.A., J.v.S.).,Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, University Utrecht, The Netherlands (P.I.W.d.B.).,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, The Netherlands (P.I.W.d.B.).,Laboratory of Clinical Chemistry and Hematology, Division Laboratories and Pharmacy, University Medical Center Utrecht, University Utrecht, The Netherlands (G.P.).,Durrer Center for Cardiogenetic Research, Netherlands Heart Institute, Utrecht (F.W.A.).,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom (F.W.A.).,Institute of Health Informatics, University College London, London, United Kingdom (F.W.A.)
| | - Folkert W den Ruijter
- Department of Cardiology, Division of Heart & Lungs, University Medical Center Utrecht, University Utrecht, The Netherlands (F.W.A., J.v.S.)
| | - Paul I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, University Utrecht, The Netherlands (P.I.W.d.B.).,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, The Netherlands (P.I.W.d.B.)
| | - Gerard Pasterkamp
- Laboratory of Experimental Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University Utrecht, The Netherlands (S.W.v.d.L., M.A.S., S.H., H.M.d.R., G.P.).,Department of Clinical Genetics, University Medical Center Utrecht, University Utrecht, The Netherlands (M.A.S.).,Laboratory of Clinical Chemistry and Hematology, Division Laboratories and Pharmacy, University Medical Center Utrecht, University Utrecht, The Netherlands (G.P.)
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35
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Moore KJ, Koplev S, Fisher EA, Tabas I, Björkegren JLM, Doran AC, Kovacic JC. Macrophage Trafficking, Inflammatory Resolution, and Genomics in Atherosclerosis: JACC Macrophage in CVD Series (Part 2). J Am Coll Cardiol 2019; 72:2181-2197. [PMID: 30360827 DOI: 10.1016/j.jacc.2018.08.2147] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 07/13/2018] [Accepted: 08/03/2018] [Indexed: 12/31/2022]
Abstract
Atherosclerosis is characterized by the retention of modified lipoproteins in the arterial wall. These modified lipoproteins activate resident macrophages and the recruitment of monocyte-derived cells, which differentiate into mononuclear phagocytes that ingest the deposited lipoproteins to become "foam cells": a hallmark of this disease. In this Part 2 of a 4-part review series covering the macrophage in cardiovascular disease, we critically review the contributions and relevant pathobiology of monocytes, macrophages, and foam cells as relevant to atherosclerosis. We also review evidence that via various pathways, a failure of the resolution of inflammation is an additional key aspect of this disease process. Finally, we consider the likely role played by genomics and biological networks in controlling the macrophage phenotype in atherosclerosis. Collectively, these data provide substantial insights on the atherosclerotic process, while concurrently offering numerous molecular and genomic candidates that appear to hold great promise for selective targeting as clinical therapies.
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Affiliation(s)
- Kathryn J Moore
- Department of Medicine, Leon H. Charney Division of Cardiology, Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, New York
| | - Simon Koplev
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Edward A Fisher
- Department of Medicine, Leon H. Charney Division of Cardiology, Marc and Ruti Bell Vascular Biology and Disease Program, New York University School of Medicine, New York, New York
| | - Ira Tabas
- Department of Medicine, Columbia University, New York, New York; Department of Pathology and Cell Biology, Columbia University, New York, New York; Department of Physiology, Columbia University, New York, New York
| | - Johan L M Björkegren
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Amanda C Doran
- Department of Medicine, Columbia University, New York, New York
| | - Jason C Kovacic
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
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36
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Identification and validation of four hub genes involved in the plaque deterioration of atherosclerosis. Aging (Albany NY) 2019; 11:6469-6489. [PMID: 31449494 PMCID: PMC6738408 DOI: 10.18632/aging.102200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 08/12/2019] [Indexed: 01/17/2023]
Abstract
In recent years, intense research has been conducted to explore the diagnostic value of mRNA expression differences in atherosclerosis (AS). Nevertheless, because various technology platforms are applied and sample sizes are small, the results are inconsistent among the studies. We conducted a comprehensive analysis of a total of 161 tissue samples from 4 published studies after evaluating 230 datasets from the Gene Expression Omnibus and ArrayExpress. Adopting the newly published robust rank aggregation approach, combined with Kyoto Encyclopedia of Genes and Genomes pathway analysis, Gene Ontology functional enrichment analysis, and protein-protein interaction network construction, we identified four significantly upregulated genes (CCL4, CCL18, MMP9 and SPP1) for diagnosing AS, even in the advanced stage. Then, we performed gene set enrichment analysis to identify the pathways that were most affected by altered mRNA expression in atherosclerotic plaques. We found that four hub genes cooperatively targeted lipid metabolism and inflammatory immune-related pathways and validated their high expression levels in ruptured plaques by qRT-PCR, western blot analysis and immunohistochemical staining. In summary, our study showed that these genes can be used as interventional targets for plaque progression, and the results suggested we should focus on small changes in these key indicators in the clinical setting.
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37
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Khan KA, McMurray JL, Mohammed F, Bicknell R. C-type lectin domain group 14 proteins in vascular biology, cancer and inflammation. FEBS J 2019; 286:3299-3332. [PMID: 31287944 PMCID: PMC6852297 DOI: 10.1111/febs.14985] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/21/2019] [Accepted: 07/05/2019] [Indexed: 02/06/2023]
Abstract
The C‐type lectin domain (CTLD) group 14 family of transmembrane glycoproteins consist of thrombomodulin, CD93, CLEC14A and CD248 (endosialin or tumour endothelial marker‐1). These cell surface proteins exhibit similar ectodomain architecture and yet mediate a diverse range of cellular functions, including but not restricted to angiogenesis, inflammation and cell adhesion. Thrombomodulin, CD93 and CLEC14A can be expressed by endothelial cells, whereas CD248 is expressed by vasculature associated pericytes, activated fibroblasts and tumour cells among other cell types. In this article, we review the current literature of these family members including their expression profiles, interacting partners, as well as established and speculated functions. We focus primarily on their roles in the vasculature and inflammation as well as their contributions to tumour immunology. The CTLD group 14 family shares several characteristic features including their ability to be proteolytically cleaved and engagement of some shared extracellular matrix ligands. Each family member has strong links to tumour development and in particular CD93, CLEC14A and CD248 have been proposed as attractive candidate targets for cancer therapy.
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Affiliation(s)
- Kabir A Khan
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Canada
| | - Jack L McMurray
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, UK
| | - Fiyaz Mohammed
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, UK
| | - Roy Bicknell
- Institutes of Cardiovascular Sciences and Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, UK
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38
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Wang CH, Shi HH, Chen LH, Li XL, Cao GL, Hu XF. Identification of Key lncRNAs Associated With Atherosclerosis Progression Based on Public Datasets. Front Genet 2019; 10:123. [PMID: 30873207 PMCID: PMC6403132 DOI: 10.3389/fgene.2019.00123] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/04/2019] [Indexed: 12/17/2022] Open
Abstract
Atherosclerosis is one of the most common type of cardiovascular disease and the prime cause of mortality in the aging population worldwide. However, the detail mechanisms and special biomarkers of atherosclerosis remain to be further investigated. Lately, long non-coding RNAs (lncRNAs) has attracted much more attention than other types of ncRNAs. In our work, we found and confirmed differently expressed lncRNAs and mRNAs in atherosclerosis by analyzing GSE28829. We performed the weighted gene co-expression network analysis (WGCNA) by analyzing GSE40231 to confirm highly correlated genes. Gene Ontology (GO) analysis were utilized to assess the potential functions of differential expressed lncRNAs in atherosclerosis. Co-expression networks were also constructed to confirm hub lncRNAs in atherosclerosis. A total of 5784 mRNAs and 654 lncRNAs were found to be dysregulated in the progression of atherosclerosis. A total of 15 lncRNA-mRNA co-expression modules were identified in this study based on WGCNA analysis. Moreover, a few lncRNAs, such as ZFAS1, LOC100506730, LOC100506691, DOCK9-AS2, RP11-6I2.3, LOC100130219, were confirmed as important lncRNAs in atherosclerosis. Taken together, bioinformatics analysis revealed these lncRNAs were involved in regulating the leukotriene biosynthetic process, gene expression, actin filament organization, t-circle formation, antigen processing, and presentation, interferon-gamma-mediated signaling pathway, and activation of GTPase activity. We believed that this study would provide potential novel therapeutic and prognostic targets for atherosclerosis.
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Affiliation(s)
- Chuan-Hui Wang
- Department of Geriatrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui-Hua Shi
- Department of Geriatrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin-Hui Chen
- Department of Neurology, Zhejiang Hospital, Zhejiang University, Hangzhou, China
| | - Xiao-Li Li
- Department of Geriatrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo-Liang Cao
- Department of Geriatrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Feng Hu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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39
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Erola P, Bonnet E, Michoel T. Learning Differential Module Networks Across Multiple Experimental Conditions. Methods Mol Biol 2019; 1883:303-321. [PMID: 30547406 DOI: 10.1007/978-1-4939-8882-2_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Module network inference is a statistical method to reconstruct gene regulatory networks, which uses probabilistic graphical models to learn modules of coregulated genes and their upstream regulatory programs from genome-wide gene expression and other omics data. Here, we review the basic theory of module network inference, present protocols for common gene regulatory network reconstruction scenarios based on the Lemon-Tree software, and show, using human gene expression data, how the software can also be applied to learn differential module networks across multiple experimental conditions.
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Affiliation(s)
- Pau Erola
- Division of Genetics and Genomics, Roslin Institute, University of Edinburgh, Midlothian, Scotland, UK
| | - Eric Bonnet
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Tom Michoel
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Midlothian, Scotland, UK.
- Current Address: Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
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40
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Wu L, Yao Q, Lin P, Li Y, Li H. Comparative transcriptomics reveals specific responding genes associated with atherosclerosis in rabbit and mouse models. PLoS One 2018; 13:e0201618. [PMID: 30067832 PMCID: PMC6070260 DOI: 10.1371/journal.pone.0201618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/18/2018] [Indexed: 11/18/2022] Open
Abstract
Mouse and rabbit are frequently employed species for atherosclerosis research. With respect to modeling human atherosclerosis, it has been observed that variations in phenotype under commonly used atherogenic conditions are partial or no congruence between two species. However, genome-wide molecular variations are still lacking. To understand the differences between rabbit and mouse in developing atherosclerosis, here from aspect of orthologs, we compared the genome-wide expression profiles of two species under the same atherosclerosis driven factors: high-fat diet or LDLR deficiency. Our results illuminated that: 1) LDLR-deficiency induced different gene expression changes in rabbit and mouse. WHHL rabbit had more significantly differential expressed genes and the most of genes were down-regulated. 2) Some genes and functions were commonly dysregulated in high-fat fed rabbit and mouse models, such as lipid metabolism and inflammation process. However, high-fat intake in rabbit produced more differentially expressed genes and more serious functional effects. 3) Specific differential expression genes were revealed for rabbit and mouse related with high-fat intake. In the aspect of lipoprotein metabolism, APOA4 and APOB was the major responding gene in rabbit and mice, respectively. The expression change of APOA4 and APOB in human atherosclerosis was more similar to rabbit, and therefore rabbit might be a better animal model for investigating human lipoprotein metabolism related diseases. In conclusion, our comparative transcriptome analysis revealed species-specific expression regulation that could partially explain the different phenotypes between rabbit and mouse, which was helpful for model selection to study atherosclerosis.
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Affiliation(s)
- Leilei Wu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qianlan Yao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Lin
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yixue Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China
| | - Hong Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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41
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Vilne B, Schunkert H. Integrating Genes Affecting Coronary Artery Disease in Functional Networks by Multi-OMICs Approach. Front Cardiovasc Med 2018; 5:89. [PMID: 30065929 PMCID: PMC6056735 DOI: 10.3389/fcvm.2018.00089] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022] Open
Abstract
Coronary artery disease (CAD) and myocardial infarction (MI) remain among the leading causes of mortality worldwide, urgently demanding a better understanding of disease etiology, and more efficient therapeutic strategies. Genetic predisposition as well as the environment and lifestyle are thought to contribute to disease risk. It is likely that non-linear and complex interactions occur between these multiple factors, involving simultaneous pathological changes in diverse cell types, tissues, and organs, at multiple molecular levels. Recent technological advances have exponentially expanded the breadth of available -omics data, from genome, epigenome, transcriptome, proteome, metabolome to even the microbiome. Integration of multiple layers of information across several -omics domains, i.e., the so-called multi-omics approach, currently holds the promise as a path toward precision medicine. Indeed, a more meaningful interpretation of genotype-phenotype relationships and the development of successful therapeutics tailored to individual patients are urgently needed. In this review, we will summarize recent findings and applications of integrative multi-omics in elucidating the etiology of CAD/MI; with a special focus on established disease susceptibility loci sequentially identified in genome-wide association studies (GWAS) over the last 10 years. Moreover, in addition to the autosomal genome, we will also consider the genetic variation in our “second genome”—the mitochondrial genome. Finally, we will summarize the current challenges in the field and point to future research directions required in order to successfully and effectively apply these approaches for precision medicine.
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Affiliation(s)
- Baiba Vilne
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
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42
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Guo J, Tao H, Li P, Li L, Zhong T, Wang L, Ma J, Chen X, Song T, Zhang H. Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds. Sci Rep 2018; 8:10405. [PMID: 29991772 PMCID: PMC6039503 DOI: 10.1038/s41598-018-28719-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. In this study, we systematically investigated the selection signatures in six phenotypically diverse goat breeds using SNPs obtained from pooled whole-genome resequencing data. More than 95.5% of 446–642 million clean reads were mapped to the latest reference goat genome, which generated a sequencing depth ranging from 22.30 to 31.75-fold for each breed. A total of 5,802,307, 6,794,020, 7,562,312, 5,325,119, 8,764,136, and 9,488,057 putative SNPs were detected in Boer, Meigu, Jintang Black, Nanjiang Yellow, Tibetan, and Tibetan cashmere goats, respectively. Based on the genome-wide FST and expected heterozygosity scores along 100-kb sliding windows, 68, 89, 44, 44, 19, and 35 outlier windows were deemed as the selection signatures in the six goat breeds. After genome annotation, several genes within the selection signals were found to be possibly associated with important traits in goats, such as coat color (IRF4, EXOC2, RALY, EIF2S2, and KITLG), high-altitude adaptation (EPAS1), growth (LDB2), and reproduction traits (KHDRBS2). In summary, we provide an improved understanding of the genetic diversity and the genomic footprints under positive selection or the adaptations to the local environments in the domestic goat genome.
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Affiliation(s)
- Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Haixi Tao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Pengfei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Tao Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China
| | - Jinying Ma
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, 850009, China
| | - Xiaoying Chen
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, 850009, China
| | - Tianzeng Song
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, 850009, China.
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Postcode 611130, China.
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43
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CD90 Identifies Adventitial Mesenchymal Progenitor Cells in Adult Human Medium- and Large-Sized Arteries. Stem Cell Reports 2018; 11:242-257. [PMID: 30008326 PMCID: PMC6067150 DOI: 10.1016/j.stemcr.2018.06.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/15/2022] Open
Abstract
Mesenchymal stem cells (MSCs) reportedly exist in a vascular niche occupying the outer adventitial layer. However, these cells have not been well characterized in vivo in medium- and large-sized arteries in humans, and their potential pathological role is unknown. To address this, healthy and diseased arterial tissues were obtained as surplus surgical specimens and freshly processed. We identified that CD90 marks a rare adventitial population that co-expresses MSC markers including PDGFRα, CD44, CD73, and CD105. However, unlike CD90, these additional markers were widely expressed by other cells. Human adventitial CD90+ cells fulfilled standard MSC criteria, including plastic adherence, spindle morphology, passage ability, colony formation, and differentiation into adipocytes, osteoblasts, and chondrocytes. Phenotypic and transcriptomic profiling, as well as adoptive transfer experiments, revealed a potential role in vascular disease pathogenesis, with the transcriptomic disease signature of these cells being represented in an aortic regulatory gene network that is operative in atherosclerosis. We identify, in situ and in vivo, adventitial CD90+ MSCs in human arteries Human adventitial CD90+ cells fulfill all criteria for an MSC population Other markers, such as CD44 and PDGFRα, were non-specific for adventitial MSCs The CD90+ MSC transcriptomic signature suggests a major role in vascular disease
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Lempiäinen H, Brænne I, Michoel T, Tragante V, Vilne B, Webb TR, Kyriakou T, Eichner J, Zeng L, Willenborg C, Franzen O, Ruusalepp A, Goel A, van der Laan SW, Biegert C, Hamby S, Talukdar HA, Foroughi Asl H, Pasterkamp G, Watkins H, Samani NJ, Wittenberger T, Erdmann J, Schunkert H, Asselbergs FW, Björkegren JLM. Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets. Sci Rep 2018; 8:3434. [PMID: 29467471 PMCID: PMC5821758 DOI: 10.1038/s41598-018-20721-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/06/2017] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified over two hundred chromosomal loci that modulate risk of coronary artery disease (CAD). The genes affected by variants at these loci are largely unknown and an untapped resource to improve our understanding of CAD pathophysiology and identify potential therapeutic targets. Here, we prioritized 68 genes as the most likely causal genes at genome-wide significant loci identified by GWAS of CAD and examined their regulatory roles in 286 metabolic and vascular tissue gene-protein sub-networks (“modules”). The modules and genes within were scored for CAD druggability potential. The scoring enriched for targets of cardiometabolic drugs currently in clinical use and in-depth analysis of the top-scoring modules validated established and revealed novel target tissues, biological processes, and druggable targets. This study provides an unprecedented resource of tissue-defined gene–protein interactions directly affected by genetic variance in CAD risk loci.
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Affiliation(s)
| | | | - Tom Michoel
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,Clinical Gene Networks AB, Stockholm, Sweden
| | - Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Baiba Vilne
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Tom R Webb
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Leicester, United Kingdom
| | - Theodosios Kyriakou
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | | | - Lingyao Zeng
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany
| | | | - Oscar Franzen
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | | | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sander W van der Laan
- Laboratory of Experimental Cardiology, Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | | | - Stephen Hamby
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Leicester, United Kingdom
| | - Husain A Talukdar
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Hassan Foroughi Asl
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | | | - Gerard Pasterkamp
- Laboratory of Experimental Cardiology, Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands.,Laboratory of Clinical Chemistry and Hematology, Division Laboratories and Pharmacy, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Leicester, United Kingdom
| | | | | | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands.,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom
| | - Johan L M Björkegren
- Clinical Gene Networks AB, Stockholm, Sweden. .,Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA. .,Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden.
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Vilne B, Skogsberg J, Foroughi Asl H, Talukdar HA, Kessler T, Björkegren JLM, Schunkert H. Network analysis reveals a causal role of mitochondrial gene activity in atherosclerotic lesion formation. Atherosclerosis 2017; 267:39-48. [PMID: 29100060 DOI: 10.1016/j.atherosclerosis.2017.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/05/2017] [Accepted: 10/18/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND AIMS Mitochondrial damage and augmented production of reactive oxygen species (ROS) may represent an intermediate step by which hypercholesterolemia exacerbates atherosclerotic lesion formation. METHODS To test this hypothesis, in mice with severe but genetically reversible hypercholesterolemia (i.e. the so called Reversa mouse model), we performed time-resolved analyses of mitochondrial transcriptome in the aortic arch employing a systems-level network approach. RESULTS During hypercholesterolemia, we observed a massive down-regulation (>28%) of mitochondrial genes, specifically at the time of rapid atherosclerotic lesion expansion and foam cell formation, i.e. between 30 and 40 weeks of age. Both phenomena - down-regulation of mitochondrial genes and lesion expansion - were largely reversible by genetically lowering plasma cholesterol (by >80%, from 427 to 54 ± 31 mg/L) at 30 weeks. Co-expression network analysis revealed that both mitochondrial signature genes were highly connected in two modules, negatively correlating with lesion size and supported as causal for coronary artery disease (CAD) in humans, as expression-associated single nucleotide polymorphisms (eSNPs) representing their genes overlapped markedly with established disease risk loci. Within these modules, we identified the transcription factor estrogen related receptor (ERR)-α and its co-factors PGC1-α and -β, i.e. two members of the peroxisome proliferator-activated receptor γ co-activator 1 family of transcription regulators, as key regulatory genes. Together, these factors are known as major orchestrators of mitochondrial biogenesis and antioxidant responses. CONCLUSIONS Using a network approach, we demonstrate how hypercholesterolemia could hamper mitochondrial activity during atherosclerosis progression and pinpoint potential therapeutic targets to counteract these processes.
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Affiliation(s)
- Baiba Vilne
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany; DZHK (German Research Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Josefin Skogsberg
- Cardiovascular Genomics Group, Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hassan Foroughi Asl
- Cardiovascular Genomics Group, Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Husain Ahammad Talukdar
- Cardiovascular Genomics Group, Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Integrated Cardio Metabolic Center (ICMC), Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Thorsten Kessler
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany; DZHK (German Research Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | - Johan L M Björkegren
- Cardiovascular Genomics Group, Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Department of Physiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Estonia; Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai New York, New York, USA; Clinical Gene Networks AB, Stockholm, Sweden.
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany; DZHK (German Research Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany.
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V A, Nayar PG, Murugesan R, S S, Krishnan J, Ahmed SSSJ. A systems biology and proteomics-based approach identifies SRC and VEGFA as biomarkers in risk factor mediated coronary heart disease. MOLECULAR BIOSYSTEMS 2017; 12:2594-604. [PMID: 27279347 DOI: 10.1039/c6mb00264a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Coronary heart disease (CHD) is the most common cause of death worldwide. The burden of CHD increases with risk factors such as smoking, hypertension, obesity and diabetes. Several studies have demonstrated the association of these classical risk factors with CHD. However, the mechanisms of these associations remain largely unclear due to the complexity of disease pathophysiology and the lack of an integrative approach that fails to provide a definite understanding of molecular linkage. To overcome these problems, we propose a novel systems biology approach that relates causative genes, interactomes and pathways to elucidate the risk factors mediating the molecular mechanisms and biomarkers for feasible diagnosis. The literature was mined to retrieve the causative genes of each risk factor and CHD to construct protein interactomes. The interactomes were examined to identify 298 common molecular signatures. The common signatures were mapped to the tissue network to synthesize a sub-network consisting of 82 proteins. Further, the dissection of the sub-network provides functional modules representing a diverse range of molecular functions, including the AKT/p13k, MAPK and wnt pathways. Also, the prioritization of functional modules identifies SRC, VEGFA and HIF1A as potential candidate markers. Further, we validate these candidates with the existing markers CRP, NOS3 and VCAM1 in the serum of 63 individuals, 33 with CHD and 30 controls, using ELISA. SRC, VEGFA, H1F1A, CRP and NOS3 were significantly altered in patients compared to controls. These results support the utility of these candidate markers for the diagnosis of CHD. Overall, our molecular observations indicate the influence of risk factors in the pathophysiology of CHD and identify serum markers for diagnosis.
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Affiliation(s)
- Alexandar V
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - Pradeep G Nayar
- Department of Cardiology, Chettinad Super Specialty Hospital, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - R Murugesan
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - Shajahan S
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Jayalakshmi Krishnan
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Shiek S S J Ahmed
- Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India.
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Kessler T, Wobst J, Wolf B, Eckhold J, Vilne B, Hollstein R, von Ameln S, Dang TA, Sager HB, Moritz Rumpf P, Aherrahrou R, Kastrati A, Björkegren JLM, Erdmann J, Lusis AJ, Civelek M, Kaiser FJ, Schunkert H. Functional Characterization of the GUCY1A3 Coronary Artery Disease Risk Locus. Circulation 2017; 136:476-489. [PMID: 28487391 DOI: 10.1161/circulationaha.116.024152] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/06/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND A chromosomal locus at 4q32.1 has been genome-wide significantly associated with coronary artery disease risk. The locus encompasses GUCY1A3, which encodes the α1 subunit of the soluble guanylyl cyclase (sGC), a key enzyme in the nitric oxide/cGMP signaling pathway. The mechanism linking common variants in this region with coronary risk is not known. METHODS Gene expression and protein expression were analyzed with quantitative polymerase chain reaction and immunoblotting, respectively. Putative allele-specific transcription factors were identified with in silico analyses and validated via allele-specific quantification of antibody-precipitated chromatin fractions. Regulatory properties of the lead risk variant region were analyzed with reporter gene assays. To assess the effect of zinc finger E box-binding homeobox 1 transcription factor (ZEB1), siRNA-mediated knockdown and overexpression experiments were performed. Association of GUCY1A3 genotype and cellular phenotypes was analyzed with vascular smooth muscle cell migration assays and platelet aggregation analyses. RESULTS Whole-blood GUCY1A3 mRNA levels were significantly lower in individuals homozygous for the lead (rs7692387) risk variant. Likewise, reporter gene assays demonstrated significantly lower GUCY1A3 promoter activity for constructs carrying this allele. In silico analyses located a DNase I hypersensitivity site to rs7692387 and predicted binding of the transcription factor ZEB1 rather to the nonrisk allele, which was confirmed experimentally. Knockdown of ZEB1 resulted in more profound reduction of nonrisk allele promoter activity and a significant reduction of endogenous GUCY1A3 expression. Ex vivo-studied platelets from homozygous nonrisk allele carriers displayed enhanced inhibition of ADP-induced platelet aggregation by the nitric oxide donor sodium nitroprusside and the phosphodiesterase 5 inhibitor sildenafil compared with homozygous risk allele carriers. Moreover, pharmacological stimulation of sGC led to reduced migration only in vascular smooth muscle cells homozygous for the nonrisk allele. In the Hybrid Mouse Diversity Panel, higher levels of GUCY1A3 expression correlated with less atherosclerosis in the aorta. CONCLUSIONS Rs7692387 is located in an intronic site that modulates GUCY1A3 promoter activity. The transcription factor ZEB1 binds preferentially to the nonrisk allele, leading to an increase in GUCY1A3 expression, higher sGC levels, and higher sGC activity after stimulation. Finally, human and mouse data link augmented sGC expression to lower risk of atherosclerosis.
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Affiliation(s)
- Thorsten Kessler
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.).
| | - Jana Wobst
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Bernhard Wolf
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Juliane Eckhold
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Baiba Vilne
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Ronja Hollstein
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Simon von Ameln
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Tan An Dang
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Hendrik B Sager
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Philipp Moritz Rumpf
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Redouane Aherrahrou
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Adnan Kastrati
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Johan L M Björkegren
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Jeanette Erdmann
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Aldons J Lusis
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Mete Civelek
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Frank J Kaiser
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.)
| | - Heribert Schunkert
- From Deutsches Herzzentrum München, Klinik für Herz-und Kreislauferkrankungen, Technische Universität München, Munich, Germany (T.K., J.W., B.W., B.V., S.V.A., T.A.D., H.B.S., P.M.R., A.K., H.S.); Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Germany (J. Eckhold, R.H., F.J.K.); Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville (R.A., M.C.); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany (A.K., H.S.); Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (J.L.M.B.); Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Estonia (J.L.M.B.); Institut für Integrative und Experimentelle Genomik and Universitäres Herzzentrum Lübeck, Universität zu Lübeck, Germany (J. Erdmann); DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany (J. Erdmann, F.J.K.); and Departments of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles (A.J.L., M.C.).
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48
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Haitjema S, Meddens CA, van der Laan SW, Kofink D, Harakalova M, Tragante V, Foroughi Asl H, van Setten J, Brandt MM, Bis JC, O’Donnell C, Cheng C, Hoefer IE, Waltenberger J, Biessen E, Jukema JW, Doevendans PA, Nieuwenhuis EE, Erdmann J, Björkegren JL, Pasterkamp G, Asselbergs FW, den Ruijter HM, Mokry M. Additional Candidate Genes for Human Atherosclerotic Disease Identified Through Annotation Based on Chromatin Organization. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.116.001664. [DOI: 10.1161/circgenetics.116.001664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 12/12/2016] [Indexed: 11/16/2022]
Abstract
Background—
As genome-wide association efforts, such as CARDIoGRAM and METASTROKE, are ongoing to reveal susceptibility loci for their underlying disease—atherosclerotic disease—identification of candidate genes explaining the associations of these loci has proven the main challenge. Many disease susceptibility loci colocalize with DNA regulatory elements, which influence gene expression through chromatin interactions. Therefore, the target genes of these regulatory elements can be considered candidate genes. Applying these biological principles, we used an alternative approach to annotate susceptibility loci and identify candidate genes for human atherosclerotic disease based on circular chromosome conformation capture followed by sequencing.
Methods and Results—
In human monocytes and coronary endothelial cells, we generated 63 chromatin interaction data sets for 37 active DNA regulatory elements that colocalize with known susceptibility loci for coronary artery disease (CARDIoGRAMplusC4D) and large artery stroke (METASTROKE). By circular chromosome conformation capture followed by sequencing, we identified a physical 3-dimensional interaction with 326 candidate genes expressed in at least 1 of these cell types, of which 294 have not been reported before. We highlight 16 genes based on expression quantitative trait loci.
Conclusions—
Our findings provide additional candidate-gene annotation for 37 disease susceptibility loci for human atherosclerotic disease that are of potential interest to better understand the complex pathophysiology of cardiovascular diseases.
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49
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Rossignoli A, Shang MM, Gladh H, Moessinger C, Foroughi Asl H, Talukdar HA, Franzén O, Mueller S, Björkegren JL, Folestad E, Skogsberg J. Poliovirus Receptor–Related 2. Arterioscler Thromb Vasc Biol 2017; 37:534-542. [DOI: 10.1161/atvbaha.116.308715] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 12/19/2016] [Indexed: 12/27/2022]
Abstract
Objective—
Recently, poliovirus receptor–related 2 (
Pvrl2
) emerged as a top gene in a global gene expression study aiming to detect plasma cholesterol–responsive genes causally related to atherosclerosis regression in hypercholesterolemic mice. PVRL2 is an adherens junction protein implied to play a role in transendothelial migration of leukocytes, a key feature in atherosclerosis development. In this study, we investigated the effect of
Pvrl2
deficiency on atherosclerosis development and transendothelial migration of leukocytes activity.
Approach and Results—
Pvrl2
-deficient mice bred onto an atherosclerosis-prone background (
Pvrl2
−/−
Ldlr
−/−
Apob
100/100
) had less atherosclerotic lesions and more stable plaques compared with littermate controls (
Pvrl2
+/+
Ldlr
−/−
Apob
100/100
).
Pvrl2
−/−
Ldlr
−/−
Apob
100/100
mice also showed a 49% decrease in transendothelial migration of leukocytes activity observed using the in vivo air pouch model. In accordance, augmented arterial wall expression of
Pvrl2
during atherosclerosis progression coincided with an increased gene expression of migrating leukocytes into the vessel wall. Both in human and mice, gene and protein expression of PVRL2 was predominantly observed in the vascular endothelium according to the immunohistochemical and gene expression data. In addition, the cholesterol responsiveness of
PVRL2
was also observed in humans.
Conclusions—
PVRL2 is a plasma cholesterol–responsive gene acting at endothelial sites of vascular inflammation that could potentially be a new therapeutic target for atherosclerosis prevention through its suggested transendothelial migration of leukocytes modulating activity.
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Affiliation(s)
- Aránzazu Rossignoli
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Ming-Mei Shang
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Hanna Gladh
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Christine Moessinger
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Hassan Foroughi Asl
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Husain Ahammad Talukdar
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Oscar Franzén
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Steffen Mueller
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Johan L.M. Björkegren
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Erika Folestad
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
| | - Josefin Skogsberg
- From the Division of Vascular Biology, Department of Medical Biochemistry and Biophysics (A.R., H.G., C.M., H.F.A., H.A.T., J.L.M.B., E.F., J.S.) and Unit of Computational Medicine, Department of Medicine (M.-M.S.), Karolinska Institutet, Stockholm, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (O.F., J.L.M.B.); and Department of Molecular Genetics and Microbiology, Stony Brook University, New
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50
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Meddens CA, Harakalova M, van den Dungen NAM, Foroughi Asl H, Hijma HJ, Cuppen EPJG, Björkegren JLM, Asselbergs FW, Nieuwenhuis EES, Mokry M. Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease. Genome Biol 2016; 17:247. [PMID: 27903283 PMCID: PMC5131449 DOI: 10.1186/s13059-016-1100-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate genes is predominantly based on genes that localize close to or within identified loci. We have recently shown that 92 of the 163 inflammatory bowel disease (IBD)-loci co-localize with non-coding DNA regulatory elements (DREs). Mutations in DREs can contribute to IBD pathogenesis through dysregulation of gene expression. Consequently, genes that are regulated by these 92 DREs are to be considered as candidate genes. This study uses circular chromosome conformation capture-sequencing (4C-seq) to systematically analyze chromatin-interactions at IBD susceptibility loci that localize to regulatory DNA. RESULTS Using 4C-seq, we identify genomic regions that physically interact with the 92 DRE that were found at IBD susceptibility loci. Since the activity of regulatory elements is cell-type specific, 4C-seq was performed in monocytes, lymphocytes, and intestinal epithelial cells. Altogether, we identified 902 novel IBD candidate genes. These include genes specific for IBD-subtypes and many noteworthy genes including ATG9A and IL10RA. We show that expression of many novel candidate genes is genotype-dependent and that these genes are upregulated during intestinal inflammation in IBD. Furthermore, we identify HNF4α as a potential key upstream regulator of IBD candidate genes. CONCLUSIONS We reveal many novel and relevant IBD candidate genes, pathways, and regulators. Our approach complements classical candidate gene identification, links novel genes to IBD and can be applied to any existing GWAS data.
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Affiliation(s)
- Claartje A. Meddens
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Hassan Foroughi Asl
- Vascular Biology Unit, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hemme J. Hijma
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - Edwin P. J. G. Cuppen
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
| | - Johan L. M. Björkegren
- Vascular Biology Unit, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
- Durrer Center for Cardiogenetic Research, Utrecht, The Netherlands
- Institute of Cardiovascular Science, University College London, London, UK
| | - Edward E. S. Nieuwenhuis
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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