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Selvarajan I, Kiema M, Huang RT, Li J, Zhu J, Pölönen P, Örd T, Õunap K, Godiwala M, Golebiewski AK, Ravindran A, Mäklin K, Toropainen A, Stolze LK, Arce M, Magnusson PU, White S, Romanoski CE, Heinäniemi M, Laakkonen JP, Fang Y, Kaikkonen MU. Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro. Arterioscler Thromb Vasc Biol 2024; 44:1330-1345. [PMID: 38602103 PMCID: PMC11111333 DOI: 10.1161/atvbaha.123.318964] [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: 01/05/2023] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND CALCRL (calcitonin receptor-like) protein is an important mediator of the endothelial fluid shear stress response, which is associated with the genetic risk of coronary artery disease. In this study, we functionally characterized the noncoding regulatory elements carrying coronary artery disease that risks single-nucleotide polymorphisms and studied their role in the regulation of CALCRL expression in endothelial cells. METHODS To functionally characterize the coronary artery disease single-nucleotide polymorphisms harbored around the gene CALCRL, we applied an integrative approach encompassing statistical, transcriptional (RNA-seq), and epigenetic (ATAC-seq [transposase-accessible chromatin with sequencing], chromatin immunoprecipitation assay-quantitative polymerase chain reaction, and electromobility shift assay) analyses, alongside luciferase reporter assays, and targeted gene and enhancer perturbations (siRNA and clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9) in human aortic endothelial cells. RESULTS We demonstrate that the regulatory element harboring rs880890 exhibits high enhancer activity and shows significant allelic bias. The A allele was favored over the G allele, particularly under shear stress conditions, mediated through alterations in the HSF1 (heat shock factor 1) motif and binding. CRISPR deletion of rs880890 enhancer resulted in downregulation of CALCRL expression, whereas HSF1 knockdown resulted in a significant decrease in rs880890-enhancer activity and CALCRL expression. A significant decrease in HSF1 binding to the enhancer region in endothelial cells was observed under disturbed flow compared with unidirectional flow. CALCRL knockdown and variant perturbation experiments indicated the role of CALCRL in mediating eNOS (endothelial nitric oxide synthase), APLN (apelin), angiopoietin, prostaglandins, and EDN1 (endothelin-1) signaling pathways leading to a decrease in cell proliferation, tube formation, and NO production. CONCLUSIONS Overall, our results demonstrate the existence of an endothelial-specific HSF (heat shock factor)-regulated transcriptional enhancer that mediates CALCRL expression. A better understanding of CALCRL gene regulation and the role of single-nucleotide polymorphisms in the modulation of CALCRL expression could provide important steps toward understanding the genetic regulation of shear stress signaling responses.
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Affiliation(s)
- Ilakya Selvarajan
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Miika Kiema
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Ru-Ting Huang
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jin Li
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jiayu Zhu
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Petri Pölönen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211, Kuopio, Finland
| | - Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Kadri Õunap
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Mehvash Godiwala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Anna Kathryn Golebiewski
- Department of Cellular and Molecular Medicine, The College of Medicine, The University of Arizona; Tucson, AZ 85721, USA
| | - Aarthi Ravindran
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Kiira Mäklin
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Anu Toropainen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Lindsey K. Stolze
- Department of Cellular and Molecular Medicine, The College of Medicine, The University of Arizona; Tucson, AZ 85721, USA
| | - Maximiliano Arce
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peetra U. Magnusson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Stephen White
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE1 3BZ, UK
| | - Casey E. Romanoski
- Department of Cellular and Molecular Medicine, The College of Medicine, The University of Arizona; Tucson, AZ 85721, USA
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211, Kuopio, Finland
| | - Johanna P. Laakkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Yun Fang
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
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2
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Zheng H, Wang S, Li X, Hu H. A computational modeling of pri-miRNA expression. PLoS One 2024; 19:e0290768. [PMID: 38165860 PMCID: PMC10760784 DOI: 10.1371/journal.pone.0290768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/15/2023] [Indexed: 01/04/2024] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in gene regulation. Most studies focus on mature miRNAs, which leaves many unknowns about primary miRNAs (pri-miRNAs). To fill the gap, we attempted to model the expression of pri-miRNAs in 1829 primary cell types, cell lines, and tissues in this study. We demonstrated that the expression of pri-miRNAs can be modeled well by the expression of specific sets of mRNAs, which we termed their associated mRNAs. These associated mRNAs differ from their corresponding target mRNAs and are enriched with specific functions. Most associated mRNAs of a miRNA are shared across conditions, while on average, about one-fifth of the associated mRNAs are condition-specific. Our study shed new light on understanding miRNA biogenesis and general gene transcriptional regulation.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
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3
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Wei Y, Yang C, Liu Y, Sun D, Li X, Wei R, Nian H. Mettl3 induced miR-338-3p expression in dendritic cells promotes antigen-specific Th17 cell response via regulation of Dusp16. FASEB J 2023; 37:e23277. [PMID: 37878342 DOI: 10.1096/fj.202300893r] [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: 05/04/2023] [Revised: 08/25/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]
Abstract
Pathogenic Th17 cells are critical drivers of multiple autoimmune diseases, including uveitis and its animal model, experimental autoimmune uveitis (EAU). However, how innate immune signals modulate pathogenic Th17 responses remains largely unknown. Here, we showed that miR-338-3p endowed dendritic cells (DCs) with an increased ability to activate interphotoreceptor retinoid-binding protein (IRBP)1-20 -specific Th17 cells by promoting the production of IL-6, IL-1β, and IL-23. In vivo administration of LV-miR-338-infected DCs promoted pathogenic Th17 responses and exacerbated EAU development. Mechanistically, dual-specificity phosphatase 16 (Dusp16) was a molecular target of miR-338-3p. miR-338-3p repressed Dusp16 and therefore strengthened the mitogen-activated protein kinase (MAPK) p38 signaling, resulting in increased production of Th17-polarizing cytokines and subsequent pathogenic Th17 responses. In addition, methyltransferase like 3 (Mettl3), a key m6A methyltransferase, mediated the upregulation of miR-338-3p in activated DCs. Together, our findings identify a vital role for Mettl3/miR-338-3p/Dusp16/p38 signaling in DCs-driven pathogenic Th17 responses and suggest a potential therapeutic avenue for uveitis and other Th17 cell-related autoimmune disorders.
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Affiliation(s)
- Yankai Wei
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Chao Yang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Yuling Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Deming Sun
- Doheny Eye Institute, Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Xiaorong Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Ruihua Wei
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Hong Nian
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
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4
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Cimen I, Natarelli L, Abedi Kichi Z, Henderson JM, Farina FM, Briem E, Aslani M, Megens RTA, Jansen Y, Mann-Fallenbuchel E, Gencer S, Duchêne J, Nazari-Jahantigh M, van der Vorst EPC, Enard W, Döring Y, Schober A, Santovito D, Weber C. Targeting a cell-specific microRNA repressor of CXCR4 ameliorates atherosclerosis in mice. Sci Transl Med 2023; 15:eadf3357. [PMID: 37910599 DOI: 10.1126/scitranslmed.adf3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
The CXC chemokine receptor 4 (CXCR4) in endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) is crucial for vascular integrity. The atheroprotective functions of CXCR4 in vascular cells may be counteracted by atherogenic functions in other nonvascular cell types. Thus, strategies for cell-specifically augmenting CXCR4 function in vascular cells are crucial if this receptor is to be useful as a therapeutic target in treating atherosclerosis and other vascular disorders. Here, we identified miR-206-3p as a vascular-specific CXCR4 repressor and exploited a target-site blocker (CXCR4-TSB) that disrupted the interaction of miR-206-3p with CXCR4 in vitro and in vivo. In vitro, CXCR4-TSB enhanced CXCR4 expression in human and murine ECs and VSMCs to modulate cell viability, proliferation, and migration. Systemic administration of CXCR4-TSB in Apoe-deficient mice enhanced Cxcr4 expression in ECs and VSMCs in the walls of blood vessels, reduced vascular permeability and monocyte adhesion to endothelium, and attenuated the development of diet-induced atherosclerosis. CXCR4-TSB also increased CXCR4 expression in B cells, corroborating its atheroprotective role in this cell type. Analyses of human atherosclerotic plaque specimens revealed a decrease in CXCR4 and an increase in miR-206-3p expression in advanced compared with early lesions, supporting a role for the miR-206-3p-CXCR4 interaction in human disease. Disrupting the miR-206-3p-CXCR4 interaction in a cell-specific manner with target-site blockers is a potential therapeutic approach that could be used to treat atherosclerosis and other vascular diseases.
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Affiliation(s)
- Ismail Cimen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Zahra Abedi Kichi
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - James M Henderson
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Floriana M Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Eva Briem
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 85152 Planegg-Martinsried, Germany
| | - Maria Aslani
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biomedical Engineering, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6200 MD Maastricht, Netherlands
| | - Yvonne Jansen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Elizabeth Mann-Fallenbuchel
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Selin Gencer
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Johan Duchêne
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Maliheh Nazari-Jahantigh
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Emiel P C van der Vorst
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, 52074 Aachen, Germany
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52062 Aachen, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 85152 Planegg-Martinsried, Germany
| | - Yvonne Döring
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Angiology, Swiss Cardiovascular Center, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland
| | - Andreas Schober
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Institute of Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council (CNR), 20090 Milan, Italy
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6229 HX Maastricht, Netherlands
- Munich Cluster for Systems Neurology (SyNergy), 81337 Munich, Germany
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5
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Bian X, Peng H, Wang Y, Guo H, Shi G. MicroRNA-22-3p alleviates atherosclerosis by mediating macrophage M2 polarization as well as inhibiting NLRP3 activation. J Int Med Res 2023; 51:3000605231197071. [PMID: 37824732 PMCID: PMC10571701 DOI: 10.1177/03000605231197071] [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: 03/07/2023] [Accepted: 08/08/2023] [Indexed: 10/14/2023] Open
Abstract
OBJECTIVE MicroRNA (miR)-22-3p is expressed in atherosclerosis (AS), but its function and regulatory mechanisms remain unclear. Therefore, the effects of miR-22-3p in AS were assessed in this study. METHODS MiR-22-3p expression was assessed in AS, and miR-22-3p target genes were predicted using sequencing transcriptomics. The effect of miR-22-3p agomir on atherosclerotic lesions in an AS mouse model were determined by Oil red O, Masson's, and sirius red staining, and by anti-smooth muscle actin and macrophage antigen-3 immunostaining. Gene expression in AS was evaluated by western blot and immunofluorescence. RESULTS MiR-22-3p was expressed in AS and control samples (32.5% and 33.9% levels, respectively, relative to total miRNA among six highly expressed miRNAs). In the mouse model of AS, miR-22-3p agomir significantly reduced lipid deposition, proliferation of aortic collagen fibres, and macrophage content. Additionally, inducible nitric oxide synthase, interleukin-6, and tumour necrosis factor-α levels were significantly reduced, and levels of arginase 1 and CD206 were significantly enhanced. MiR-22-3p was found to target janus kinase 1(JAK1), and significantly inhibited the activation of NLR family pyrin domain containing 3 (NLRP3) and JAK1 in mice. CONCLUSIONS MiR-22-3p appears to reduce the inflammatory response in AS, which might be achieved by inducing the M2 macrophage phenotype and suppressing NLRP3 activation via JAK1.
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Affiliation(s)
- Xiaoyan Bian
- Department of Ultrasound, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Ultrasound, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Haoyang Peng
- Department of Ultrasound, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yin Wang
- Department of Orthopaedics, Shijiazhuang People’s Hospital, Shijiazhuang, Hebei, China
| | - Hongjiang Guo
- Department of Ultrasound, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Gaofeng Shi
- Department of Ultrasound, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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6
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Yu Z, Yin J, Tang Z, Hu T, Wang Z, Chen Y, Liu T, Zhang W. Non-coding RNAs are key players and promising therapeutic targets in atherosclerosis. Front Cell Dev Biol 2023; 11:1237941. [PMID: 37719883 PMCID: PMC10502512 DOI: 10.3389/fcell.2023.1237941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/22/2023] [Indexed: 09/19/2023] Open
Abstract
Cardiovascular disease (CVD) is the primary cause of death in humans. Atherosclerosis (AS) is the most common CVD and a major cause of many CVD-related fatalities. AS has numerous risk factors and complex pathogenesis, and while it has long been a research focus, most mechanisms underlying its progression remain unknown. Noncoding RNAs (ncRNAs) represent an important focus in epigenetics studies and are critical biological regulators that form a complex network of gene regulation. Abnormal ncRNA expression disrupts the normal function of tissues or cells, leading to disease development. A large body of evidence suggests that ncRNAs are involved in all stages of atherosclerosis, from initiation to progression, and that some are significantly differentially expressed during AS development, suggesting that they may be powerful markers for screening AS or potential treatment targets. Here, we review the role of ncRNAs in AS development and recent developments in the use of ncRNAs for AS-targeted therapy, providing evidence for ncRNAs as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Zhun Yu
- School of Clinical Medical, Changchun University of Chinese Medicine, Jilin, China
| | - JinZhu Yin
- Cardiology Department, Affiliated Hospital of Changchun University of Chinese Medicine, Jilin, China
| | - ZhiTong Tang
- Department of Massage, Affiliated Hospital of Changchun University of Chinese Medicine, Jilin, China
| | - Ting Hu
- Internal Medicine of Chinese Medicine, Affiliated Hospital of Changchun University of Chinese Medicine, Jilin, China
| | - ZhuoEr Wang
- School of Clinical Medical, Changchun University of Chinese Medicine, Jilin, China
| | - Ying Chen
- Cardiology Department, Affiliated Hospital of Changchun University of Chinese Medicine, Jilin, China
| | - Tianjia Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Jilin, China
| | - Wei Zhang
- Orthopedics Department, The Third Affiliated Hospital of Changchun University of Chinese Medicine, Jilin, China
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7
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Örd T, Lönnberg T, Nurminen V, Ravindran A, Niskanen H, Kiema M, Õunap K, Maria M, Moreau PR, Mishra PP, Palani S, Virta J, Liljenbäck H, Aavik E, Roivainen A, Ylä-Herttuala S, Laakkonen JP, Lehtimäki T, Kaikkonen MU. Dissecting the polygenic basis of atherosclerosis via disease-associated cell state signatures. Am J Hum Genet 2023; 110:722-740. [PMID: 37060905 PMCID: PMC10183377 DOI: 10.1016/j.ajhg.2023.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/21/2023] [Indexed: 04/17/2023] Open
Abstract
Coronary artery disease (CAD) is a pandemic disease where up to half of the risk is explained by genetic factors. Advanced insights into the genetic basis of CAD require deeper understanding of the contributions of different cell types, molecular pathways, and genes to disease heritability. Here, we investigate the biological diversity of atherosclerosis-associated cell states and interrogate their contribution to the genetic risk of CAD by using single-cell and bulk RNA sequencing (RNA-seq) of mouse and human lesions. We identified 12 disease-associated cell states that we characterized further by gene set functional profiling, ligand-receptor prediction, and transcription factor inference. Importantly, Vcam1+ smooth muscle cell state genes contributed most to SNP-based heritability of CAD. In line with this, genetic variants near smooth muscle cell state genes and regulatory elements explained the largest fraction of CAD-risk variance between individuals. Using this information for variant prioritization, we derived a hybrid polygenic risk score (PRS) that demonstrated improved performance over a classical PRS. Our results provide insights into the biological mechanisms associated with CAD risk, which could make a promising contribution to precision medicine and tailored therapeutic interventions in the future.
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Affiliation(s)
- Tiit Örd
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Valtteri Nurminen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Aarthi Ravindran
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Miika Kiema
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kadri Õunap
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maleeha Maria
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Pierre R Moreau
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland
| | - Senthil Palani
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland
| | - Jenni Virta
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland
| | - Heidi Liljenbäck
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland; Turku Center for Disease Modeling, University of Turku, 20520 Turku, Finland
| | - Einari Aavik
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Anne Roivainen
- Turku PET Centre, University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland; Turku Center for Disease Modeling, University of Turku, 20520 Turku, Finland; Turku PET Centre, Turku University Hospital, 20520 Turku, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Johanna P Laakkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland.
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8
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Giannella A, Castelblanco E, Zambon CF, Basso D, Hernandez M, Ortega E, Alonso N, Mauricio D, Avogaro A, Ceolotto G, Vigili de Kreutzenberg S. Circulating Small Noncoding RNA Profiling as a Potential Biomarker of Atherosclerotic Plaque Composition in Type 1 Diabetes. Diabetes Care 2023; 46:551-560. [PMID: 36577032 PMCID: PMC10020028 DOI: 10.2337/dc22-1441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Cardiovascular disease (CVD) accounts for most deaths in patients with type 1 diabetes (T1D); however, the determinants of plaque composition are unknown. miRNAs regulate gene expression, participate in the development of atherosclerosis, and represent promising CVD biomarkers. This study analyzed the circulating miRNA expression profile in T1D with either carotid calcified (CCP) or fibrous plaque (CFP). RESEARCH DESIGN AND METHODS Circulating small noncoding RNAs were sequenced and quantified using next-generation sequencing and bioinformatic analysis in an exploratory set of 26 subjects with T1D with CCP and in 25 with CFP. Then, in a validation set of 40 subjects with CCP, 40 with CFP, and 24 control subjects with T1D, selected miRNA expression was measured by digital droplet PCR. Putative gene targets enriched for pathways implicated in atherosclerosis/vascular calcification/diabetes were analyzed. The patients' main clinical characteristics were also recorded. RESULTS miR-503-5p, let-7d-5p, miR-106b-3p, and miR-93-5p were significantly upregulated, while miR-10a-5p was downregulated in patients with CCP compared with CFP (all fold change >±1.5; P < 0.05). All candidate miRNAs showed a significant correlation with LDL-cholesterol, direct for the upregulated and inverse for the downregulated miRNA, in CCP. Many target genes of upregulated miRNAs in CCP participate in osteogenic differentiation, apoptosis, inflammation, cholesterol metabolism, and extracellular matrix organization. CONCLUSIONS These findings characterize miRNAs and their signature in the regulatory network of carotid plaque phenotype in T1D, providing new insights into plaque pathophysiology and possibly novel biomarkers of plaque composition.
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Affiliation(s)
| | - Esmeralda Castelblanco
- Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
- Unitat de Suport a la Recerca Barcelona, Institut Universitari d’Investigació en Atenció Primària Jordi Gol i Gurina, Barcelona, Spain
| | | | - Daniela Basso
- Department of Medicine, University of Padova, Padova, Italy
| | - Marta Hernandez
- Department of Endocrinology & Nutrition, Hospital Arnau de Vilanova and Institut d’Investigació Biomédica de Lleida, Lleida, Spain
| | - Emilio Ortega
- Department of Endocrinology & Nutrition, Diabetes Unit, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Center for Biomedical Research on Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
| | - Nuria Alonso
- Department of Endocrinology and Nutrition, Health Sciences Research Institute and University Hospital Germans Trias i Pujol, Badalona, Spain
- CIBERDEM, Barcelona, Spain
| | - Didac Mauricio
- Unitat de Suport a la Recerca Barcelona, Institut Universitari d’Investigació en Atenció Primària Jordi Gol i Gurina, Barcelona, Spain
- CIBERDEM, Barcelona, Spain
- Department of Endocrinology and Nutrition, Hospital de la Santa Creu i Sant Pau and Sant Pau Biomedical Research Institute, Barcelona, Spain
- Faculty of Medicine, University of Vic–Central University of Catalonia, Vic, Spain
| | - Angelo Avogaro
- Department of Medicine, University of Padova, Padova, Italy
- Corresponding authors: Saula Vigili de Kreutzenberg, , and Angelo Avogaro,
| | | | - Saula Vigili de Kreutzenberg
- Department of Medicine, University of Padova, Padova, Italy
- Corresponding authors: Saula Vigili de Kreutzenberg, , and Angelo Avogaro,
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9
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Sun Z, Wu Y, Gao F, Li H, Wang C, Du L, Dong L, Jiang Y. In situ detection of exosomal RNAs for cancer diagnosis. Acta Biomater 2023; 155:80-98. [PMID: 36343908 DOI: 10.1016/j.actbio.2022.10.061] [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: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Exosomes are considered as biomarkers reflecting the physiological state of the human body. Studies have revealed that the expression levels of specific exosomal RNAs are closely associated with certain cancers. Thus, detection of exosomal RNA offers a new avenue for liquid biopsy of cancers. Many exosomal RNA detection methods based on various principles have been developed, and most of the methods detect the extracted RNAs after lysing exosomes. Besides complex and time-consuming extraction steps, a major drawback of this approach is the degradation of the extracted RNAs in the absence of plasma membrane and cytosol. In addition, there is considerable loss of RNAs during their extraction. In situ detection of exosomal RNAs can avoid these drawbacks, thus allowing higher diagnostic reliability. In this paper, in situ detection of exosomal RNAs was systematically reviewed from the perspectives of detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, and involved functional materials. Furthermore, the limitations and possible improvements of the current in situ detection methods for exosomal RNAs towards the clinical diagnostic application are discussed. This review aims to provide a valuable reference for the development of in situ exosomal RNA detection strategies for non-invasive diagnosis of cancers. STATEMENT OF SIGNIFICANCE: Certain RNAs have been identified as valuable biomarkers for some cancers, and sensitive detection of cancer-related RNAs is expected to achieve better diagnostic efficacy. Currently, the detection of exosomal RNAs is receiving increasing attention due to their high stability and significant concentration differences between patients and healthy individuals. In situ detection of exosomal RNAs has greater diagnostic reliability due to the avoidance of RNA degradation and loss. However, this mode is still limited by some factors such as detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, etc. This review focuses on the progress of in situ detection of exosomal RNAs and aims to promote the development of this field.
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Affiliation(s)
- Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Yanqiu Wu
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Fucheng Gao
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Hui Li
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, China.
| | - Lun Dong
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan 250012, China.
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan 250061, China.
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10
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Korvenlaita N, Gómez‐Budia M, Scoyni F, Pistono C, Giudice L, Eamen S, Loppi S, de Sande AH, Huremagic B, Bouvy‐Liivrand M, Heinäniemi M, Kaikkonen MU, Cheng L, Hill AF, Kanninen KM, Jenster GW, van Royen ME, Ramiro L, Montaner J, Batkova T, Mikulik R, Giugno R, Jolkkonen J, Korhonen P, Malm T. Dynamic release of neuronal extracellular vesicles containing miR-21a-5p is induced by hypoxia. J Extracell Vesicles 2023; 12:e12297. [PMID: 36594832 PMCID: PMC9809533 DOI: 10.1002/jev2.12297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hypoxia induces changes in the secretion of extracellular vesicles (EVs) in several non-neuronal cells and pathological conditions. EVs are packed with biomolecules, such as microRNA(miR)-21-5p, which respond to hypoxia. However, the true EV association of miR-21-5p, and its functional or biomarker relevance, are inadequately characterised. Neurons are extremely sensitive cells, and it is not known whether the secretion of neuronal EVs and miR-21-5p are altered upon hypoxia. Here, we characterised the temporal EV secretion profile and cell viability of neurons under hypoxia. Hypoxia induced a rapid increase of miR-21a-5p secretion in the EVs, which preceded the elevation of hypoxia-induced tissue or cellular miR-21a-5p. Prolonged hypoxia induced cell death and the release of morphologically distinct EVs. The EVs protected miR-21a-5p from enzymatic degradation but a remarkable fraction of miR-21a-5p remained fragile and non-EV associated. The increase in miR-21a-5p secretion may have biomarker potential, as high blood levels of miR-21-5p in stroke patients were associated with significant disability at hospital discharge. Our data provides an understanding of the dynamic regulation of EV secretion from neurons under hypoxia and provides a candidate for the prediction of recovery from ischemic stroke.
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Affiliation(s)
- Nea Korvenlaita
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Mireia Gómez‐Budia
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Flavia Scoyni
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Cristiana Pistono
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Luca Giudice
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland,Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly
| | - Shaila Eamen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Sanna Loppi
- Department of ImmunologyUniversity of ArizonaTucsonArizonaUSA
| | - Ana Hernández de Sande
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Benjamin Huremagic
- Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly,Department of Human GeneticsKU LeuvenLeuvenFlandersBelgium
| | | | | | - Minna U. Kaikkonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Lesley Cheng
- Department of Biochemistry and ChemistrySchool of Agriculture Biomedicine & EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Andrew F. Hill
- Department of Biochemistry and ChemistrySchool of Agriculture Biomedicine & EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia,La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia,Institute for Health and SportVictoria UniversityMelbourneVictoriaAustralia
| | - Katja M. Kanninen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Guido W. Jenster
- Department of UrologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Martin E. van Royen
- Department of PathologyErasmus University Medical CenterRotterdamThe Netherlands
| | - Laura Ramiro
- Neurovascular Research LaboratoryVall d'Hebron Institute of Research (VHIR)Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Montaner
- Neurovascular Research LaboratoryVall d'Hebron Institute of Research (VHIR)Universitat Autònoma de BarcelonaBarcelonaSpain,Institute de Biomedicine of SevilleIBiS/Hospital Universitario Virgen del Rocío/CSIC/University of Seville & Department of NeurologyHospital Universitario Virgen MacarenaSevilleAndalucíaSpain
| | - Tereza Batkova
- BioVendor‐laboratorni medicina a.s.BrnoCzech Republic,International Clinical Research CenterNeurological DepartmentSt. Anne's University Hospital and Masaryk UniversityBrnoCzech Republic
| | - Robert Mikulik
- International Clinical Research CenterNeurological DepartmentSt. Anne's University Hospital and Masaryk UniversityBrnoCzech Republic
| | - Rosalba Giugno
- Department of Computer ScienceUniversity of VeronaVeronaVenetoItaly
| | - Jukka Jolkkonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Paula Korhonen
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
| | - Tarja Malm
- University of Eastern FinlandA.I. Virtanen Institute for Molecular SciencesKuopioFinland
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11
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There is urgent need to treat atherosclerotic cardiovascular disease risk earlier, more intensively, and with greater precision: A review of current practice and recommendations for improved effectiveness. Am J Prev Cardiol 2022; 12:100371. [PMID: 36124049 PMCID: PMC9482082 DOI: 10.1016/j.ajpc.2022.100371] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/10/2022] [Accepted: 08/05/2022] [Indexed: 12/12/2022] Open
Abstract
Atherosclerotic cardiovascular disease (ASCVD) is epidemic throughout the world and is etiologic for such acute cardiovascular events as myocardial infarction, ischemic stroke, unstable angina, and death. ASCVD also impacts risk for dementia, chronic kidney disease peripheral arterial disease and mobility, impaired sexual response, and a host of other visceral impairments that adversely impact the quality and rate of progression of aging. The relationship between low-density lipoprotein cholesterol (LDL-C) and risk for ASCVD is one of the most highly established and investigated issues in the entirety of modern medicine. Elevated LDL-C is a necessary condition for atherogenesis induction. Basic scientific investigation, prospective longitudinal cohorts, and randomized clinical trials have all validated this association. Yet despite the enormous number of clinical trials which support the need for reducing the burden of atherogenic lipoprotein in blood, the percentage of high and very high-risk patients who achieve risk stratified LDL-C target reductions is low and has remained low for the last thirty years. Atherosclerosis is a preventable disease. As clinicians, the time has come for us to take primordial and primary prevention more serously. Despite a plethora of therapeutic approaches, the large majority of patients at risk for ASCVD are poorly or inadequately treated, leaving them vulnerable to disease progression, acute cardiovascular events, and poor aging due to loss of function in multiple visceral organs. Herein we discuss the need to greatly intensify efforts to reduce risk, decrease disease burden, and provide more comprehensive and earlier risk assessment to optimally prevent ASCVD and its complications. Evidence is presented to support that treatment should aim for far lower goals in cholesterol management, should take into account many more factors than commonly employed today and should begin significantly earlier in life.
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12
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Du M, Espinosa-Diez C, Liu M, Ahmed IA, Mahan S, Wei J, Handen AL, Chan SY, Gomez D. miRNA/mRNA co-profiling identifies the miR-200 family as a central regulator of SMC quiescence. iScience 2022; 25:104169. [PMID: 35465051 PMCID: PMC9018390 DOI: 10.1016/j.isci.2022.104169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/01/2022] [Accepted: 03/24/2022] [Indexed: 12/14/2022] Open
Abstract
miRNAs are versatile regulators of smooth muscle cell (SMC) fate and behavior in vascular development and disease. Targeted loss-of-function studies have established the relevance of specific miRNAs in controlling SMC differentiation or mediating phenotypic modulation. Our goal was to characterize SMC miRNAome and its contribution to transcriptome changes during phenotypic modulation. Small RNA sequencing revealed that dedifferentiation led to the differential expression of over 50 miRNAs in cultured SMC. miRNA/mRNA comparison predicted that over a third of SMC transcript expression was regulated by differentially expressed miRNAs. Our screen identified the miR-200 cluster as highly downregulated during dedifferentiation. miR-200 maintains SMC quiescence and represses proliferation, migration, and neointima formation, in part by targeting Quaking, a central SMC phenotypic switching mediator. Our study unraveled the substantial contribution of miRNAs in regulating the SMC transcriptome and identified the miR-200 cluster as a pro-quiescence mechanism and a potential inhibitor of vascular restenosis.
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Affiliation(s)
- Mingyuan Du
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Vascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Cristina Espinosa-Diez
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mingjun Liu
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ibrahim Adeola Ahmed
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sidney Mahan
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jianxin Wei
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Adam L Handen
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Stephen Y Chan
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Delphine Gomez
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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13
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Santovito D, Weber C. Non-canonical features of microRNAs: paradigms emerging from cardiovascular disease. Nat Rev Cardiol 2022; 19:620-638. [PMID: 35304600 DOI: 10.1038/s41569-022-00680-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
Research showing that microRNAs (miRNAs) are versatile regulators of gene expression has instigated tremendous interest in cardiovascular research. The overwhelming majority of studies are predicated on the dogmatic notion that miRNAs regulate the expression of specific target mRNAs by inhibiting mRNA translation or promoting mRNA decay in the RNA-induced silencing complex (RISC). These efforts mostly identified and dissected contributions of multiple regulatory networks of miRNA-target mRNAs to cardiovascular pathogenesis. However, evidence from studies in the past decade indicates that miRNAs also operate beyond this canonical paradigm, featuring non-conventional regulatory functions and cellular localizations that have a pathophysiological role in cardiovascular disease. In this Review, we highlight the functional relevance of atypical miRNA biogenesis and localization as well as RISC heterogeneity. Moreover, we delineate remarkable non-canonical examples of miRNA functionality, including direct interactions with proteins beyond the Argonaute family and their role in transcriptional regulation in the nucleus and in mitochondria. We scrutinize the relevance of non-conventional biogenesis and non-canonical functions of miRNAs in cardiovascular homeostasis and pathology, and contextualize how uncovering these non-conventional properties can expand the scope of translational research in the cardiovascular field and beyond.
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Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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14
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Chatzopoulou F, Kyritsis KA, Papagiannopoulos CI, Galatou E, Mittas N, Theodoroula NF, Papazoglou AS, Karagiannidis E, Chatzidimitriou M, Papa A, Sianos G, Angelis L, Chatzidimitriou D, Vizirianakis IS. Dissecting miRNA–Gene Networks to Map Clinical Utility Roads of Pharmacogenomics-Guided Therapeutic Decisions in Cardiovascular Precision Medicine. Cells 2022; 11:cells11040607. [PMID: 35203258 PMCID: PMC8870388 DOI: 10.3390/cells11040607] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs) create systems networks and gene-expression circuits through molecular signaling and cell interactions that contribute to health imbalance and the emergence of cardiovascular disorders (CVDs). Because the clinical phenotypes of CVD patients present a diversity in their pathophysiology and heterogeneity at the molecular level, it is essential to establish genomic signatures to delineate multifactorial correlations, and to unveil the variability seen in therapeutic intervention outcomes. The clinically validated miRNA biomarkers, along with the relevant SNPs identified, have to be suitably implemented in the clinical setting in order to enhance patient stratification capacity, to contribute to a better understanding of the underlying pathophysiological mechanisms, to guide the selection of innovative therapeutic schemes, and to identify innovative drugs and delivery systems. In this article, the miRNA–gene networks and the genomic signatures resulting from the SNPs will be analyzed as a method of highlighting specific gene-signaling circuits as sources of molecular knowledge which is relevant to CVDs. In concordance with this concept, and as a case study, the design of the clinical trial GESS (NCT03150680) is referenced. The latter is presented in a manner to provide a direction for the improvement of the implementation of pharmacogenomics and precision cardiovascular medicine trials.
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Affiliation(s)
- Fani Chatzopoulou
- Laboratory of Microbiology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.C.); (A.P.); (D.C.)
- Labnet Laboratories, Department of Molecular Biology and Genetics, 54638 Thessaloniki, Greece
| | - Konstantinos A. Kyritsis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (K.A.K.); (C.I.P.); (N.F.T.)
| | - Christos I. Papagiannopoulos
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (K.A.K.); (C.I.P.); (N.F.T.)
| | - Eleftheria Galatou
- Department of Life & Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
| | - Nikolaos Mittas
- Department of Chemistry, International Hellenic University, 65404 Kavala, Greece;
| | - Nikoleta F. Theodoroula
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (K.A.K.); (C.I.P.); (N.F.T.)
| | - Andreas S. Papazoglou
- 1st Cardiology Department, AHEPA University General Hospital of Thessaloniki, 54636 Thessaloniki, Greece; (A.S.P.); (E.K.); (G.S.)
| | - Efstratios Karagiannidis
- 1st Cardiology Department, AHEPA University General Hospital of Thessaloniki, 54636 Thessaloniki, Greece; (A.S.P.); (E.K.); (G.S.)
| | - Maria Chatzidimitriou
- Department of Biomedical Sciences, School of Health Sciences, International Hellenic University, 57400 Thessaloniki, Greece;
| | - Anna Papa
- Laboratory of Microbiology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.C.); (A.P.); (D.C.)
| | - Georgios Sianos
- 1st Cardiology Department, AHEPA University General Hospital of Thessaloniki, 54636 Thessaloniki, Greece; (A.S.P.); (E.K.); (G.S.)
| | - Lefteris Angelis
- Department of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Dimitrios Chatzidimitriou
- Laboratory of Microbiology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.C.); (A.P.); (D.C.)
| | - Ioannis S. Vizirianakis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (K.A.K.); (C.I.P.); (N.F.T.)
- Department of Life & Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
- Correspondence: or
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15
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Ren DY, Yuan XR, Tu CX, Shen JL, Li YW, Yan AH, Ru Y, Han HY, Yang YM, Liu Y, Li HY. Long Noncoding RNA 00472: A Novel Biomarker in Human Diseases. Front Pharmacol 2021; 12:726908. [PMID: 34987381 PMCID: PMC8722734 DOI: 10.3389/fphar.2021.726908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in human diseases. They control gene expression levels and influence various biological processes through multiple mechanisms. Functional abnormalities in lncRNAs are strongly associated with occurrence and development of various diseases. LINC00472, which is located on chromosome 6q13, is involved in several human diseases, particularly cancers of the breast, lung, liver, osteosarcoma, bladder, colorectal, ovarian, pancreatic and stomach. Importantly, LINC00472 can be used as a biomarker for breast cancer cell sensitivity to chemotherapeutic regimens, including doxorubicin. LINC00472 is regulated by microRNAs and several signaling pathways. However, the significance of LINC00472 in human diseases has not been clearly established. In this review, we elucidate on the significance of LINC00472 in various human diseases, indicating that LINC00472 may be a diagnostic, prognostic as well as therapeutic target for these diseases.
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Affiliation(s)
- Dan-yang Ren
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Xin-rong Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Cai-xia Tu
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Jian-ling Shen
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Yun-wei Li
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Ai-hua Yan
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Yi Ru
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Hui-yun Han
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Yan-ming Yang
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Yan Liu
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
| | - Hui-ying Li
- Pharmaceutical Preparation Section, Children’s Hospital of Kunming Medical University, Kunming, China
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