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Dergunov AD, Nosova EV, Rozhkova AV, Vinogradina MA, Baserova VB, Popov MA, Limborska SA, Dergunova LV. Differential Expression of Subsets of Genes Related to HDL Metabolism and Atherogenesis in the Peripheral Blood in Coronary Artery Disease. Curr Issues Mol Biol 2023; 45:6823-6841. [PMID: 37623250 PMCID: PMC10452992 DOI: 10.3390/cimb45080431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Differential expression of genes (DEGs) in coronary artery disease (CAD) and the association between transcript level and high-density lipoprotein cholesterol (HDL-C) were studied with 76 male patients with CAD and 63 control patients. The transcript level of genes related to HDL metabolism (24 genes) and atherosclerosis-prone (41 genes) in RNA isolated from peripheral blood mononuclear cells was measured by real-time RT-PCR. Twenty-eight DEGs were identified. The expression of cholesterol transporters, ALB, APOA1, and LCAT was down-regulated, while the expression of AMN, APOE, LDLR, LPL, PLTP, PRKACA, and CETP was up-regulated. The systemic inflammation in CAD is evidenced by the up-regulation of IL1B, TLR8, CXCL5, and TNFRSF1A. For the controls, TLR8 and SOAT1 were negative predictors of the HDL-C level. For CAD patients, PRKACG, PRKCQ, and SREBF1 were positive predictors, while PRKACB, LCAT, and S100A8 were negative predictors. For CAD patients, the efficiency of reverse cholesterol transport is 73-79%, and intracellular free cholesterol seems to accumulate at hyperalphalipoproteinemia. Both atheroprotective (via S100A8) and proatherogenic (via SREBF1, LCAT, PRKACG, PRKACB, and PRKCQ) associations of gene expression with HDL-C determine HDL functionality in CAD patients. The selected key genes and involved pathways may represent HDL-specific targets for the diagnosis and treatment of CAD and atherosclerosis.
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Affiliation(s)
- Alexander D. Dergunov
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigsky Street 10, Moscow 101990, Russia;
| | - Elena V. Nosova
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (E.V.N.); (A.V.R.); (M.A.V.); (S.A.L.); (L.V.D.)
| | - Alexandra V. Rozhkova
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (E.V.N.); (A.V.R.); (M.A.V.); (S.A.L.); (L.V.D.)
| | - Margarita A. Vinogradina
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (E.V.N.); (A.V.R.); (M.A.V.); (S.A.L.); (L.V.D.)
| | - Veronika B. Baserova
- National Medical Research Center for Therapy and Preventive Medicine, Petroverigsky Street 10, Moscow 101990, Russia;
| | - Mikhail A. Popov
- Moscow Regional Research and Clinical Institute MONIKI, Moscow 129110, Russia;
| | - Svetlana A. Limborska
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (E.V.N.); (A.V.R.); (M.A.V.); (S.A.L.); (L.V.D.)
| | - Liudmila V. Dergunova
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (E.V.N.); (A.V.R.); (M.A.V.); (S.A.L.); (L.V.D.)
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Dergunova LV, Vinogradina MA, Filippenkov IB, Limborska SA, Dergunov AD. Circular RNAs Variously Participate in Coronary Atherogenesis. Curr Issues Mol Biol 2023; 45:6682-6700. [PMID: 37623241 PMCID: PMC10453518 DOI: 10.3390/cimb45080422] [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: 06/29/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Over the past decade, numerous studies have shown that circular RNAs (circRNAs) play a significant role in coronary artery atherogenesis and other cardiovascular diseases. They belong to the class of non-coding RNAs and arise as a result of non-canonical splicing of premature RNA, which results in the formation of closed single-stranded circRNA molecules that lack 5'-end caps and 3'-end poly(A) tails. circRNAs have broad post-transcriptional regulatory activity. Acting as a sponge for miRNAs, circRNAs compete with mRNAs for binding to miRNAs, acting as competing endogenous RNAs. Numerous circRNAs are involved in the circRNA-miRNA-mRNA regulatory axes associated with the pathogenesis of cardiomyopathy, chronic heart failure, hypertension, atherosclerosis, and coronary artery disease. Recent studies have shown that сirc_0001445, circ_0000345, circ_0093887, сircSmoc1-2, and circ_0003423 are involved in the pathogenesis of coronary artery disease (CAD) with an atheroprotective effect, while circ_0002984, circ_0029589, circ_0124644, circ_0091822, and circ_0050486 possess a proatherogenic effect. With their high resistance to endonucleases, circRNAs are promising diagnostic biomarkers and therapeutic targets. This review aims to provide updated information on the involvement of atherogenesis-related circRNAs in the pathogenesis of CAD. We also discuss the main modern approaches to detecting and studying circRNA-miRNA-mRNA interactions, as well as the prospects for using circRNAs as biomarkers and therapeutic targets for the treatment of cardiovascular diseases.
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Affiliation(s)
- Liudmila V. Dergunova
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Margarita A. Vinogradina
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Ivan B. Filippenkov
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Svetlana A. Limborska
- Laboratory of Human Molecular Genetics, National Research Center “Kurchatov Institute”, Kurchatov Sq. 2, Moscow 123182, Russia; (M.A.V.); (I.B.F.); (S.A.L.)
| | - Alexander D. Dergunov
- Laboratory of Structural Fundamentals of Lipoprotein Metabolism, National Medical Research Center for Therapy and Preventive Medicine, Petroverigsky Street 10, Moscow 101990, Russia;
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Yang Y, Cai Y, Zhang Y, Yi X, Xu Z. Identification of Molecular Subtypes and Key Genes of Atherosclerosis Through Gene Expression Profiles. Front Mol Biosci 2021; 8:628546. [PMID: 33996893 PMCID: PMC8113832 DOI: 10.3389/fmolb.2021.628546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Atherosclerotic cardiovascular disease (ASCVD) caused by atherosclerosis (AS) is one of the highest causes of mortality worldwide. Although there have been many studies on AS, its etiology remains unclear. In order to carry out molecular characterization of different types of AS, we retrieved two datasets composed of 151 AS samples and 32 normal samples from the Gene Expression Omnibus database. Using the non-negative matrix factorization (NMF) algorithm, we successfully divided the 151 AS samples into two subgroups. We then compared the molecular characteristics between the two groups using weighted gene co-expression analysis (WGCNA) and identified six key modules associated with the two subgroups. Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analysis were used to identify the potential functions and pathways associated with the modules. In addition, we used the cytoscape software to construct and visualize protein-protein networks so as to identify key genes in the modules of interest. Three hub genes including PTGER3, GNAI1, and IGFBP5 were further screened using the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) algorithms. Since the modules were associated with immune pathways, we performed immune cell infiltration analysis. We discovered a significant difference in the level of immune cell infiltration by naïve B cells, CD8 T cells, T regulatory cells (Tregs), resting NK cells, Monocytes, Macrophages M0, Macrophages M1, and Macrophages M2 between the two subgroups. In addition, we observed the three hub genes were positively correlated with Tregs but negatively correlated with Macrophages M0. We also found that the three key genes are differentially expressed between normal and diseased tissue, as well as in the different subgroups. Receiver operating characteristic (ROC) results showed a good performance in the validation dataset. These results may provide novel insight into cellular and molecular characteristics of AS and potential markers for diagnosis and targeted therapy.
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Affiliation(s)
- Yujia Yang
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yue Cai
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuan Zhang
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xu Yi
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhiqiang Xu
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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Zalewski DP, Ruszel KP, Stępniewski A, Gałkowski D, Bogucki J, Kołodziej P, Szymańska J, Płachno BJ, Zubilewicz T, Feldo M, Kocki J, Bogucka-Kocka A. Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens. Int J Mol Sci 2021; 22:3200. [PMID: 33801150 PMCID: PMC8004090 DOI: 10.3390/ijms22063200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 01/10/2023] Open
Abstract
Several human tissues are investigated in studies of molecular biomarkers associated with diseases development. Special attention is focused on the blood and its components due to combining abundant information about systemic responses to pathological processes as well as high accessibility. In the current study, transcriptome profiles of peripheral blood mononuclear cells (PBMCs) were used to compare differentially expressed genes between patients with lower extremities arterial disease (LEAD), abdominal aortic aneurysm (AAA) and chronic venous disease (CVD). Gene expression patterns were generated using the Ion S5XL next-generation sequencing platform and were analyzed using DESeq2 and UVE-PLS methods implemented in R programming software. In direct pairwise analysis, 21, 58 and 10 differentially expressed genes were selected from the comparison of LEAD vs. AAA, LEAD vs. CVD and AAA vs. CVD patient groups, respectively. Relationships between expression of dysregulated genes and age, body mass index, creatinine levels, hypertension and medication were identified using Spearman rank correlation test and two-sided Mann-Whitney U test. The functional analysis, performed using DAVID website tool, provides potential implications of selected genes in pathological processes underlying diseases studied. Presented research provides new insight into differences of pathogenesis in LEAD, AAA and CVD, and selected genes could be considered as potential candidates for biomarkers useful in diagnosis and differentiation of studied diseases.
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Affiliation(s)
- Daniel P. Zalewski
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland;
| | - Karol P. Ruszel
- Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland; (K.P.R.); (J.K.)
| | - Andrzej Stępniewski
- Ecotech Complex Analytical and Programme Centre for Advanced Environmentally Friendly Technologies, University of Marie Curie-Skłodowska, 39 Głęboka St., 20-612 Lublin, Poland;
| | - Dariusz Gałkowski
- Department of Pathology and Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, One Robert Wood Johnson Place, New Brunswick, NJ 08903-0019, USA;
| | - Jacek Bogucki
- Chair and Department of Organic Chemistry, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland;
| | - Przemysław Kołodziej
- Laboratory of Diagnostic Parasitology, Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland;
| | - Jolanta Szymańska
- Department of Integrated Paediatric Dentistry, Chair of Integrated Dentistry, Medical University of Lublin, 6 Chodźki St., 20-093 Lublin, Poland;
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Cracow, Poland;
| | - Tomasz Zubilewicz
- Chair and Department of Vascular Surgery and Angiology, Medical University of Lublin, 11 Staszica St., 20-081 Lublin, Poland; (T.Z.); (M.F.)
| | - Marcin Feldo
- Chair and Department of Vascular Surgery and Angiology, Medical University of Lublin, 11 Staszica St., 20-081 Lublin, Poland; (T.Z.); (M.F.)
| | - Janusz Kocki
- Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland; (K.P.R.); (J.K.)
| | - Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland;
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5
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Abstract
Atherosclerotic cardiovascular disease (ASCVD) proceeds through a series of stages: initiation, progression (or regression), and complications. By integrating known biology regarding molecular signatures of each stage with recent advances in high-dimensional molecular data acquisition platforms (to assay the genome, epigenome, transcriptome, proteome, metabolome, and gut microbiome), snapshots of each phase of atherosclerotic cardiovascular disease development can be captured. In this review, we will summarize emerging approaches for assessment of atherosclerotic cardiovascular disease risk in humans using peripheral blood molecular signatures and molecular imaging approaches. We will then discuss the potential (and challenges) for these snapshots to be integrated into a personalized movie providing dynamic readouts of an individual's atherosclerotic cardiovascular disease risk status throughout the life course.
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Affiliation(s)
- Matthew Nayor
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Kemar J. Brown
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ramachandran S. Vasan
- Sections of Preventive Medicine & Epidemiology, and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA; Department of Epidemiology, Boston University School of Public Health; Boston University Center for Computing and Data Sciences
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Navarro E, Mallén A, Cruzado JM, Torras J, Hueso M. Unveiling ncRNA regulatory axes in atherosclerosis progression. Clin Transl Med 2020; 9:5. [PMID: 32009226 PMCID: PMC6995802 DOI: 10.1186/s40169-020-0256-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.
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Affiliation(s)
- Estanislao Navarro
- Independent Researcher, Barcelona, Spain. .,Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
| | - Adrian Mallén
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Josep M Cruzado
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Joan Torras
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Miguel Hueso
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
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Bogucka-Kocka A, Zalewski DP, Ruszel KP, Stępniewski A, Gałkowski D, Bogucki J, Komsta Ł, Kołodziej P, Zubilewicz T, Feldo M, Kocki J. Dysregulation of MicroRNA Regulatory Network in Lower Extremities Arterial Disease. Front Genet 2019; 10:1200. [PMID: 31827490 PMCID: PMC6892359 DOI: 10.3389/fgene.2019.01200] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/29/2019] [Indexed: 01/12/2023] Open
Abstract
Atherosclerosis and its comorbidities are the major contributors to the global burden of death worldwide. Lower extremities arterial disease (LEAD) is a common manifestation of atherosclerotic disease of arteries of lower extremities. MicroRNAs belong to epigenetic factors that regulate gene expression and have not yet been extensively studied in LEAD. We aimed to indicate the most promising microRNA and gene expression signatures of LEAD, to identify interactions between microRNA and genes and to describe potential effect of modulated gene expression. High-throughput sequencing was employed to examine microRNAome and transcriptome of peripheral blood mononuclear cells of patients with LEAD, in relation to controls. Statistical significance of microRNAs and genes analysis results was evaluated using DESeq2 and uninformative variable elimination by partial least squares methods. Altered expression of 26 microRNAs (hsa-let-7f-1-3p, hsa-miR-34a-5p, -122-5p, -3591-3p, -34a-3p, -1261, -21-5p, -15a-5p, -548d-5p, -34b-5p, -424-3p, -548aa, -548t-3p, -4423-3p, -196a-5p, -330-3p, -766-3p, -30e-3p, -125b-5p, -1301-3p, -3184-5p, -423-3p, -339-3p, -138-5p, -99a-3p, and -6087) and 14 genes (AK5, CD248, CDS2, FAM129A, FBLN2, GGT1, NOG, NRCAM, PDE7A, RP11-545E17.3, SLC12A2, SLC16A10, SLC4A10, and ZSCAN18) were the most significantly differentially expressed in LEAD group compared to controls. Discriminative value of revealed microRNAs and genes were confirmed by receiver operating characteristic analysis. Dysregulations of 26 microRNAs and 14 genes were used to propose novel biomarkers of LEAD. Regulatory interactions between biomarker microRNAs and genes were studied in silico using R multiMiR package. Functional analysis of genes modulated by proposed biomarker microRNAs was performed using DAVID 6.8 tools and revealed terms closely related to atherosclerosis and, interestingly, the processes involving nervous system. The study provides new insight into microRNA-dependent regulatory mechanisms involved in pathology of LEAD. Proposed microRNA and gene biomarkers of LEAD may provide new diagnostic and therapeutic opportunities.
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Affiliation(s)
- Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Medical University of Lublin, Lublin, Poland
| | - Daniel P Zalewski
- Chair and Department of Biology and Genetics, Medical University of Lublin, Lublin, Poland
| | - Karol P Ruszel
- Department of Clinical Genetics, Chair of Medical Genetics, Medical University of Lublin, Lublin, Poland
| | - Andrzej Stępniewski
- Ecotech Complex, Analytical and Programme Centre for Advanced Environmentally-Friendly Technologies, University of Marie Curie-Sklodowska, Lublin, Poland
| | - Dariusz Gałkowski
- Department of Pathology and Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Jacek Bogucki
- Department of Clinical Genetics, Chair of Medical Genetics, Medical University of Lublin, Lublin, Poland
| | - Łukasz Komsta
- Chair and Department of Medicinal Chemistry, Medical University of Lublin, Lublin, Poland
| | - Przemysław Kołodziej
- Chair and Department of Biology and Genetics, Medical University of Lublin, Lublin, Poland
| | - Tomasz Zubilewicz
- Department of Vascular Surgery and Angiology, Medical University of Lublin, Lublin, Poland
| | - Marcin Feldo
- Department of Vascular Surgery and Angiology, Medical University of Lublin, Lublin, Poland
| | - Janusz Kocki
- Department of Clinical Genetics, Chair of Medical Genetics, Medical University of Lublin, Lublin, Poland
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Hamledari H, Sajjadi SF, Alikhah A, Boroumand MA, Behmanesh M. ASGR1 but not FOXM1 expression decreases in the peripheral blood mononuclear cells of diabetic atherosclerotic patients. J Diabetes Complications 2019; 33:539-546. [PMID: 31202960 DOI: 10.1016/j.jdiacomp.2019.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/22/2019] [Accepted: 05/11/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND The ASGR1 was recently shown to play a key role in the development of coronary artery disease (CAD), but its exact mechanism of action in the CAD pathogenesis is not yet known. This study evaluates the possible association between the expression level of ASGR1 and its downstream transcription factor FOXM1 in the inflammatory cells of peripheral blood (PBMC) and the pathogenesis of CAD in the Diabetic condition. METHODS Blood samples were taken from the candidates who had visited the Tehran Heart Center and had underwent diagnostic tests with respect to diabetes and CAD. The peripheral blood cells were harvested, RNA was extracted, and cDNA was synthesized. The qRT-PCR was performed on 79 cDNA samples taken from 49 CAD+ patients and 30 CAD- patients. RESULTS In this study, we observed a significant decrease of ASGR1 expression in the PBMC of CAD+ patients compared to the CAD- patients. We did not identify any considerable differences in the expression of FOXM1 in patients' subgroups with respect to the diabetes and CAD. CONCLUSION The results of our study determine the association of ASGR1 expression and CAD pathogenesis. However, we do not know whether this result is the cause or the effect of CAD.
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Affiliation(s)
- Homa Hamledari
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyedeh Fatemeh Sajjadi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Asieh Alikhah
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Evidence of association of circulating epigenetic-sensitive biomarkers with suspected coronary heart disease evaluated by Cardiac Computed Tomography. PLoS One 2019; 14:e0210909. [PMID: 30673762 PMCID: PMC6343931 DOI: 10.1371/journal.pone.0210909] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/03/2019] [Indexed: 12/22/2022] Open
Abstract
Circulating biomarkers available in clinical practice do not allow to stratify patients with coronary heart disease (CHD) prior the onset of a clinically relevant event. We evaluated the methylation status of specific genomic segments and gene expression in peripheral blood of patients undergoing Cardiac Computed Tomography (CCT) for CHD (n = 95). We choose to investigate cholesterol metabolism. Methylation and gene expression of low density lipoprotein receptor (LDLR), sterol regulatory element-binding factor 2 (SREBF2) and ATP-binding cassette transporter 1 (ABCA1) were evaluated by qRT-PCR. Calcium score (CACS), stenosis degree, total plaque volume (TPV), calcified plaque volume (CPV), non-calcified plaque volume (NCPV) and plaque burden (PB) were assessed in all CHD patients (n = 65). The percentage of methylation at the specific analyzed segment of LDLR promoter was higher in CHD patients vs healthy subjects (HS) (n = 30) (p = 0.001). LDLR, SREBF2 and ABCA1 mRNAs were up-regulated in CHD patients vs HS (p = 0.02; p = 0.019; p = 0.008). SREBF2 was overexpressed in patients with coronary stenosis ≥50% vs subjects with stenosis <50% (p = 0.036). After adjustment for risk factors and clinical features, ABCA1 (p = 0.005) and SREBF2 (p = 0.010) gene expression were identified as independent predictors of CHD and severity. ROC curve analysis revealed a good performance of ABCA1 on predicting CHD (AUC = 0.768; p<0.001) and of SREBF2 for the prediction of disease severity (AUC = 0.815; p<0.001). Moreover, adjusted multivariate analysis demonstrated SREBF2 as independent predictor of CPV, NCPV and TPV (p = 0.022; p = 0.002 and p = 0.006) and ABCA1 as independent predictor of NCPV and TPV (p = 0.002 and p = 0.013). CHD presence and characteristics are related to selected circulating transcriptional and epigenetic-sensitive biomarkers linked to cholesterol pathway. More extensive analysis of CHD phenotypes and circulating biomarkers might improve and personalize cardiovascular risk stratification in the clinical settings.
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10
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Ferronato S, Scuro A, Fochi S, Orlandi E, Gomez-Lira M, Olivato S, Mazzucco S, Turco A, Romanelli MG. Expression of TLR4-PTGE2 signaling genes in atherosclerotic carotid plaques and peripheral blood. Mol Biol Rep 2018; 46:1317-1321. [PMID: 30421129 DOI: 10.1007/s11033-018-4478-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/07/2018] [Indexed: 01/01/2023]
Abstract
Toll-like receptor 4 (TLR4)/prostaglandine synthetase 2 (PTGS2) signaling plays a relevant role in atherosclerotic plaque vulnerability. The purpose of this study was to check the gene expression of 6 genes participating to TLR4/PTGS2 signaling (TLR4, PTGS2, ACSL4, PTGER3, PTGER4, and EPRAP) in carotid plaques and blood samples from the same individual and to evaluate these genes as biomarker of plaque progression. We investigated differential gene expression by qRT-PCR in 62 atherosclerotic patients' carotid plaques and corresponding blood sample. A very weak or no correlation was observed in the overall population or analyzing asymptomatic patients. These analyzed genes are most likely not suitable for inclusion in the clinical routine as biomarkers of plaque instability.
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Affiliation(s)
- S Ferronato
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
| | - A Scuro
- Department of Surgery, Dentistry, Pediatrics and Gynaecology, Unit of Vascular and Endovascular Surgery, University of Verona, Verona, Italy
| | - S Fochi
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
| | - E Orlandi
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
| | - M Gomez-Lira
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy.
| | - S Olivato
- Section of Neurophatology, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Verona, Italy
| | - S Mazzucco
- Department of Clinical Neurosciences, Centre for Prevention of Stroke and Dementia Nuffield, University of Oxford, Oxford, UK
| | - A Turco
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
| | - M G Romanelli
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Strada Le Grazie, 8, 37134, Verona, Italy
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11
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Lin M, Zhang Y, Niu Z, Chi Y, Huang Q. Transcriptomic responses of peripheral blood cells to coronary artery disease. Biosci Trends 2018; 12:354-359. [PMID: 30146615 DOI: 10.5582/bst.2018.01078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Transcriptomic response of peripheral blood cells to coronary artery diseases (CAD) is a long recognized phenomenon. Currently, accumulating evidence indicates that such response having significant clinical utility in CAD-associated events determination. In this review, we summarized the existing data of transcriptomic biomarkers at mRNA, microRNA, long non-coding RNA, and circular RNA for the diagnosis, progression and outcome prediction and treatment response of CAD. Furthermore, we also discussed the functional significance on the gene expression patterns caused by CAD, and emphasized the importance of inflammatory pathways in CAD tissues-blood cells interaction. Based on the current knowledge, we proposed a perspective on the future strategies to further improve the robustness and reproducibility of transcriptomic biomarkers in the personalized medicine of CAD patients.
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Affiliation(s)
- Mingshan Lin
- Department of Cardiovascular Surgery, Qingdao Municipal Hospital
| | - Yuan Zhang
- Department of Cardiovascular Surgery, Qingdao Municipal Hospital
| | - Zhaozhuo Niu
- Department of Cardiovascular Surgery, Qingdao Municipal Hospital
| | - Yifan Chi
- Department of Cardiovascular Surgery, Qingdao Municipal Hospital
| | - Qiang Huang
- Department of Cardiovascular Surgery, Qingdao Municipal Hospital
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12
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Lygirou V, Latosinska A, Makridakis M, Mullen W, Delles C, Schanstra JP, Zoidakis J, Pieske B, Mischak H, Vlahou A. Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease. J Transl Med 2018; 16:104. [PMID: 29665821 PMCID: PMC5905170 DOI: 10.1186/s12967-018-1476-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/06/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis. METHODS LC-MS/MS was employed to analyze plasma from 32 subjects (19 cases of various CVD phenotypes and 13 controls) in two steps: discovery (13 cases and 8 controls) and test (6 cases and 5 controls) set analysis. Following label-free quantification, the detected proteins were correlated to existing plasma proteomics datasets (plasma proteome database; PPD) and functionally annotated (Cytoscape, Ingenuity Pathway Analysis). Differential expression was defined based on identification confidence (≥ 2 peptides per protein), statistical significance (Mann-Whitney p value ≤ 0.05) and a minimum of twofold change. RESULTS Peptides detected in at least 50% of samples per group were considered, resulting in a total of 3796 identified proteins (838 proteins based on ≥ 2 peptides). Pathway annotation confirmed the functional relevance of the findings (representation of complement cascade, fibrin clot formation, platelet degranulation, etc.). Correlation of the relative abundance of the proteins identified in the discovery set with their reported concentrations in the PPD was significant, confirming the validity of the quantification method. The discovery set analysis revealed 100 differentially expressed proteins between cases and controls, 39 of which were verified (≥ twofold change) in the test set. These included proteins already studied in the context of CVD (such as apolipoprotein B, alpha-2-macroglobulin), as well as novel findings (such as low density lipoprotein receptor related protein 2 [LRP2], protein SZT2) for which a mechanism of action is suggested. CONCLUSIONS This proteomic study provides a comprehensive dataset to be used for integrative and functional studies in the field. The observed protein changes reflect known CVD-related processes (e.g. lipid uptake, inflammation) but also novel hypotheses for further investigation including a potential pleiotropic role of LPR2 but also links of SZT2 to CVD.
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Affiliation(s)
- Vasiliki Lygirou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece
| | | | - Manousos Makridakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jerome Zoidakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece
| | - Burkert Pieske
- Deutsches Herzzentrum Berlin, Augustenburger Pl. 1, 13353, Berlin, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece.
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