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Bonet F, Hernandez-Torres F, Ramos-Sánchez M, Quezada-Feijoo M, Bermúdez-García A, Daroca T, Alonso-Villa E, García-Padilla C, Mangas A, Toro R. Unraveling the Etiology of Dilated Cardiomyopathy through Differential miRNA-mRNA Interactome. Biomolecules 2024; 14:524. [PMID: 38785931 PMCID: PMC11117812 DOI: 10.3390/biom14050524] [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: 04/01/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Dilated cardiomyopathy (DCM) encompasses various acquired or genetic diseases sharing a common phenotype. The understanding of pathogenetic mechanisms and the determination of the functional effects of each etiology may allow for tailoring different therapeutic strategies. MicroRNAs (miRNAs) have emerged as key regulators in cardiovascular diseases, including DCM. However, their specific roles in different DCM etiologies remain elusive. Here, we applied mRNA-seq and miRNA-seq to identify the gene and miRNA signature from myocardial biopsies from four patients with DCM caused by volume overload (VCM) and four with ischemic DCM (ICM). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used for differentially expressed genes (DEGs). The miRNA-mRNA interactions were identified by Pearson correlation analysis and miRNA target-prediction programs. mRNA-seq and miRNA-seq were validated by qRT-PCR and miRNA-mRNA interactions were validated by luciferase assays. We found 112 mRNAs and five miRNAs dysregulated in VCM vs. ICM. DEGs were positively enriched for pathways related to the extracellular matrix (ECM), mitochondrial respiration, cardiac muscle contraction, and fatty acid metabolism in VCM vs. ICM and negatively enriched for immune-response-related pathways, JAK-STAT, and NF-kappa B signaling. We identified four pairs of negatively correlated miRNA-mRNA: miR-218-5p-DDX6, miR-218-5p-TTC39C, miR-218-5p-SEMA4A, and miR-494-3p-SGMS2. Our study revealed novel miRNA-mRNA interaction networks and signaling pathways for VCM and ICM, providing novel insights into the development of these DCM etiologies.
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Affiliation(s)
- Fernando Bonet
- Medicine Department, School of Medicine, University of Cádiz (UCA), 11003 Cádiz, Spain; (F.B.); (E.A.-V.); (A.M.)
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, 11009 Cádiz, Spain
| | - Francisco Hernandez-Torres
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Mónica Ramos-Sánchez
- Cardiology Department, Central de la Cruz Roja Hospital, 28003 Madrid, Spain; (M.R.-S.); (M.Q.-F.)
- Medicine Department, School of Medicine, Alfonso X EL Sabio University, 28691 Madrid, Spain
| | - Maribel Quezada-Feijoo
- Cardiology Department, Central de la Cruz Roja Hospital, 28003 Madrid, Spain; (M.R.-S.); (M.Q.-F.)
- Medicine Department, School of Medicine, Alfonso X EL Sabio University, 28691 Madrid, Spain
| | - Aníbal Bermúdez-García
- Cardiovascular Surgery Department, Puerta del Mar University Hospital, 11009 Cádiz, Spain (T.D.)
| | - Tomás Daroca
- Cardiovascular Surgery Department, Puerta del Mar University Hospital, 11009 Cádiz, Spain (T.D.)
| | - Elena Alonso-Villa
- Medicine Department, School of Medicine, University of Cádiz (UCA), 11003 Cádiz, Spain; (F.B.); (E.A.-V.); (A.M.)
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, 11009 Cádiz, Spain
| | | | - Alipio Mangas
- Medicine Department, School of Medicine, University of Cádiz (UCA), 11003 Cádiz, Spain; (F.B.); (E.A.-V.); (A.M.)
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, 11009 Cádiz, Spain
- Internal Medicine Department, Puerta del Mar University Hospital, 11009 Cádiz, Spain
| | - Rocio Toro
- Medicine Department, School of Medicine, University of Cádiz (UCA), 11003 Cádiz, Spain; (F.B.); (E.A.-V.); (A.M.)
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, 11009 Cádiz, Spain
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2
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Jia Y, Zhang RN, Li YJ, Guo BY, Wang JL, Liu SY. Bioinformatics analysis and identification of potential key genes and pathways in the pathogenesis of nonischemic cardiomyopathy. Medicine (Baltimore) 2024; 103:e37898. [PMID: 38669428 PMCID: PMC11049792 DOI: 10.1097/md.0000000000037898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Nonischemic cardiomyopathy (NICM) is a major cause of advanced heart failure, and the morbidity and mortality associated with NICM are serious medical problems. However, the etiology of NICM is complex and the related mechanisms involved in its pathogenesis remain unclear. The microarray datasets GSE1869 and GSE9128 retrieved from the Gene Expression Omnibus database were used to identify differentially expressed genes (DEGs) between NICM and normal samples. The co-expressed genes were identified using Venn diagrams. Kyoto Encyclopedia of Genes and Genomes pathway analyses and gene ontology enrichment were used to clarify biological functions and signaling pathways. Analysis of protein-protein interaction networks using Search Tool for the Retrieval of Interacting Genes/Proteins online to define the hub genes associated with NICM pathogenesis. A total of 297 DEGs were identified from GSE1869, 261 of which were upregulated genes and 36 were downregulated genes. A total of 360 DEGs were identified from GSE9128, 243 of which were upregulated genes and 117 were downregulated genes. In the 2 datasets, the screening identified 36 co-expressed DEGs. Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology analysis showed that DEGs were mainly enriched in pantothenate and CoA biosynthesis, beta-alanine metabolism, kinetochore, G-protein beta/gamma-subunit complex, and other related pathways. The PPI network analysis revealed that DUSP6, EGR1, ZEB2, and XPO1 are the 4 hub genes of interest in the 2 datasets. Bioinformatics analysis of hub genes and key signaling pathways is an effective way to elucidate the mechanisms involved in the development of NICM. The results will facilitate further studies on the pathogenesis and therapeutic targets of NICM.
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Affiliation(s)
- Yan Jia
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Rui-Ning Zhang
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yong-Jun Li
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bing-Yan Guo
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jian-Long Wang
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Su-Yun Liu
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Broman MT, Nadadur RD, Perez-Cervantes C, Burnicka-Turek O, Lazarevic S, Gams A, Laforest B, Steimle JD, Iddir S, Wang Z, Smith L, Mazurek SR, Olivey HE, Zhou P, Gadek M, Shen KM, Khan Z, Theisen JW, Yang XH, Ikegami K, Efimov IR, Pu WT, Weber CR, McNally EM, Svensson EC, Moskowitz IP. A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network. Circulation 2024; 149:1205-1230. [PMID: 38189150 PMCID: PMC11152454 DOI: 10.1161/circulationaha.123.066804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND The relationship between heart failure (HF) and atrial fibrillation (AF) is clear, with up to half of patients with HF progressing to AF. The pathophysiological basis of AF in the context of HF is presumed to result from atrial remodeling. Upregulation of the transcription factor FOG2 (friend of GATA2; encoded by ZFPM2) is observed in human ventricles during HF and causes HF in mice. METHODS FOG2 expression was assessed in human atria. The effect of adult-specific FOG2 overexpression in the mouse heart was evaluated by whole animal electrophysiology, in vivo organ electrophysiology, cellular electrophysiology, calcium flux, mouse genetic interactions, gene expression, and genomic function, including a novel approach for defining functional transcription factor interactions based on overlapping effects on enhancer noncoding transcription. RESULTS FOG2 is significantly upregulated in the human atria during HF. Adult cardiomyocyte-specific FOG2 overexpression in mice caused primary spontaneous AF before the development of HF or atrial remodeling. FOG2 overexpression generated arrhythmia substrate and trigger in cardiomyocytes, including calcium cycling defects. We found that FOG2 repressed atrial gene expression promoted by TBX5. FOG2 bound a subset of GATA4 and TBX5 co-bound genomic locations, defining a shared atrial gene regulatory network. FOG2 repressed TBX5-dependent transcription from a subset of co-bound enhancers, including a conserved enhancer at the Atp2a2 locus. Atrial rhythm abnormalities in mice caused by Tbx5 haploinsufficiency were rescued by Zfpm2 haploinsufficiency. CONCLUSIONS Transcriptional changes in the atria observed in human HF directly antagonize the atrial rhythm gene regulatory network, providing a genomic link between HF and AF risk independent of atrial remodeling.
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Affiliation(s)
- Michael T. Broman
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Rangarajan D. Nadadur
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Carlos Perez-Cervantes
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Ozanna Burnicka-Turek
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Sonja Lazarevic
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Anna Gams
- Department of Biomedical Engineering, George Washington University
| | - Brigitte Laforest
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Jeffrey D. Steimle
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Sabrina Iddir
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Zhezhen Wang
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Linsin Smith
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Stefan R. Mazurek
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Harold E. Olivey
- Department of Biology, Indiana University Northwest, Gary, IN 46408
| | | | - Margaret Gadek
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Kaitlyn M. Shen
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Zoheb Khan
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Joshua W.M. Theisen
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Xinan H. Yang
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Kohta Ikegami
- Division of Molecular and Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Igor R. Efimov
- Department of Biomedical Engineering, George Washington University
| | - William T. Pu
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, 02115
| | | | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University, 303 E. Superior, SQ5-516, Chicago, IL 60611
| | | | - Ivan P. Moskowitz
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
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4
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Wang L, Sun T, Liu X, Wang Y, Qiao X, Chen N, Liu F, Zhou X, Wang H, Shen H. Myocarditis: A multi-omics approach. Clin Chim Acta 2024; 554:117752. [PMID: 38184138 DOI: 10.1016/j.cca.2023.117752] [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: 12/14/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Myocarditis, an inflammatory condition of weakened heart muscles often triggered by a variety of causes, that can result in heart failure and sudden death. Novel ways to enhance our understanding of myocarditis pathogenesis is available through newer modalities (omics). In this review, we examine the roles of various biomolecules and associated functional pathways across genomics, transcriptomics, proteomics, and metabolomics in the pathogenesis of myocarditis. Our analysis further explores the reproducibility and variability intrinsic to omics studies, underscoring the necessity and significance of employing a multi-omics approach to gain profound insights into myocarditis pathogenesis. This integrated strategy not only enhances our understanding of the disease, but also confirms the critical importance of a holistic multi-omics approach in disease analysis.
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Affiliation(s)
- Lulu Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Tao Sun
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang 212000, Jiangsu, China
| | - Xiaolan Liu
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Yan Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiaorong Qiao
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Nuo Chen
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Fangqian Liu
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiaoxiang Zhou
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Hua Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Hongxing Shen
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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5
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Yu S, Sun Z, Wang X, Ju T, Wang C, Liu Y, Qu Z, Liu K, Mei Z, Li N, Lu M, Wu F, Huang M, Pang X, Jia Y, Li Y, Zhang Y, Dou S, Jiang J, Li X, Yang B, Du W. Mettl13 protects against cardiac contractile dysfunction by negatively regulating C-Cbl-mediated ubiquitination of SERCA2a in ischemic heart failure. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2786-2804. [PMID: 37450238 DOI: 10.1007/s11427-022-2351-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/14/2023] [Indexed: 07/18/2023]
Abstract
Ischemic heart failure (HF) remains a leading cause of morbidity and mortality. Maintaining homeostasis of cardiac function and preventing cardiac remodeling deterioration are critical to halting HF progression. Methyltransferase-like protein 13 (Mettl13) has been shown to regulate protein translation efficiency by acting as a protein lysine methyltransferase, but its role in cardiac pathology remains unexplored. This study aims to characterize the roles and mechanisms of Mettl13 in cardiac contractile function and HF. We found that Mettl13 was downregulated in the failing hearts of mice post-myocardial infarction (MI) and in a cellular model of oxidative stress. Cardiomyocyte-specific overexpression of Mettl13 mediated by AAV9-Mettl13 attenuated cardiac contractile dysfunction and fibrosis in response to MI, while silencing of Mettl13 impaired cardiac function in normal mice. Moreover, Mettl13 overexpression abrogated the reduction in cell shortening, Ca2+ transient amplitude and SERCA2a protein levels in the cardiomyocytes of adult mice with MI. Conversely, knockdown of Mettl13 impaired the contractility of cardiomyocytes, and decreased Ca2+ transient amplitude and SERCA2a protein expression in vivo and in vitro. Mechanistically, Mettl13 impaired the stability of c-Cbl by inducing lysine methylation of c-Cbl, which in turn inhibited ubiquitination-dependent degradation of SERCA2a. Furthermore, the inhibitory effects of knocking down Mettl13 on SERCA2a protein expression and Ca2+ transients were partially rescued by silencing c-Cbl in H2O2-treated cardiomyocytes. In conclusion, our study uncovers a novel mechanism that involves the Mettl13/c-Cbl/SERCA2a axis in regulating cardiac contractile function and remodeling, and identifies Mettl13 as a novel therapeutic target for ischemic HF.
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Affiliation(s)
- Shuting Yu
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - ZhiYong Sun
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiuzhu Wang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Tiantian Ju
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Changhao Wang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yingqi Liu
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Zhezhe Qu
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - KuiWu Liu
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Zhongting Mei
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Na Li
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Meixi Lu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Fan Wu
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Min Huang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaochen Pang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yingqiong Jia
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Ying Li
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yaozhi Zhang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Shunkang Dou
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Jianhao Jiang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xin Li
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Baofeng Yang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China.
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, 150081, China.
- Research Unit of Noninfectious Chronic Diseases in Frigid Zone, Chinese Academy of Medical Sciences, 2019RU070, Harbin, 150081, China.
| | - Weijie Du
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China.
- Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, 150081, China.
- Research Unit of Noninfectious Chronic Diseases in Frigid Zone, Chinese Academy of Medical Sciences, 2019RU070, Harbin, 150081, China.
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Zheng PF, Hong XQ, Liu ZY, Zheng ZF, Liu P, Chen LZ. m6A regulator-mediated RNA methylation modification patterns are involved in the regulation of the immune microenvironment in ischaemic cardiomyopathy. Sci Rep 2023; 13:5904. [PMID: 37041267 PMCID: PMC10090050 DOI: 10.1038/s41598-023-32919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/04/2023] [Indexed: 04/13/2023] Open
Abstract
The role of RNA N6-methyladenosine (m6A) modification in the regulation of the immune microenvironment in ischaemic cardiomyopathy (ICM) remains largely unclear. This study first identified differential m6A regulators between ICM and healthy samples, and then systematically evaluated the effects of m6A modification on the characteristics of the immune microenvironment in ICM, including the infiltration of immune cells, the human leukocyte antigen (HLA) gene, and HALLMARKS pathways. A total of seven key m6A regulators, including WTAP, ZCH3H13, YTHDC1, FMR1, FTO, RBM15 and YTHDF3, were identified using a random forest classifier. A diagnostic nomogram based on these seven key m6A regulators could effectively distinguish patients with ICM from healthy subjects. We further identified two distinct m6A modification patterns (m6A cluster-A and m6A cluster-B) that are mediated by these seven regulators. Meanwhile, we also noted that one m6A regulator, WTAP, was gradually upregulated, while the others were gradually downregulated in the m6A cluster-A vs. m6A cluster-B vs. healthy subjects. In addition, we observed that the degree of infiltration of the activated dendritic cells, macrophages, natural killer (NK) T cells, and type-17 T helper (Th17) cells gradually increased in m6A cluster-A vs. m6A cluster-B vs. healthy subjects. Furthermore, m6A regulators, including FTO, YTHDC1, YTHDF3, FMR1, ZC3H13, and RBM15 were significantly negatively correlated with the above-mentioned immune cells. Additionally, several differential HLA genes and HALLMARKS signalling pathways between the m6A cluster-A and m6A cluster-B groups were also identified. These results suggest that m6A modification plays a key role in the complexity and diversity of the immune microenvironment in ICM, and seven key m6A regulators, including WTAP, ZCH3H13, YTHDC1, FMR1, FTO, RBM15, and YTHDF3, may be novel biomarkers for the accurate diagnosis of ICM. Immunotyping of patients with ICM will help to develop immunotherapy strategies with a higher level of accuracy for patients with a significant immune response.
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Affiliation(s)
- Peng-Fei Zheng
- Cardiology Department, Hunan Provincial People's Hospital, No. 61 West Jiefang Road, Furong District, ChangshaHunan, 410000, China
- Clinical Research Center for Heart Failure in Hunan Province, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
- Epidemiology Department, Hunan Provincial People's Hospital, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
| | - Xiu-Qin Hong
- Clinical Research Center for Heart Failure in Hunan Province, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
- Epidemiology Department, Hunan Provincial People's Hospital, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
| | - Zheng-Yu Liu
- Cardiology Department, Hunan Provincial People's Hospital, No. 61 West Jiefang Road, Furong District, ChangshaHunan, 410000, China
- Clinical Research Center for Heart Failure in Hunan Province, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
- Epidemiology Department, Hunan Provincial People's Hospital, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
| | - Zhao-Fen Zheng
- Cardiology Department, Hunan Provincial People's Hospital, No. 61 West Jiefang Road, Furong District, ChangshaHunan, 410000, China
- Clinical Research Center for Heart Failure in Hunan Province, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
- Epidemiology Department, Hunan Provincial People's Hospital, No. 61 West Jiefang Road, Furong District, Changsha, 410000, Hunan, China
| | - Peng Liu
- Department of Cardiology, The Central Hospital of ShaoYang, No. 36 QianYuan Lane, Daxiang District, Shaoyang, 422000, Hunan, China.
| | - Lu-Zhu Chen
- Department of Cardiology, The Central Hospital of ShaoYang, No. 36 QianYuan Lane, Daxiang District, Shaoyang, 422000, Hunan, China.
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7
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Drakos SG, Badolia R, Makaju A, Kyriakopoulos CP, Wever-Pinzon O, Tracy CM, Bakhtina A, Bia R, Parnell T, Taleb I, Ramadurai DKA, Navankasattusas S, Dranow E, Hanff TC, Tseliou E, Shankar TS, Visker J, Hamouche R, Stauder EL, Caine WT, Alharethi R, Selzman CH, Franklin S. Distinct Transcriptomic and Proteomic Profile Specifies Patients Who Have Heart Failure With Potential of Myocardial Recovery on Mechanical Unloading and Circulatory Support. Circulation 2023; 147:409-424. [PMID: 36448446 PMCID: PMC10062458 DOI: 10.1161/circulationaha.121.056600] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/25/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Extensive evidence from single-center studies indicates that a subset of patients with chronic advanced heart failure (HF) undergoing left ventricular assist device (LVAD) support show significantly improved heart function and reverse structural remodeling (ie, termed "responders"). Furthermore, we recently published a multicenter prospective study, RESTAGE-HF (Remission from Stage D Heart Failure), demonstrating that LVAD support combined with standard HF medications induced remarkable cardiac structural and functional improvement, leading to high rates of LVAD weaning and excellent long-term outcomes. This intriguing phenomenon provides great translational and clinical promise, although the underlying molecular mechanisms driving this recovery are largely unknown. METHODS To identify changes in signaling pathways operative in the normal and failing human heart and to molecularly characterize patients who respond favorably to LVAD unloading, we performed global RNA sequencing and phosphopeptide profiling of left ventricular tissue from 93 patients with HF undergoing LVAD implantation (25 responders and 68 nonresponders) and 12 nonfailing donor hearts. Patients were prospectively monitored through echocardiography to characterize their myocardial structure and function and identify responders and nonresponders. RESULTS These analyses identified 1341 transcripts and 288 phosphopeptides that are differentially regulated in cardiac tissue from nonfailing control samples and patients with HF. In addition, these unbiased molecular profiles identified a unique signature of 29 transcripts and 93 phosphopeptides in patients with HF that distinguished responders after LVAD unloading. Further analyses of these macromolecules highlighted differential regulation in 2 key pathways: cell cycle regulation and extracellular matrix/focal adhesions. CONCLUSIONS This is the first study to characterize changes in the nonfailing and failing human heart by integrating multiple -omics platforms to identify molecular indices defining patients capable of myocardial recovery. These findings may guide patient selection for advanced HF therapies and identify new HF therapeutic targets.
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Affiliation(s)
- Stavros G. Drakos
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Rachit Badolia
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Aman Makaju
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Christos P. Kyriakopoulos
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Omar Wever-Pinzon
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Christopher M. Tracy
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Anna Bakhtina
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Ryan Bia
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Timothy Parnell
- Bioinformatics Core, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States
| | - Iosif Taleb
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Dinesh K. A. Ramadurai
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Sutip Navankasattusas
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Elizabeth Dranow
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Thomas C. Hanff
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Eleni Tseliou
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Thirupura S. Shankar
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Joseph Visker
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Rana Hamouche
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
| | - Elizabeth L. Stauder
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - William T. Caine
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Rami Alharethi
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Craig H. Selzman
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Utah Transplantation Affiliated Hospitals (U.T.A.H.) Cardiac Transplant Program (University of Utah, Intermountain Medical Center, Salt Lake VA Medical Center), Salt Lake City, Utah, United States
| | - Sarah Franklin
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah, United States
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States
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8
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Hindmarch CCT, Tian L, Xiong PY, Potus F, Bentley RET, Al-Qazazi R, Prins KW, Archer SL. An integrated proteomic and transcriptomic signature of the failing right ventricle in monocrotaline induced pulmonary arterial hypertension in male rats. Front Physiol 2022; 13:966454. [PMID: 36388115 PMCID: PMC9664166 DOI: 10.3389/fphys.2022.966454] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/19/2022] [Indexed: 01/25/2023] Open
Abstract
Aim: Pulmonary arterial hypertension (PAH) is an obstructive pulmonary vasculopathy that results in death from right ventricular failure (RVF). There is limited understanding of the molecular mechanisms of RVF in PAH. Methods: In a PAH-RVF model induced by injection of adult male rats with monocrotaline (MCT; 60 mg/kg), we performed mass spectrometry to identify proteins that change in the RV as a consequence of PAH induced RVF. Bioinformatic analysis was used to integrate our previously published RNA sequencing data from an independent cohort of PAH rats. Results: We identified 1,277 differentially regulated proteins in the RV of MCT rats compared to controls. Integration of MCT RV transcriptome and proteome data sets identified 410 targets that are concordantly regulated at the mRNA and protein levels. Functional analysis of these data revealed enriched functions, including mitochondrial metabolism, cellular respiration, and purine metabolism. We also prioritized 15 highly enriched protein:transcript pairs and confirmed their biological plausibility as contributors to RVF. We demonstrated an overlap of these differentially expressed pairs with data published by independent investigators using multiple PAH models, including the male SU5416-hypoxia model and several male rat strains. Conclusion: Multiomic integration provides a novel view of the molecular phenotype of RVF in PAH which includes dysregulation of pathways involving purine metabolism, mitochondrial function, inflammation, and fibrosis.
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Affiliation(s)
- Charles Colin Thomas Hindmarch
- QCPU, Queen’s Cardiopulmonary Unit, Translational Institute of Medicine (TIME), Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Lian Tian
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Ping Yu Xiong
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Francois Potus
- Pulmonary Hypertension Research Group, Centre de Recherche de l’Institut Universitaire de Cardiologie et Pneumologie de Quebec, Quebec City, QC, Canada
| | | | - Ruaa Al-Qazazi
- Department of Medicine, Queen’s University, Kingston, ON, Canada
| | - Kurt W. Prins
- Cardiovascular Division, Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Stephen L. Archer
- QCPU, Queen’s Cardiopulmonary Unit, Translational Institute of Medicine (TIME), Department of Medicine, Queen’s University, Kingston, ON, Canada,Department of Medicine, Queen’s University, Kingston, ON, Canada,*Correspondence: Stephen L. Archer,
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9
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Höcht C, Allo MA, Polizio AH, Morettón MA, Carranza A, Chiappetta DA, Choi MR. New and developing pharmacotherapies for hypertension. Expert Rev Cardiovasc Ther 2022; 20:647-666. [PMID: 35880547 DOI: 10.1080/14779072.2022.2105204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
INTRODUCTION Despite the significant contribution of hypertension to the global burden of disease, disease control remains poor worldwide. Considering this unmet clinical need, several new antihypertensive drugs with novel mechanisms of action are under development. AREAS COVERED The present review summarizes the recent advances in the development of emerging pharmacological agents for the management of hypertension. The latest technological innovations in the design of optimized formulations of available antihypertensive drugs and the potential role of the modification of intestinal microbiota to improve blood pressure (BP) control are also covered. EXPERT OPINION Significant efforts have been made to develop new antihypertensive agents with novel actions that target the main mechanisms involved in resistant hypertension. Sacubitril/valsartan may emerge as a potential first-line drug due to its superiority over renin angiotensin system inhibitors, and SGLT2 inhibitors can reduce BP in difficult-to-control hypertensive patients with type 2 diabetes. In addition, firibastat and aprocitentan may expand the therapeutic options for resistant hypertension by novel mechanism of actions. Since gut dysbiosis not only leads to hypertension but also causes direct target organ damage, prebiotics and probiotics could represent a potential strategy to prevent or reduce the development of hypertension and to contribute to BP control.
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Affiliation(s)
- Christian Höcht
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Farmacología, Buenos Aires, Argentinaa.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Tecnología Farmacéutica y Biofarmacia (InTecFyB), Buenos Aires, Argentinab
| | - Miguel A Allo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Farmacología, Buenos Aires, Argentinaa.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Tecnología Farmacéutica y Biofarmacia (InTecFyB), Buenos Aires, Argentinab
| | - Ariel Héctor Polizio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Farmacología, Buenos Aires, Argentinaa.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Tecnología Farmacéutica y Biofarmacia (InTecFyB), Buenos Aires, Argentinab
| | - Marcela A Morettón
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Tecnología Farmacéutica y Biofarmacia (InTecFyB), Buenos Aires, Argentinab.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Tecnología Farmacéutica, Buenos Aires, Argentinac.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Andrea Carranza
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Farmacología, Buenos Aires, Argentinaa.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Instituto Alberto C. Taquini de Investigaciones en Medicina Traslacional (IATIMET), Buenos Aires, Argentinae
| | - Diego A Chiappetta
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Tecnología Farmacéutica y Biofarmacia (InTecFyB), Buenos Aires, Argentinab.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Tecnología Farmacéutica, Buenos Aires, Argentinac.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Marcelo Roberto Choi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad de Buenos Aires, Instituto Alberto C. Taquini de Investigaciones en Medicina Traslacional (IATIMET), Buenos Aires, Argentinae.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Biológicas, Buenos Aires, Argentina f
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10
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Kalesinskas L, Gupta S, Khatri P. Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology. PLoS Comput Biol 2022; 18:e1010260. [PMID: 35759523 PMCID: PMC9269905 DOI: 10.1371/journal.pcbi.1010260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 07/08/2022] [Accepted: 05/29/2022] [Indexed: 01/07/2023] Open
Abstract
A major limitation of gene expression biomarker studies is that they are not reproducible as they simply do not generalize to larger, real-world, heterogeneous populations. Frequentist multi-cohort gene expression meta-analysis has been frequently used as a solution to this problem to identify biomarkers that are truly differentially expressed. However, the frequentist meta-analysis framework has its limitations-it needs at least 4-5 datasets with hundreds of samples, is prone to confounding from outliers and relies on multiple-hypothesis corrected p-values. To address these shortcomings, we have created a Bayesian meta-analysis framework for the analysis of gene expression data. Using real-world data from three different diseases, we show that the Bayesian method is more robust to outliers, creates more informative estimates of between-study heterogeneity, reduces the number of false positive and false negative biomarkers and selects more generalizable biomarkers with less data. We have compared the Bayesian framework to a previously published frequentist framework and have developed a publicly available R package for use.
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Affiliation(s)
- Laurynas Kalesinskas
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, United States of America
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Sanjana Gupta
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, United States of America
- * E-mail:
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11
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Lu Y, An L, Taylor MRG, Chen QM. Nrf2 signaling in heart failure: expression of Nrf2, Keap1, antioxidant, and detoxification genes in dilated or ischemic cardiomyopathy. Physiol Genomics 2022; 54:115-127. [PMID: 35073209 PMCID: PMC8897001 DOI: 10.1152/physiolgenomics.00079.2021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Increased levels of oxidative stress have been found with heart failure. Whether failing hearts express antioxidant and detoxification enzymes have not been addressed systematically. Nrf2 gene encodes a transcription factor that regulates the expression of antioxidant and detoxification genes. Using RNA-Seq data set from explanted hearts of 37 patients with dilated cardiomyopathy (DCM), 13 patients with ischemic cardiomyopathy (ICM), and 14 nonfailure (NF) donors as a control, we addressed whether failing hearts change the expression of Nrf2, its negative regulator Keap1, and antioxidant or detoxification genes. Significant increases in the ratio of Nrf2 to Keap1 were found to associate with DCM or ICM. Antioxidant genes showed decreased expression in both types of heart failure, including NQO1, SOD1, GPX3, GPX4, GSR, PRDX1, and TXNRD1. Detoxification enzymes, GCLM and EPHX1, also showed decreased expression, whereas the CYP1B1 transcript was elevated in both DCM and ICM. The genes encoding metal-binding protein ferritin were decreased, whereas five out of 12 metallothionein genes showed elevated expression. Our finding on Nrf2 gene expression has been validated by meta-analysis of seven independent data sets of microarray or RNA-Seq for differential gene expression in DCM and ICM from NF controls. In conclusion, minor elevation of Nrf2 gene expression is not coupled to increases in antioxidant and detoxification genes, supporting an impairment of Nrf2 signaling in patients with heart failure. Decreases in multiple antioxidant and detoxification genes are consistent with the observed increases of oxidative stress in failing hearts.
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Affiliation(s)
- Yingying Lu
- 1Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, Arizona,2Interdisciplanary Program in Statistics and Data Science, University of Arizona, Tucson, Arizona
| | - Lingling An
- 3Department of Biosystems Engineering, University of Arizona, Tucson, Arizona
| | - Matthew R. G. Taylor
- 4Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Qin M. Chen
- 1Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, Arizona
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12
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Sharma P, Liu Chung Ming C, Wang X, Bienvenu LA, Beck D, Figtree GA, Boyle A, Gentile C. Biofabrication of advanced in vitro3D models to study ischaemic and doxorubicin-induced myocardial damage. Biofabrication 2022; 14. [PMID: 34983029 DOI: 10.1088/1758-5090/ac47d8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 11/11/2022]
Abstract
Current preclinicalin vitroandin vivomodels of cardiac injury typical of myocardial infarction (MI, or heart attack) and drug induced cardiotoxicity mimic only a few aspects of these complex scenarios. This leads to a poor translation of findings from the bench to the bedside. In this study, we biofabricated for the first time advancedin vitromodels of MI and doxorubicin (DOX) induced injury by exposing cardiac spheroids (CSs) to pathophysiological changes in oxygen (O2) levels or DOX treatment. Then, contractile function and cell death was analyzed in CSs in control versus I/R and DOX CSs. For a deeper dig into cell death analysis, 3D rendering analyses and mRNA level changes of cardiac damage-related genes were compared in control versus I/R and DOX CSs. Overall,in vitroCSs recapitulated major features typical of thein vivoMI and drug induced cardiac damages, such as adapting intracellular alterations to O2concentration changes and incubation with cardiotoxic drug, mimicking the contraction frequency and fractional shortening and changes in mRNA expression levels for genes regulating sarcomere structure, calcium transport, cell cycle, cardiac remodelling and signal transduction. Taken together, our study supports the use of I/R and DOX CSs as advancedin vitromodels to study MI and DOX-induced cardiac damage by recapitulating their complex in vivoscenario.
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Affiliation(s)
- Poonam Sharma
- The University of Newcastle Faculty of Health and Medicine, Kookaburra Cct, New Lambton Heights, New South Wales, 2305, AUSTRALIA
| | - Clara Liu Chung Ming
- University of Technology Sydney Faculty of Engineering, Building 11, Level 10, Room 115, University of Technology Sydney, Ultimo, Sydney, Ultimo, Sydney, New South Wales, 2007, AUSTRALIA
| | - Xiaowei Wang
- Baker Heart and Diabetes Institute South Australia, 75 Commercial Road, Melbourne, Victoria, 3004, AUSTRALIA
| | - Laura A Bienvenu
- Baker Heart and Diabetes Institute South Australia, 75 Commercial Road, Melbourne, Victoria, 3004, AUSTRALIA
| | - Domink Beck
- University of Technology Sydney Faculty of Engineering, Building 11, Level 10, Room 115, University of Technology Sydney, Ultimo, Sydney, Ultimo, Sydney, New South Wales, 2007, AUSTRALIA
| | - Gemma A Figtree
- , The University of Sydney Faculty of Medicine and Health, Reserve Rd, Sydney, New South Wales, 2000, AUSTRALIA
| | - Andrew Boyle
- The University of Newcastle Faculty of Health and Medicine, Kookaburra Cct, New Lambton Heights, New South Wales, 2305, AUSTRALIA
| | - Carmine Gentile
- University of Technology Sydney Faculty of Engineering, Building 11, Level 10, Room 115, 81 Broadway St, Ultimo, Sydney, Ultimo, Sydney, New South Wales, 2007, AUSTRALIA
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13
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Bai Z, Sun H, Li X, Wu J, Yuan H, Zhang G, Yang H, Shi H. Time-ordered dysregulated ceRNA networks reveal disease progression and diagnostic biomarkers in ischemic and dilated cardiomyopathy. Cell Death Discov 2021; 7:296. [PMID: 34657123 PMCID: PMC8520530 DOI: 10.1038/s41420-021-00687-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 09/10/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Ischemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM) are the two main causes of heart failure (HF). Despite similar clinical characteristics and common “HF pathways”, ICM and DCM are expected to have different personalized treatment strategies. The underlying mechanisms of ICM and DCM have yet to be fully elucidated. The present study developed a novel computational method for identifying dysregulated long noncoding RNA (lncRNA)–microRNA (miRNA)–mRNA competing endogenous RNA (ceRNA) triplets. Time-ordered dysregulated ceRNA networks were subsequently constructed to reveal the possible disease progression of ICM and DCM based on the method. Biological functional analysis indicated that ICM and DCM had similar features during myocardial remodeling, whereas their characteristics differed during progression. Specifically, disturbance of myocardial energy metabolism may be the main characteristic during DCM progression, whereas early inflammation and response to oxygen are the characteristics that may be specific to ICM. In addition, several panels of diagnostic biomarkers for differentiating non-heart failure (NF) and ICM (NF-ICM), NF-DCM, and ICM-DCM were identified. Our study reveals biological differences during ICM and DCM progression and provides potential diagnostic biomarkers for ICM and DCM.
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Affiliation(s)
- Ziyi Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoran Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiuhong Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Hao Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guangde Zhang
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
| | - Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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14
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Zhang Q, He Y, Xu H, Li L, Guo Y, Zhang J, Cheng L, Yu H, Dai Y, Yang Q, Yang Z, Li C, Zhang S, Zhu S, Luo B, Gao Y. Modulation of STIM1 by a risk insertion/deletion polymorphism underlying genetics susceptibility to sudden cardiac death originated from coronary artery disease. Forensic Sci Int 2021; 328:111010. [PMID: 34592581 DOI: 10.1016/j.forsciint.2021.111010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022]
Abstract
Stromal interaction molecule 1 (STIM1), as a dynamic calcium signal transducer and key regulator of cardiomyocyte Ca2+ homeostasis, has been implicated in various pathological processes related to sudden cardiac death originated from coronary artery disease (SCD-CAD). In this study, we performed a systematic variant screening on promoter region of STIM1 to filter potential functional genetic variations. Based on the screening results, a 5-bp insertion/deletion (indel) polymorphism (rs3061890) in promoter region of STIM1 was selected as the candidate variant. We investigated the association of rs3061890 with SCD-CAD susceptibility in Chinese Han populations. The homozygote del/del genotype significantly increased risk for SCD-CAD as compared with the ins/ins genotype (odds ratio, 2.86 [95% confidence interval, 1.69-4.29]; P = 2.3 × 10-5). Compared with the common allele, the 5-bp deletion risk allele exhibited lower transcriptional capacity in luciferase assays. Intriguingly, genotype-phenotype correlation studies using human myocardium tissue samples revealed that the expression of STIM1 was associated with the genotype of rs3061890. Computational prediction combined with electrophoretic mobility shift (EMSA) and chromatin immunoprecipitation (ChIP) assays provided convincing evidence for stronger binding affinity of ELF1 (E74 like ETS transcription factor 1) with the deletion allele promoter. Taken together, our findings implied an allele-specific mechanism of regulating the transcription of STIM1 via ELF1, which contribute to SCD-CAD susceptibility. rs3061890 may thus considered as a candidate genetic marker for SCD-CAD prediction and prevention.
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Affiliation(s)
- Qing Zhang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
| | - Yan He
- Department of Epidemiology, Medical College of Soochow University, Suzhou, China.
| | - Hongfei Xu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
| | - Lijuan Li
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
| | - Yadong Guo
- Department of Forensic Sciences, School of Basic Medical Sciences, Central South University, Changsha, China.
| | - Jianhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China.
| | - Lei Cheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Huan Yu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
| | - Yunda Dai
- Department of Forensic Pathology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Qi Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
| | - Zhenzhen Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China.
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, Shanghai, China.
| | - Shaohua Zhu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
| | - Bin Luo
- Department of Forensic Pathology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China.
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15
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Zhu W, Wang W, Angsutararux P, Mellor RL, Isom LL, Nerbonne JM, Silva JR. Modulation of the effects of class Ib antiarrhythmics on cardiac NaV1.5-encoded channels by accessory NaVβ subunits. JCI Insight 2021; 6:e143092. [PMID: 34156986 PMCID: PMC8410097 DOI: 10.1172/jci.insight.143092] [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: 08/07/2020] [Accepted: 06/17/2021] [Indexed: 01/28/2023] Open
Abstract
Native myocardial voltage-gated sodium (NaV) channels function in macromolecular complexes comprising a pore-forming (α) subunit and multiple accessory proteins. Here, we investigated the impact of accessory NaVβ1 and NaVβ3 subunits on the functional effects of 2 well-known class Ib antiarrhythmics, lidocaine and ranolazine, on the predominant NaV channel α subunit, NaV1.5, expressed in the mammalian heart. We showed that both drugs stabilized the activated conformation of the voltage sensor of domain-III (DIII-VSD) in NaV1.5. In the presence of NaVβ1, the effect of lidocaine on the DIII-VSD was enhanced, whereas the effect of ranolazine was abolished. Mutating the main class Ib drug-binding site, F1760, affected but did not abolish the modulation of drug block by NaVβ1/β3. Recordings from adult mouse ventricular myocytes demonstrated that loss of Scn1b (NaVβ1) differentially affected the potencies of lidocaine and ranolazine. In vivo experiments revealed distinct ECG responses to i.p. injection of ranolazine or lidocaine in WT and Scn1b-null animals, suggesting that NaVβ1 modulated drug responses at the whole-heart level. In the human heart, we found that SCN1B transcript expression was 3 times higher in the atria than ventricles, differences that could, in combination with inherited or acquired cardiovascular disease, dramatically affect patient response to class Ib antiarrhythmic therapies.
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Affiliation(s)
- Wandi Zhu
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Wei Wang
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Paweorn Angsutararux
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Rebecca L Mellor
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Lori L Isom
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jeanne M Nerbonne
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jonathan R Silva
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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16
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Nguyen N, Souza T, Verheijen MCT, Gmuender H, Selevsek N, Schlapbach R, Kleinjans J, Jennen D. Translational Proteomics Analysis of Anthracycline-Induced Cardiotoxicity From Cardiac Microtissues to Human Heart Biopsies. Front Genet 2021; 12:695625. [PMID: 34211507 PMCID: PMC8239409 DOI: 10.3389/fgene.2021.695625] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/24/2021] [Indexed: 01/17/2023] Open
Abstract
Anthracyclines, including doxorubicin, idarubicin, and epirubicin, are common antitumor drugs as well as well-known cardiotoxic agents. This study analyzed the proteomics alteration in cardiac tissues caused by these 3 anthracyclines analogs. The in vitro human cardiac microtissues were exposed to drugs in 2 weeks; the proteomic data were measured at 7 time points. The heart biopsy data were collected from heart failure patients, in which some patients underwent anthracycline treatment. The anthracyclines-affected proteins were separately identified in the in vitro and in vivo dataset using the WGCNA method. These proteins engage in different cellular pathways including translation, metabolism, mitochondrial function, muscle contraction, and signaling pathways. From proteins detected in 2 datasets, a protein-protein network was established with 4 hub proteins, and 7 weighted proteins from both cardiac microtissue and human biopsies data. These 11 proteins, which involve in mitochondrial functions and the NF-κB signaling pathway, could provide insights into the anthracycline toxic mechanism. Some of them, such as HSPA5, BAG3, and SH3BGRL, are cardiac therapy targets or cardiotoxicity biomarkers. Other proteins, such as ATP5F1B and EEF1D, showed similar responses in both the in vitro and in vivo data. This suggests that the in vitro outcomes could link to clinical phenomena in proteomic analysis.
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Affiliation(s)
- Nhan Nguyen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Terezinha Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Marcha C T Verheijen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | | | | | - Ralph Schlapbach
- Functional Genomics Center, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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17
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Luo X, Yin J, Dwyer D, Yamawaki T, Zhou H, Ge H, Han CY, Shkumatov A, Snyder K, Ason B, Li CM, Homann O, Stolina M. Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction. Sci Rep 2021; 11:11839. [PMID: 34088950 PMCID: PMC8178406 DOI: 10.1038/s41598-021-91214-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Heart failure with reduced ejection fraction (HFrEF) constitutes 50% of HF hospitalizations and is characterized by high rates of mortality. To explore the underlying mechanisms of HFrEF etiology and progression, we studied the molecular and cellular differences in four chambers of non-failing (NF, n = 10) and HFrEF (n = 12) human hearts. We identified 333 genes enriched within NF heart subregions and often associated with cardiovascular disease GWAS variants. Expression analysis of HFrEF tissues revealed extensive disease-associated transcriptional and signaling alterations in left atrium (LA) and left ventricle (LV). Common left heart HFrEF pathologies included mitochondrial dysfunction, cardiac hypertrophy and fibrosis. Oxidative stress and cardiac necrosis pathways were prominent within LV, whereas TGF-beta signaling was evident within LA. Cell type composition was estimated by deconvolution and revealed that HFrEF samples had smaller percentage of cardiomyocytes within the left heart, higher representation of fibroblasts within LA and perivascular cells within the left heart relative to NF samples. We identified essential modules associated with HFrEF pathology and linked transcriptome discoveries with human genetics findings. This study contributes to a growing body of knowledge describing chamber-specific transcriptomics and revealed genes and pathways that are associated with heart failure pathophysiology, which may aid in therapeutic target discovery.
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Affiliation(s)
- Xin Luo
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Jun Yin
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Denise Dwyer
- Department of Cardiometabolic Disorders, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Tracy Yamawaki
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Hong Zhou
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Hongfei Ge
- Department of Cardiometabolic Disorders, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Chun-Ya Han
- Department of Cardiometabolic Disorders, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Artem Shkumatov
- TS&BA Pathology, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Karen Snyder
- Clinical Biomarkers, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Brandon Ason
- Department of Cardiometabolic Disorders, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Chi-Ming Li
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Oliver Homann
- Genome Analysis Unit, Amgen Research, 1120 Veterans BLVD, South San Francisco, CA, 94010, USA
| | - Marina Stolina
- Department of Cardiometabolic Disorders, Amgen Research, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA.
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18
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Ramirez Flores RO, Lanzer JD, Holland CH, Leuschner F, Most P, Schultz J, Levinson RT, Saez‐Rodriguez J. Consensus Transcriptional Landscape of Human End-Stage Heart Failure. J Am Heart Assoc 2021; 10:e019667. [PMID: 33787284 PMCID: PMC8174362 DOI: 10.1161/jaha.120.019667] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Background Transcriptomic studies have contributed to fundamental knowledge of myocardial remodeling in human heart failure (HF). However, the key HF genes reported are often inconsistent between studies, and systematic efforts to integrate evidence from multiple patient cohorts are lacking. Here, we aimed to provide a framework for comprehensive comparison and analysis of publicly available data sets resulting in an unbiased consensus transcriptional signature of human end-stage HF. Methods and Results We curated and uniformly processed 16 public transcriptomic studies of left ventricular samples from 263 healthy and 653 failing human hearts. First, we evaluated the degree of consistency between studies by using linear classifiers and overrepresentation analysis. Then, we meta-analyzed the deregulation of 14 041 genes to extract a consensus signature of HF. Finally, to functionally characterize this signature, we estimated the activities of 343 transcription factors, 14 signaling pathways, and 182 micro RNAs, as well as the enrichment of 5998 biological processes. Machine learning approaches revealed conserved disease patterns across all studies independent of technical differences. These consistent molecular changes were prioritized with a meta-analysis, functionally characterized and validated on external data. We provide all results in a free public resource (https://saezlab.shinyapps.io/reheat/) and exemplified usage by deciphering fetal gene reprogramming and tracing the potential myocardial origin of the plasma proteome markers in patients with HF. Conclusions Even though technical and sampling variability confound the identification of differentially expressed genes in individual studies, we demonstrated that coordinated molecular responses during end-stage HF are conserved. The presented resource is crucial to complement findings in independent studies and decipher fundamental changes in failing myocardium.
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Affiliation(s)
- Ricardo O. Ramirez Flores
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
| | - Jan D. Lanzer
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Christian H. Holland
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Florian Leuschner
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
| | - Patrick Most
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
- Center for Translational MedicineJefferson UniversityPhiladelphiaPA
| | - Jobst‐Hendrik Schultz
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Rebecca T. Levinson
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Julio Saez‐Rodriguez
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
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19
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Dougherty BV, Rawls KD, Kolling GL, Vinnakota KC, Wallqvist A, Papin JA. Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model. Cell Rep 2021; 34:108836. [PMID: 33691118 DOI: 10.1016/j.celrep.2021.108836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/07/2021] [Accepted: 02/17/2021] [Indexed: 11/28/2022] Open
Abstract
In diseased states, the heart can shift to use different carbon substrates, measured through changes in uptake of metabolites by imaging methods or blood metabolomics. However, it is not known whether these measured changes are a result of transcriptional changes or external factors. Here, we explore transcriptional changes in late-stage heart failure using publicly available data integrated with a model of heart metabolism. First, we present a heart-specific genome-scale metabolic network reconstruction (GENRE), iCardio. Next, we demonstrate the utility of iCardio in interpreting heart failure gene expression data by identifying tasks inferred from differential expression (TIDEs), which represent metabolic functions associated with changes in gene expression. We identify decreased gene expression for nitric oxide (NO) and N-acetylneuraminic acid (Neu5Ac) synthesis as common metabolic markers of heart failure. The methods presented here for constructing a tissue-specific model and identifying TIDEs can be extended to multiple tissues and diseases of interest.
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Affiliation(s)
- Bonnie V Dougherty
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Kristopher D Rawls
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Glynis L Kolling
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA
| | - Kalyan C Vinnakota
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
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20
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Zhang K, Wu M, Qin X, Wen P, Wu Y, Zhuang J. Asporin is a Potential Promising Biomarker for Common Heart Failure. DNA Cell Biol 2021; 40:303-315. [PMID: 33605799 DOI: 10.1089/dna.2020.5995] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heart failure (HF) is the end-stage of various diseases, especially ischemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM). We aimed to investigate the common molecular mechanism of ICM and DCM. Differentially expressed genes (DEGs) of ICM or DCM samples compared with control were identified in GSE1869, GSE5406, GSE57338, GSE79962, GSE116250, and GSE46224 datasets. Functional enrichment analysis and protein-protein network analysis of the coregulated DEGs in at least four datasets were performed using the online tools of DAVID, the Metascape database, and the STRING database. Hub genes of HF were identified and validated by western blotting (WB) and immunohistochemistry in our tissue microarray (TMA). Seventy-four coregulated ICM and 126 coregulated DCM relevant DEGs were identified. Moreover, 59 common genes between ICM and DCM relevant DEGs were obtained, which were mainly involved in cardiac fibrosis and several signal pathways, such as Wnt signal pathway, PI3K-Akt signal pathway, and HIF-1A signal pathway. Among the six hub genes with top degrees, asporin (ASPN) had a relatively higher correlation with LVEF. Finally, TMA and WB results revealed that the ASPN protein was significantly increased in ICM and DCM left ventricular samples. The present study revealed some common molecular mechanisms of HF with different causes. Furthermore, ASPN may be a potential promising biomarker for HF.
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Affiliation(s)
- Kai Zhang
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Min Wu
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xianyu Qin
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Pengju Wen
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yueheng Wu
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jian Zhuang
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
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21
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Kyriazis ID, Hoffman M, Gaignebet L, Lucchese AM, Markopoulou E, Palioura D, Wang C, Bannister TD, Christofidou-Solomidou M, Oka SI, Sadoshima J, Koch WJ, Goldberg IJ, Yang VW, Bialkowska AB, Kararigas G, Drosatos K. KLF5 Is Induced by FOXO1 and Causes Oxidative Stress and Diabetic Cardiomyopathy. Circ Res 2021; 128:335-357. [PMID: 33539225 PMCID: PMC7870005 DOI: 10.1161/circresaha.120.316738] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022]
Abstract
RATIONALE Diabetic cardiomyopathy (DbCM) is a major complication in type-1 diabetes, accompanied by altered cardiac energetics, impaired mitochondrial function, and oxidative stress. Previous studies indicate that type-1 diabetes is associated with increased cardiac expression of KLF5 (Krüppel-like factor-5) and PPARα (peroxisome proliferator-activated receptor) that regulate cardiac lipid metabolism. OBJECTIVE In this study, we investigated the involvement of KLF5 in DbCM and its transcriptional regulation. METHODS AND RESULTS KLF5 mRNA levels were assessed in isolated cardiomyocytes from cardiovascular patients with diabetes and were higher compared with nondiabetic individuals. Analyses in human cells and diabetic mice with cardiomyocyte-specific FOXO1 (Forkhead box protein O1) deletion showed that FOXO1 bound directly on the KLF5 promoter and increased KLF5 expression. Diabetic mice with cardiomyocyte-specific FOXO1 deletion had lower cardiac KLF5 expression and were protected from DbCM. Genetic, pharmacological gain and loss of KLF5 function approaches and AAV (adeno-associated virus)-mediated Klf5 delivery in mice showed that KLF5 induces DbCM. Accordingly, the protective effect of cardiomyocyte FOXO1 ablation in DbCM was abolished when KLF5 expression was rescued. Similarly, constitutive cardiomyocyte-specific KLF5 overexpression caused cardiac dysfunction. KLF5 caused oxidative stress via direct binding on NADPH oxidase (NOX)4 promoter and induction of NOX4 (NADPH oxidase 4) expression. This was accompanied by accumulation of cardiac ceramides. Pharmacological or genetic KLF5 inhibition alleviated superoxide formation, prevented ceramide accumulation, and improved cardiac function in diabetic mice. CONCLUSIONS Diabetes-mediated activation of cardiomyocyte FOXO1 increases KLF5 expression, which stimulates NOX4 expression, ceramide accumulation, and causes DbCM.
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Affiliation(s)
- Ioannis D. Kyriazis
- Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, 19131, USA
| | - Matthew Hoffman
- Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, 19131, USA
| | - Lea Gaignebet
- Charité – Universitätsmedizin Berlin, Berlin 10115, Germany
| | - Anna Maria Lucchese
- Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, 19131, USA
| | - Eftychia Markopoulou
- Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, 19131, USA
| | - Dimitra Palioura
- Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, 19131, USA
| | - Chao Wang
- The Scripps Research Institute, Jupiter, FL, 33458m USA
| | | | - Melpo Christofidou-Solomidou
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Shin-ichi Oka
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07101, USA
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07101, USA
| | - Walter J. Koch
- Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, 19131, USA
| | - Ira J. Goldberg
- Division of Endocrinology, Diabetes and Metabolism, New York University School of Medicine, New York, NY, 10016, USA
| | - Vincent W. Yang
- School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | | | - Georgios Kararigas
- Charité – Universitätsmedizin Berlin, Berlin 10115, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin 10785, Germany
- Department of Physiology, Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
| | - Konstantinos Drosatos
- Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, 19131, USA
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22
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McTiernan CF, Lemster BH, Bedi KC, Margulies KB, Moravec CS, Hsieh PN, Shusterman V, Saba S. Circadian Pattern of Ion Channel Gene Expression in Failing Human Hearts. Circ Arrhythm Electrophysiol 2020; 14:e009254. [PMID: 33301345 DOI: 10.1161/circep.120.009254] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ventricular tachyarrhythmias and sudden cardiac death show a circadian pattern of occurrence in patients with heart failure. In the rodent ventricle, a significant portion of genes, including some ion channels, shows a circadian pattern of expression. However, genes that define electrophysiological properties in failing human heart ventricles have not been examined for a circadian expression pattern. METHODS Ventricular tissue samples were collected from patients at the time of cardiac transplantation. Two sets of samples (n=37 and 46, one set with a greater arrhythmic history) were selected to generate pseudo-time series according to their collection time. A third set (n=27) of samples was acquired from the nonfailing ventricles of brain-dead donors. The expression of 5 known circadian clock genes and 19 additional ion channel genes plausibly important to electrophysiological properties were analyzed by real-time polymerase chain reaction and then analyzed for the percentage of expression variation attributed to a 24-hour circadian pattern. RESULTS The 5 known circadian clock gene transcripts showed a strong circadian expression pattern. Compared with rodent hearts, the human circadian clock gene transcripts showed a similar temporal order of acrophases but with a ≈7.6 hours phase shift. Five of the ion channel genes also showed strong circadian expression. Comparable studies of circadian clock gene expression in samples recovered from nonheart failure brain-dead donors showed acrophase shifts, or weak or complete loss of circadian rhythmicity, suggesting alterations in circadian gene expression. CONCLUSIONS Ventricular tissue from failing human hearts display a circadian pattern of circadian clock gene expression but phase-shifted relative to rodent hearts. At least 5 ion channels show a circadian expression pattern in the ventricles of failing human hearts, which may underlie a circadian pattern of ventricular tachyarrhythmia/sudden cardiac death. Nonfailing hearts from brain-dead donors show marked differences in circadian clock gene expression patterns, suggesting fundamental deviations from circadian expression.
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Affiliation(s)
- Charles F McTiernan
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA (C.F.M., B.H.L., S.S.)
| | - Bonnie H Lemster
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA (C.F.M., B.H.L., S.S.)
| | - Kenneth C Bedi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.C.B)
| | - Kenneth B Margulies
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.B.M.)
| | - Christine S Moravec
- Department of Cardiovascular Medicine, Cleveland Clinic Foundation, OH (C.S.M.)
| | | | | | - Samir Saba
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA (C.F.M., B.H.L., S.S.)
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23
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Zhao J, Yang S, Jing R, Jin H, Hu Y, Wang J, Gu M, Niu H, Zhang S, Chen L, Hua W. Plasma Metabolomic Profiles Differentiate Patients With Dilated Cardiomyopathy and Ischemic Cardiomyopathy. Front Cardiovasc Med 2020; 7:597546. [PMID: 33240942 PMCID: PMC7683512 DOI: 10.3389/fcvm.2020.597546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/22/2020] [Indexed: 12/31/2022] Open
Abstract
Dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) are common causes of heart failure (HF). Though they share similar clinical characteristics, their differential effects on cardiovascular metabolomics have yet to be elucidated. In this study, we applied a comprehensive metabolomics platform to plasma samples of HF patients with different etiology (38 patients with DCM and 18 patients with ICM) and 20 healthy controls. Significant differences in metabolomics profiling were shown among two cardiomyopathy groups and healthy controls. Two hundred thirty three dysregulated metabolites were identified between DCM vs. healthy controls, and 204 dysregulated metabolites between ICM patients and healthy controls. They have 140 metabolites in common, with fold-changes in the same direction in both groups. Pathway analysis found the commonalities of HF pathways as well as disease-specific metabolic signatures. In addition, we found that a combination panel of 6 metabolites including 1-pyrroline-2-carboxylate, norvaline, lysophosphatidylinositol (16:0/0:0), phosphatidylglycerol (6:0/8:0), fatty acid esters of hydroxy fatty acid (24:1), and phosphatidylcholine (18:0/18:3) may have the potential to differentiate patients with DCM and ICM.
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Affiliation(s)
- Junhan Zhao
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengwen Yang
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Heart Center & Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ran Jing
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Han Jin
- Peking University First Hospital, Beijing, China
| | - Yiran Hu
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wang
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Gu
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongxia Niu
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shu Zhang
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liang Chen
- State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Hua
- State Key Laboratory of Cardiovascular Disease, Arrhythmia Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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24
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Abstract
PURPOSE OF REVIEW The goal of this review is to summarize the state of big data analyses in the study of heart failure (HF). We discuss the use of big data in the HF space, focusing on "omics" and clinical data. We address some limitations of this data, as well as their future potential. RECENT FINDINGS Omics are providing insight into plasmal and myocardial molecular profiles in HF patients. The introduction of single cell and spatial technologies is a major advance that will reshape our understanding of cell heterogeneity and function as well as tissue architecture. Clinical data analysis focuses on HF phenotyping and prognostic modeling. Big data approaches are increasingly common in HF research. The use of methods designed for big data, such as machine learning, may help elucidate the biology underlying HF. However, important challenges remain in the translation of this knowledge into improvements in clinical care.
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Affiliation(s)
- Jan D Lanzer
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Internal Medicine II, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Leuschner
- Department of Cardiology, Medical University Hospital, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany
| | - Rafael Kramann
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rebecca T Levinson
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Internal Medicine II, Heidelberg University Hospital, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany.
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25
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Mollanoori H, Rahmati Y, Hassani B, Esmaeili S, Amini K, Teimourian S. Screening the underlying molecular mechanisms involved in the development of heart failure. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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26
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Fajarda O, Duarte-Pereira S, Silva RM, Oliveira JL. Merging microarray studies to identify a common gene expression signature to several structural heart diseases. BioData Min 2020; 13:8. [PMID: 32670412 PMCID: PMC7346458 DOI: 10.1186/s13040-020-00217-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Heart disease is the leading cause of death worldwide. Knowing a gene expression signature in heart disease can lead to the development of more efficient diagnosis and treatments that may prevent premature deaths. A large amount of microarray data is available in public repositories and can be used to identify differentially expressed genes. However, most of the microarray datasets are composed of a reduced number of samples and to obtain more reliable results, several datasets have to be merged, which is a challenging task. The identification of differentially expressed genes is commonly done using statistical methods. Nonetheless, these methods are based on the definition of an arbitrary threshold to select the differentially expressed genes and there is no consensus on the values that should be used. RESULTS Nine publicly available microarray datasets from studies of different heart diseases were merged to form a dataset composed of 689 samples and 8354 features. Subsequently, the adjusted p-value and fold change were determined and by combining a set of adjusted p-values cutoffs with a list of different fold change thresholds, 12 sets of differentially expressed genes were obtained. To select the set of differentially expressed genes that has the best accuracy in classifying samples from patients with heart diseases and samples from patients with no heart condition, the random forest algorithm was used. A set of 62 differentially expressed genes having a classification accuracy of approximately 95% was identified. CONCLUSIONS We identified a gene expression signature common to different cardiac diseases and supported our findings by showing their involvement in the pathophysiology of the heart. The approach used in this study is suitable for the identification of gene expression signatures, and can be extended to different diseases.
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Affiliation(s)
- Olga Fajarda
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Sara Duarte-Pereira
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Raquel M. Silva
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
- Current Address: Universidade Católica Portuguesa, Faculdade de Medicina Dentária, CIIS-Centro de Investigação Interdisciplinar em Saúde, Campus de Viseu, Viseu, 3504-505 Portugal
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27
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Zhou J, Zhang W, Wei C, Zhang Z, Yi D, Peng X, Peng J, Yin R, Zheng Z, Qi H, Wei Y, Wen T. Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure. BMC Med Genomics 2020; 13:93. [PMID: 32620106 PMCID: PMC7333416 DOI: 10.1186/s12920-020-00750-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Left-sided heart failure (HF) is documented as a key prognostic factor in HF. However, the relative molecular mechanisms underlying left-sided HF is unknown. The purpose of this study is to unearth significant modules, pivotal genes and candidate regulatory components governing the progression of left-sided HF by bioinformatical analysis. METHODS A total of 319 samples in GSE57345 dataset were used for weighted gene correlation network analysis (WGCNA). ClusterProfiler package in R was used to conduct functional enrichment for genes uncovered from the modules of interest. Regulatory networks of genes were built using Cytoscape while Enrichr database was used for identification of transcription factors (TFs). The MCODE plugin was used for identifying hub genes in the modules of interest and their validation was performed based on GSE1869 dataset. RESULTS A total of six significant modules were identified. Notably, the blue module was confirmed as the most crucially associated with left-sided HF, ischemic heart disease (ISCH) and dilated cardiomyopathy (CMP). Functional enrichment conveyed that genes belonging to this module were mainly those driving the extracellular matrix-associated processes such as extracellular matrix structural constituent and collagen binding. A total of seven transcriptional factors, including Suppressor of Zeste 12 Protein Homolog (SUZ12) and nuclear factor erythroid 2 like 2 (NFE2L2), adrenergic receptor (AR), were identified as possible regulators of coexpression genes identified in the blue module. A total of three key genes (OGN, HTRA1 and MXRA5) were retained after validation of their prognostic value in left-sided HF. The results of functional enrichment confirmed that these key genes were primarily involved in response to transforming growth factor beta and extracellular matrix. CONCLUSION We uncovered a candidate gene signature correlated with HF, ISCH and CMP in the left ventricle, which may help provide better prognosis and therapeutic decisions and in HF, ISCH and CMP patients.
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Affiliation(s)
- Jiamin Zhou
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Wei Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Chunying Wei
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Zhiliang Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Dasong Yi
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Xiaoping Peng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Jingtian Peng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Ran Yin
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Zeqi Zheng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Hongmei Qi
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Yunfeng Wei
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China
| | - Tong Wen
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi province, China.
- Hypertension Research Institute of Jiangxi Province, Nanchang, 330006, China.
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28
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Haywood ME, Cocciolo A, Porter KF, Dobrinskikh E, Slavov D, Graw SL, Reece TB, Ambardekar AV, Bristow MR, Mestroni L, Taylor MRG. Transcriptome signature of ventricular arrhythmia in dilated cardiomyopathy reveals increased fibrosis and activated TP53. J Mol Cell Cardiol 2020; 139:124-134. [PMID: 31958463 PMCID: PMC7144813 DOI: 10.1016/j.yjmcc.2019.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 12/19/2019] [Accepted: 12/29/2019] [Indexed: 12/21/2022]
Abstract
AIMS One-third of DCM patients experience ventricular tachycardia (VT), but a clear biological basis for this has not been established. The purpose of this study was to identify transcriptome signatures and enriched pathways in the hearts of dilated cardiomyopathy (DCM) patients with VT. METHODS AND RESULTS We used RNA-sequencing in explanted heart tissue from 49 samples: 19 DCM patients with VT, 16 DCM patients without VT, and 14 non-failing controls. We compared each DCM cohort to the controls and identified the genes that were differentially expressed in DCM patients with VT but not without VT. Differentially expressed genes were evaluated using pathway analysis, and pathways of interest were investigated by qRT-PCR validation, Western blot, and microscopy. There were 590 genes differentially expressed in DCM patients with VT that are not differentially expressed in patients without VT. These genes were enriched for genes in the TGFß1 and TP53 signaling pathways. Increased fibrosis and activated TP53 signaling was demonstrated in heart tissue of DCM patients with VT. CONCLUSIONS Our study supports that distinct biological mechanisms distinguish ventricular arrhythmia in DCM patients.
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Affiliation(s)
- Mary E Haywood
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA.
| | - Andrea Cocciolo
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Kadijah F Porter
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - Evgenia Dobrinskikh
- Division of Renal Diseases and Hypertension, Department of Medicine University of Colorado, Aurora, CO, USA.
| | - Dobromir Slavov
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - Sharon L Graw
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - T Brett Reece
- Department of Cardiothoracic Surgery, University of Colorado Hospital, Aurora, CO, USA.
| | - Amrut V Ambardekar
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA.
| | - Michael R Bristow
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA.
| | - Luisa Mestroni
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA; Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - Matthew R G Taylor
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA; Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
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29
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Watanabe T, Okada H, Kanamori H, Miyazaki N, Tsujimoto A, Takada C, Suzuki K, Naruse G, Yoshida A, Nawa T, Tanaka T, Kawasaki M, Ito H, Ogura S, Okura H, Fujiwara T, Fujiwara H, Takemura G. In situ nuclear DNA methylation in dilated cardiomyopathy: an endomyocardial biopsy study. ESC Heart Fail 2020; 7:493-502. [PMID: 31971668 DOI: 10.1002/ehf2.12593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 11/12/2022] Open
Abstract
AIMS Although distinct DNA methylation patterns have been reported, its localization and roles remain to be defined in heart failure. We investigated the cellular and subcellular localization of DNA methylation and its pathophysiological significance in human failing hearts. METHODS AND RESULTS Using left ventricular (LV) endomyocardial biopsy specimens from 75 patients with dilated cardiomyopathy (DCM; age: 58 ± 14 years old, %female: 32%) and 20 patients without heart failure (controls; age: 56 ± 17 years old, %female: 45%), we performed immunohistochemistry and immunoelectron microscopy for methylated DNA, 5-methylcytosine (5-mC). We next investigated possible relations of the incidence of 5-mC-positive (%5-mC+ ) cardiomyocytes with clinicopathological parameters. Immunopositivity for 5-mC was detected in the cardiomyocytes and other cell types. The %5-mC+ cardiomyocytes was significantly greater in DCM hearts than in controls (57 ± 13% in DCM vs. 25 ± 12% in controls, P < 0.0001). The localization of 5-mC immunopositivity in cardiomyocyte nuclei coincided well with that of heterochromatin, as confirmed by immunoelectron microscopy. Substantial DNA methylation was also observed in interstitial non-cardiomyocytes, but the incidences did not differ between control and DCM hearts (39 ± 7.9% in DCM vs. 41 ± 10% in controls, P = 0.4099). In DCM patients, the %5-mC+ cardiomyocytes showed a significant inverse correlation with LV functional parameters such as heart rate (r = 0.2391, P = 0.0388), end-diastolic pressure (r = 0.2397, P = 0.0397), and ejection fraction (r = -0.2917, P = 0.0111) and a positive correlation with LV dilatation (volume index at diastole; r = 0.2442, P = 0.0347; and volume index at systole; r = 0.3136, P = 0.0062) and LV hypertrophy (mass index; r = 0.2287, P = 0.0484)-that is, LV remodelling parameters. No significant correlations between DNA methylation and the histological parameters of the biopsies, including cardiomyocyte hypertrophy, fibrosis, and inflammatory cell infiltration, were noted. CONCLUSIONS The present study revealed increased nuclear DNA methylation in cardiomyocytes, but not other cell types, from DCM hearts, with predominant localization in the heterochromatin. Its significant relations with LV functional and remodelling parameters imply a pathophysiological significance of DNA methylation in heart failure.
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Affiliation(s)
- Takatomo Watanabe
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan.,Department of Informative Clinical Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hideshi Okada
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan.,Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiromitsu Kanamori
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Nagisa Miyazaki
- Department of Internal Medicine, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, 501-0296, Japan
| | - Akiko Tsujimoto
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Chihiro Takada
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kodai Suzuki
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Genki Naruse
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akihiro Yoshida
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takahide Nawa
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Toshiki Tanaka
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Masanori Kawasaki
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyasu Ito
- Department of Informative Clinical Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Shinji Ogura
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyuki Okura
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takako Fujiwara
- Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | | | - Genzou Takemura
- Department of Internal Medicine, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, 501-0296, Japan
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30
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Defining decreased protein succinylation of failing human cardiac myofibrils in ischemic cardiomyopathy. J Mol Cell Cardiol 2019; 138:304-317. [PMID: 31836543 DOI: 10.1016/j.yjmcc.2019.11.159] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Succinylation is a post-translational modification of protein lysine residues with succinyl groups derived from succinyl CoA. Succinylation is considered a significant post-translational modification with the potential to impact protein function which is highly conserved across numerous species. The role of succinylation in the heart, especially in heart failure and myofibril mechanics, remains largely unexplored. Mechanical parameters were measured in myofibrils isolated from failing hearts of ischemic cardiomyopathy patients and non-failing donor controls. We employed mass spectrometry to quantify differential protein expression in myofibrils from failing ischemic cardiomyopathy hearts compared to non-failing hearts. In addition, we combined peptide enrichment by immunoprecipitation with liquid chromatography tandem mass spectrometry to quantitatively analyze succinylated lysine residues in these myofibrils. Several key parameters of sarcomeric mechanical interactions were altered in myofibrils isolated from failing ischemic cardiomyopathy hearts, including lower resting tension and a faster rate of activation. Of the 100 differentially expressed proteins, 46 showed increased expression in ischemic heart failure, while 54 demonstrated decreased expression in ischemic heart failure. Our quantitative succinylome analysis identified a total of 572 unique succinylated lysine sites located on 181 proteins, with 307 significantly changed succinylation events. We found that 297 succinyl-Lys demonstrated decreased succinylation on 104 proteins, while 10 residues demonstrated increased succinylation on 4 proteins. Investigating succinyl CoA generation, enzyme activity assays demonstrated that α-ketoglutarate dehydrogenase and succinate dehydrogenase activities were significantly decreased in ischemic heart failure. An activity assay for succinyl CoA synthetase demonstrated a significant increase in ischemic heart failure. Taken together, our findings support the hypothesis that succinyl CoA production is decreased and succinyl CoA turnover is increased in ischemic heart failure, potentially resulting in an overall decrease in the mitochondrial succinyl CoA pool, which may contribute to decreased myofibril protein succinylation in heart failure.
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31
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Niu X, Zhang J, Zhang L, Hou Y, Pu S, Chu A, Bai M, Zhang Z. Weighted Gene Co-Expression Network Analysis Identifies Critical Genes in the Development of Heart Failure After Acute Myocardial Infarction. Front Genet 2019; 10:1214. [PMID: 31850068 PMCID: PMC6889910 DOI: 10.3389/fgene.2019.01214] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/04/2019] [Indexed: 12/13/2022] Open
Abstract
Background: The development of heart failure (HF) remains a common complication following an acute myocardial infarction (AMI), and is associated with substantial adverse outcomes. However, the specific predictive biomarkers and candidate therapeutic targets for post-infarction HF have not been fully established. We sought to perform a weighted gene co-expression network analysis (WGCNA) to identify key modules, hub genes, and possible regulatory targets involved in the development of HF following AMI. Methods: Genes exhibiting the most (top 50%) variation in expression levels across samples in a GSE59867 dataset were imported to the WGCNA. Gene Ontology and pathway enrichment analyses were performed on genes identified in the key module by Metascape. Gene regulatory networks were constructed using the microarray probe reannotation and bioinformatics database. Hub genes were screened out from the key module and validated using other datasets. Results: A total of 10,265 most varied genes and six modules were identified between AMI patients who developed HF within 6 months of follow-up and those who did not. Specifically, the blue module was found to be the most significantly related to the development of post-infarction HF. Functional enrichment analysis revealed that the blue module was primarily associated with the inflammatory response, immune system, and apoptosis. Seven transcriptional factors, including SPI1, ZBTB7A, IRF8, PPARG, P65, KLF4, and Fos, were identified as potential regulators of the expression of genes identified in the blue module. Further, non-coding RNAs, including miR-142-3p and LINC00537, were identified as having close interactions with genes from the blue module. A total of six hub genes (BCL3, HCK, PPIF, S100A9, SERPINA1, and TBC1D9B) were identified and validated for their predictive value in identifying future HFs. Conclusions: By using the WGCNA, we provide new insights into the underlying molecular mechanism and molecular markers correlated with HF development following an AMI, which may serve to improve risk stratification, therapeutic decisions, and prognosis prediction in AMI patients.
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Affiliation(s)
- Xiaowei Niu
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,The Quality Improvement Project for the Diagnosis and Treatment of Complicated Cardiovascular and Cerebrovascular Diseases (2018), The First Hospital of Lanzhou University, Lanzhou, China
| | - Jingjing Zhang
- Department of Internal Medicine, Baiyin Second People's Hospital, Baiyin, China
| | - Lanlan Zhang
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,The Quality Improvement Project for the Diagnosis and Treatment of Complicated Cardiovascular and Cerebrovascular Diseases (2018), The First Hospital of Lanzhou University, Lanzhou, China
| | - Yangfan Hou
- Department of Digestive, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuangshuang Pu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Aiai Chu
- Department of Cardiology, Gansu Provincial Hospital, Lanzhou, China
| | - Ming Bai
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,The Quality Improvement Project for the Diagnosis and Treatment of Complicated Cardiovascular and Cerebrovascular Diseases (2018), The First Hospital of Lanzhou University, Lanzhou, China
| | - Zheng Zhang
- Heart Center, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, China.,The Quality Improvement Project for the Diagnosis and Treatment of Complicated Cardiovascular and Cerebrovascular Diseases (2018), The First Hospital of Lanzhou University, Lanzhou, China
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32
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Rieger AC, Myerburg RJ, Florea V, Tompkins BA, Natsumeda M, Premer C, Khan A, Schulman IH, Vidro-Casiano M, DiFede DL, Heldman AW, Mitrani R, Hare JM. Genetic determinants of responsiveness to mesenchymal stem cell injections in non-ischemic dilated cardiomyopathy. EBioMedicine 2019; 48:377-385. [PMID: 31648988 PMCID: PMC6838383 DOI: 10.1016/j.ebiom.2019.09.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Non-ischemic dilated cardiomyopathy (NIDCM) responds variably to intramyocardial injection of mesenchymal stem cells (MSCs). We hypothesized that NIDCM genotype may influence responsiveness to MSC therapy and performed genotyping on all patients in the POSEIDON-DCM trial. METHODS POSEIDON-DCM patients (n = 34) underwent genetic sequence analysis and deletion/duplication testing. The results were classified as positive for pathological variants (PV+; n = 8), negative for any variants (V-; n = 6), or as variants of uncertain significance (VUS; n = 20). All outcomes of therapy were analysed for each category of genetic results. FINDINGS The 3 groups were indistinguishable at baseline with regard to ejection fraction (EF), demographics, medication use, or functional parameters. V- patients had an increase in EF at 12 months: +13.6% (IQR = +7.8%; +20.5%; p = 0.002), compared with VUS (+6.5%; IQR = +0.9%, +11.1%; p = 0.005) and PV+(-5.9%; IQR = -12.7%, +1.0; p = 0.2; p = 0.01 between groups). Six-minute walk distance improved in V- patients, but not in VUS and PV+. V- patients improved MLHFQ, compared to the other 2 groups, which did not improve over time. EPCCFUs increased by 9.7 ± 1.9 in V- (p = 0.009) compared to VUS and PV+ patients. V- patients had one-year survival (100%) compared with VUS (85%) and PV+ (40%; p = 0.015 log-rank). Similarly, MACE rates were lower in V- (0%) than PV+ (61.9%) or VUS (42.2%; p = 0.021 log-rank). INTERPRETATION Our findings support the concept that the genetic profile of NIDCM patients plays a role in responsiveness to MSC therapy, with V- patients more likely to benefit and the converse for PV+. This observation emphasizes the need for further genetic studies, because of important implications for the management of NIDCM syndromes.
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Affiliation(s)
- Angela C Rieger
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Robert J Myerburg
- Cardiovascular Division, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Victoria Florea
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Bryon A Tompkins
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States; Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Makoto Natsumeda
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Courtney Premer
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Aisha Khan
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ivonne H Schulman
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States; Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Mayra Vidro-Casiano
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Darcy L DiFede
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Alan W Heldman
- Cardiovascular Division, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Raul Mitrani
- Cardiovascular Division, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Joshua M Hare
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States; Cardiovascular Division, University of Miami Miller School of Medicine, Miami, FL, United States.
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Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure. Nat Commun 2019; 10:2760. [PMID: 31235787 PMCID: PMC6591478 DOI: 10.1038/s41467-019-10591-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
Heart failure is a leading cause of mortality, yet our understanding of the genetic interactions underlying this disease remains incomplete. Here, we harvest 1352 healthy and failing human hearts directly from transplant center operating rooms, and obtain genome-wide genotyping and gene expression measurements for a subset of 313. We build failing and non-failing cardiac regulatory gene networks, revealing important regulators and cardiac expression quantitative trait loci (eQTLs). PPP1R3A emerges as a regulator whose network connectivity changes significantly between health and disease. RNA sequencing after PPP1R3A knockdown validates network-based predictions, and highlights metabolic pathway regulation associated with increased cardiomyocyte size and perturbed respiratory metabolism. Mice lacking PPP1R3A are protected against pressure-overload heart failure. We present a global gene interaction map of the human heart failure transition, identify previously unreported cardiac eQTLs, and demonstrate the discovery potential of disease-specific networks through the description of PPP1R3A as a central regulator in heart failure. The genetic and pathogenetic basis of heart failure is incompletely understood. Here, the authors present a high-fidelity tissue collection from rapidly preserved failing and non-failing control hearts which are used for eQTL mapping and network analysis, resulting in the prioritization of PPP1R3A as a heart failure gene.
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Pepin ME, Ha CM, Crossman DK, Litovsky SH, Varambally S, Barchue JP, Pamboukian SV, Diakos NA, Drakos SG, Pogwizd SM, Wende AR. Genome-wide DNA methylation encodes cardiac transcriptional reprogramming in human ischemic heart failure. J Transl Med 2019; 99:371-386. [PMID: 30089854 PMCID: PMC6515060 DOI: 10.1038/s41374-018-0104-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 02/07/2023] Open
Abstract
Ischemic cardiomyopathy (ICM) is the clinical endpoint of coronary heart disease and a leading cause of heart failure. Despite growing demands to develop personalized approaches to treat ICM, progress is limited by inadequate knowledge of its pathogenesis. Since epigenetics has been implicated in the development of other chronic diseases, the current study was designed to determine whether transcriptional and/or epigenetic changes are sufficient to distinguish ICM from other etiologies of heart failure. Specifically, we hypothesize that genome-wide DNA methylation encodes transcriptional reprogramming in ICM. RNA-sequencing analysis was performed on human ischemic left ventricular tissue obtained from patients with end-stage heart failure, which enriched known targets of the polycomb methyltransferase EZH2 compared to non-ischemic hearts. Combined RNA sequencing and genome-wide DNA methylation analysis revealed a robust gene expression pattern consistent with suppression of oxidative metabolism, induced anaerobic glycolysis, and altered cellular remodeling. Lastly, KLF15 was identified as a putative upstream regulator of metabolic gene expression that was itself regulated by EZH2 in a SET domain-dependent manner. Our observations therefore define a novel role of DNA methylation in the metabolic reprogramming of ICM. Furthermore, we identify EZH2 as an epigenetic regulator of KLF15 along with DNA hypermethylation, and we propose a novel mechanism through which coronary heart disease reprograms the expression of both intermediate enzymes and upstream regulators of cardiac metabolism such as KLF15.
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Affiliation(s)
- Mark E. Pepin
- 0000000106344187grid.265892.2Dept of Pathology, Div of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35294 USA ,0000000106344187grid.265892.2Dept of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Chae-Myeong Ha
- 0000000106344187grid.265892.2Dept of Pathology, Div of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - David K. Crossman
- 0000000106344187grid.265892.2Dept of Genetics, Heflin Center for Genomic Science, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Silvio H. Litovsky
- 0000000106344187grid.265892.2Dept of Pathology, Div of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Sooryanarayana Varambally
- 0000000106344187grid.265892.2Dept of Pathology, Div of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Joseph P. Barchue
- 0000000106344187grid.265892.2Dept of Medicine, Div of Cardiovascular Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Salpy V. Pamboukian
- 0000000106344187grid.265892.2Dept of Medicine, Div of Cardiovascular Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Nikolaos A. Diakos
- 0000 0001 2193 0096grid.223827.eDept of Internal Medicine, Div of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah, Salt Lake City, UT 84108 USA
| | - Stavros G. Drakos
- 0000 0001 2193 0096grid.223827.eDept of Internal Medicine, Div of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah, Salt Lake City, UT 84108 USA
| | - Steven M. Pogwizd
- 0000000106344187grid.265892.2Dept of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294 USA ,0000000106344187grid.265892.2Dept of Medicine, Div of Cardiovascular Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Adam R. Wende
- 0000000106344187grid.265892.2Dept of Pathology, Div of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35294 USA ,0000000106344187grid.265892.2Dept of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294 USA
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Maimouni S, Issa N, Cheng S, Ouaari C, Cheema A, Kumar D, Byers S. Tumor suppressor RARRES1- A novel regulator of fatty acid metabolism in epithelial cells. PLoS One 2018; 13:e0208756. [PMID: 30557378 PMCID: PMC6296515 DOI: 10.1371/journal.pone.0208756] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 11/20/2018] [Indexed: 12/31/2022] Open
Abstract
Retinoic acid receptor responder 1 (RARRES1) is silenced in many cancers and is differentially expressed in metabolism associated diseases, such as hepatic steatosis, hyperinsulinemia and obesity. Here we report a novel function of RARRES1 in metabolic reprogramming of epithelial cells. Using non-targeted LC-MS, we discovered that RARRES1 depletion in epithelial cells caused a global increase in lipid synthesis. RARRES1-depleted cells rewire glucose metabolism by switching from aerobic glycolysis to glucose-dependent de novo lipogenesis (DNL). Treatment with fatty acid synthase (FASN) inhibitor, C75, reversed the effects of RARRES1 depletion. The increased DNL in RARRES1-depleted normal breast and prostate epithelial cells proved advantageous to the cells during starvation, as the increase in fatty acid availability lead to more oxidized fatty acids (FAO), which were used for mitochondrial respiration. Expression of RARRES1 in several common solid tumors is also contextually correlated with expression of fatty acid metabolism genes and fatty acid-regulated transcription factors. Pathway enrichment analysis led us to determine that RARRES1 is regulated by peroxisome proliferating activated receptor (PPAR) signaling. These findings open up a new avenue for metabolic reprogramming and identify RARRES1 as a potential target for cancers and other diseases with impaired fatty acid metabolism.
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Affiliation(s)
- Sara Maimouni
- Department of Biochemical, Molecular and Cellular Biology, Georgetown University, Washington, District of Columbia, United States of America
| | - Naiem Issa
- Georgetown-Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia, United States of America
| | - Selina Cheng
- Georgetown-Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia, United States of America
| | - Chokri Ouaari
- Georgetown-Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia, United States of America
- University of the District of Columbia, Washington, District of Columbia, United States of America
| | - Amrita Cheema
- Georgetown-Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia, United States of America
| | - Deepak Kumar
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, North Carolina, United States of America
| | - Stephen Byers
- Department of Biochemical, Molecular and Cellular Biology, Georgetown University, Washington, District of Columbia, United States of America
- Georgetown-Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia, United States of America
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Sweet ME, Cocciolo A, Slavov D, Jones KL, Sweet JR, Graw SL, Reece TB, Ambardekar AV, Bristow MR, Mestroni L, Taylor MRG. Transcriptome analysis of human heart failure reveals dysregulated cell adhesion in dilated cardiomyopathy and activated immune pathways in ischemic heart failure. BMC Genomics 2018; 19:812. [PMID: 30419824 PMCID: PMC6233272 DOI: 10.1186/s12864-018-5213-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/31/2018] [Indexed: 01/17/2023] Open
Abstract
Background Current heart failure (HF) treatment is based on targeting symptoms and left ventricle dysfunction severity, relying on a common HF pathway paradigm to justify common treatments for HF patients. This common strategy may belie an incomplete understanding of heterogeneous underlying mechanisms and could be a barrier to more precise treatments. We hypothesized we could use RNA-sequencing (RNA-seq) in human heart tissue to delineate HF etiology-specific gene expression signatures. Results RNA-seq from 64 human left ventricular samples: 37 dilated (DCM), 13 ischemic (ICM), and 14 non-failing (NF). Using a multi-analytic approach including covariate adjustment for age and sex, differentially expressed genes (DEGs) were identified characterizing HF and disease-specific expression. Pathway analysis investigated enrichment for biologically relevant pathways and functions. DCM vs NF and ICM vs NF had shared HF-DEGs that were enriched for the fetal gene program and mitochondrial dysfunction. DCM-specific DEGs were enriched for cell-cell and cell-matrix adhesion pathways. ICM-specific DEGs were enriched for cytoskeletal and immune pathway activation. Using the ICM and DCM DEG signatures from our data we were able to correctly classify the phenotypes of 24/31 ICM and 32/36 DCM samples from publicly available replication datasets. Conclusions Our results demonstrate the commonality of mitochondrial dysfunction in end-stage HF but more importantly reveal key etiology-specific signatures. Dysfunctional cell-cell and cell-matrix adhesion signatures typified DCM whereas signals related to immune and fibrotic responses were seen in ICM. These findings suggest that transcriptome signatures may distinguish end-stage heart failure, shedding light on underlying biological differences between ICM and DCM. Electronic supplementary material The online version of this article (10.1186/s12864-018-5213-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mary E Sweet
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA
| | - Andrea Cocciolo
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Dobromir Slavov
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado, Aurora, CO, USA
| | - Joseph R Sweet
- Department of Statistics, E. & J. Gallo, Modesto, CA, USA
| | - Sharon L Graw
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - T Brett Reece
- Department of Cardiothoracic Surgery, University of Colorado Hospital, Aurora, CO, USA
| | - Amrut V Ambardekar
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Michael R Bristow
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Luisa Mestroni
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA.,Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Matthew R G Taylor
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA. .,Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
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Tompkins BA, Rieger AC, Florea V, Banerjee MN, Natsumeda M, Nigh ED, Landin AM, Rodriguez GM, Hatzistergos KE, Schulman IH, Hare JM. Comparison of Mesenchymal Stem Cell Efficacy in Ischemic Versus Nonischemic Dilated Cardiomyopathy. J Am Heart Assoc 2018; 7:JAHA.117.008460. [PMID: 30005555 PMCID: PMC6064862 DOI: 10.1161/jaha.117.008460] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background Ischemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM) differ in histopathology and prognosis. Although transendocardial delivery of mesenchymal stem cells is safe and provides cardiovascular benefits in both, a comparison of mesenchymal stem cell efficacy in ICM versus DCM has not been done. Methods and Results We conducted a subanalysis of 3 single‐center, randomized, and blinded clinical trials: (1) TAC‐HFT (Transendocardial Autologous Mesenchymal Stem Cells and Mononuclear Bone Marrow Cells in Ischemic Heart Failure Trial); (2) POSEIDON (A Phase I/II, Randomized Pilot Study of the Comparative Safety and Efficacy of Transendocardial Injection of Autologous Mesenchymal Stem Cells Versus Allogeneic Mesenchymal Stem Cells in Patients With Chronic Ischemic Left Ventricular Dysfunction Secondary to Myocardial Infarction); and (3) POSEIDON‐DCM (Percutaneous Stem Cell Injection Delivery Effects on Neomyogenesis in Dilated Cardiomyopathy). Baseline and 1‐year cardiac structure and function and quality‐of‐life data were compared in a post hoc pooled analysis including ICM (n=46) and DCM (n=33) patients who received autologous or allogeneic mesenchymal stem cells. Ejection fraction improved in DCM by 7% (within‐group, P=0.002) compared to ICM (1.5%; within‐group, P=0.14; between‐group, P=0.003). Similarly, stroke volume increased in DCM by 10.59 mL (P=0.046) versus ICM (−0.2 mL; P=0.73; between‐group, P=0.02). End‐diastolic volume improved only in ICM (10.6 mL; P=0.04) and end‐systolic volume improved only in DCM (17.8 mL; P=0.049). The sphericity index decreased only in ICM (−0.04; P=0.0002). End‐diastolic mass increased in ICM (23.1 g; P<0.0001) versus DCM (−4.1 g; P=0.34; between‐group, P=0.007). The 6‐minute walk test improved in DCM (31.1 m; P=0.009) and ICM (36.3 m; P=0.006) with no between‐group difference (P=0.79). The New York Heart Association class improved in DCM (P=0.005) and ICM (P=0.02; between‐group P=0.20). The Minnesota Living with Heart Failure Questionnaire improved in DCM (−19.5; P=0.002) and ICM (−6.4; P=0.03; δ between‐group difference P=0.042) patients. Conclusions Mesenchymal stem cell therapy is beneficial in DCM and ICM patients, despite variable effects on cardiac phenotypic outcomes. Whereas cardiac function improved preferentially in DCM patients, ICM patients experienced reverse remodeling. Mesenchymal stem cell therapy enhanced quality of life and functional capacity in both etiologies. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifiers: TAC‐HFT: NCT00768066, POSEIDON: NCT01087996, POSEIDON‐DCM: NCT01392625.
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Affiliation(s)
- Bryon A Tompkins
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL.,Department of Surgery, University of Miami Miller School of Medicine, Miami, FL
| | - Angela C Rieger
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Victoria Florea
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Monisha N Banerjee
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL.,Department of Surgery, University of Miami Miller School of Medicine, Miami, FL
| | - Makoto Natsumeda
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Evan D Nigh
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Ana Marie Landin
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Gianna M Rodriguez
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL
| | | | - Ivonne Hernandez Schulman
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL.,Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, FL
| | - Joshua M Hare
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL .,Cardiovascular Division, University of Miami Miller School of Medicine, Miami, FL
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38
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Wang J, Wang F, Zhu J, Song M, An J, Li W. Transcriptome Profiling Reveals PHLDA1 as a Novel Molecular Marker for Ischemic Cardiomyopathy. J Mol Neurosci 2018; 65:102-109. [PMID: 29736818 PMCID: PMC5978804 DOI: 10.1007/s12031-018-1066-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/11/2018] [Indexed: 12/13/2022]
Abstract
Ischemic cardiomyopathy (ICM) represents a worldwide health issue owning to its high sudden death rate. Easy diagnosis and effective treatment of ICM are still lacking. Identification of novel molecular markers will help illustrate the pathophysiology of ICM and facilitate its diagnosis and targeted treatment. Transcription profiling could be an easy and efficient way for identifying new markers. However, the mega data in the available database may contain a large number of false-positive hits. To identify the true marker for ICM, we systematically compared available microarray datasets in the GEO database and identified 26 genes that are shared by all datasets. We further verified the expression pattern of these 26 genes in ICM rat model. Only 12 genes show significant differential expression in our animal model. Among them, we focused on PHLDA1, a well-documented pro-apoptotic factor. Expression of PHLDA1 was elevated in both ischemic cardiac cell lines and in rat model. Overexpression of PHLDA1 promotes apoptosis of cardiac muscle cell. Meanwhile, PHLDA1 not only inhibited AKT pathway, but also activated p53 pathway. We thus confirmed PHLDA1 as a true molecular marker for ICM.
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Affiliation(s)
- Jinhui Wang
- Clinical Laboratory, The First Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Feifei Wang
- Clinical Laboratory, The First Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Jingbin Zhu
- Orthopedics, The First Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Mei Song
- Clinical Laboratory, The First Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Jinghong An
- Clinical Laboratory, The First Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Weimin Li
- Cardiology, The First Hospital of Harbin, Harbin, Heilongjiang Province, China.
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39
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Li Y, Jiang Q, Ding Z, Liu G, Yu P, Jiang G, Yu Z, Yang C, Qian J, Jiang H, Zou Y. Identification of a Common Different Gene Expression Signature in Ischemic Cardiomyopathy. Genes (Basel) 2018; 9:genes9010056. [PMID: 29361784 PMCID: PMC5793207 DOI: 10.3390/genes9010056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/09/2018] [Accepted: 01/16/2018] [Indexed: 01/25/2023] Open
Abstract
The molecular mechanisms underlying the development of ischemic cardiomyopathy (ICM) remain poorly understood. Gene expression profiling is helpful to discover the molecular changes taking place in ICM. The aim of this study was to identify the genes that are significantly changed during the development of heart failure caused by ICM. The differentially expressed genes (DEGs) were identified from 162 control samples and 227 ICM patients. PANTHER was used to perform gene ontology (GO), and Reactome for pathway enrichment analysis. A protein–protein interaction network was established using STRING and Cytoscape. A further validation was performed by real-time polymerase chain reaction (RT-PCR). A total of 255 common DEGs was found. Gene ontology, pathway enrichment, and protein–protein interaction analysis showed that nucleic acid-binding proteins, enzymes, and transcription factors accounted for a great part of the DEGs, while immune system signaling and cytokine signaling displayed the most significant changes. Furthermore, seven hub genes and nine transcription factors were identified. Interestingly, the top five upregulated DEGs were located on chromosome Y, and four of the top five downregulated DEGs were involved in immune and inflammation signaling. Further, the top DEGs were validated by RT-PCR in human samples. Our study explored the possible molecular mechanisms of heart failure caused by ischemic heart disease.
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Affiliation(s)
- Yana Li
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Qiu Jiang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Zhiwen Ding
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Guijian Liu
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Peng Yu
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Guoliang Jiang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Ziqing Yu
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Chunjie Yang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Juying Qian
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Hong Jiang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
- Shanghai Institute of clinical bioinformatics, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Yunzeng Zou
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
- Institutes of Biomedical Sciences, Fudan University, 130 Dong'an Road, Shanghai 200032, China.
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40
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Nair NU, Das A, Amit U, Robinson W, Park SG, Basu M, Lugo A, Leor J, Ruppin E, Hannenhalli S. Putative functional genes in idiopathic dilated cardiomyopathy. Sci Rep 2018; 8:66. [PMID: 29311597 PMCID: PMC5758757 DOI: 10.1038/s41598-017-18524-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/12/2017] [Indexed: 12/16/2022] Open
Abstract
Idiopathic dilated cardiomyopathy (DCM) is a complex disorder with a genetic and an environmental component involving multiple genes, many of which are yet to be discovered. We integrate genetic, epigenetic, transcriptomic, phenotypic, and evolutionary features into a method - Hridaya, to infer putative functional genes underlying DCM in a genome-wide fashion, using 213 human heart genomes and transcriptomes. Many genes identified by Hridaya are experimentally shown to cause cardiac complications. We validate the top predicted genes, via five different genome-wide analyses: First, the predicted genes are associated with cardiovascular functions. Second, their knockdowns in mice induce cardiac abnormalities. Third, their inhibition by drugs cause cardiac side effects in human. Fourth, they tend to have differential exon usage between DCM and normal samples. Fifth, analyzing 213 individual genotypes, we show that regulatory polymorphisms of the predicted genes are associated with elevated risk of cardiomyopathy. The stratification of DCM patients based on cardiac expression of the functional genes reveals two subgroups differing in key cardiac phenotypes. Integrating predicted functional genes with cardiomyocyte drug treatment experiments reveals novel potential drug targets. We provide a list of investigational drugs that target the newly identified functional genes that may lead to cardiac side effects.
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Affiliation(s)
- Nishanth Ulhas Nair
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA.
| | - Avinash Das
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Uri Amit
- The Neufeld Cardiac Research Institute, Tel Aviv University, Tel Aviv-Yafo, Israel
- Tamman Cardiovascular Research Institute, Sheba Medical Center, Ramat Gan, Israel
- The Dr. Pinchas Borenstein Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Radiation Oncology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Welles Robinson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Seung Gu Park
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Mahashweta Basu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Alex Lugo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Jonathan Leor
- The Neufeld Cardiac Research Institute, Tel Aviv University, Tel Aviv-Yafo, Israel
- Tamman Cardiovascular Research Institute, Sheba Medical Center, Ramat Gan, Israel
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, 20742, USA.
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41
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Dhingra R, Vasan RS. Biomarkers in cardiovascular disease: Statistical assessment and section on key novel heart failure biomarkers. Trends Cardiovasc Med 2017; 27:123-133. [PMID: 27576060 PMCID: PMC5253084 DOI: 10.1016/j.tcm.2016.07.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 07/23/2016] [Accepted: 07/23/2016] [Indexed: 12/11/2022]
Abstract
Cardiovascular disease (CVD) is a leading cause of death worldwide and continues to increase in prevalence compared to previous decades, in part because of the aging of the world population. Atherosclerotic CVD starts at a very young age and progresses over time allowing sufficient time for screening and early detection of the condition. Advances in biomarker research and developments related to CVD over the past 30 years have led to more sensitive screening methods, a greater emphasis on its early detection and diagnosis, and improved treatments resulting in more favorable clinical outcomes in the community. However, the use of biomarkers for different purposes in CVD remains an important area of research that has been explored by scientists over the years and many new developments are still underway. Therefore, a detailed description of all CVD biomarkers that are currently been used or investigated for future use in the field of cardiovascular medicine is out of scope for any review article. In the present review, we do not intend to replicate the information from previous exhaustive review on biomarkers, but highlight key statistical and clinical issues with an emphasis on methods to evaluate the incremental yield of biomarkers, including their clinical utility, a prerequisite before any putative novel biomarker is utilized in clinical practice. In addition, we will summarize information regarding recent novel heart failure biomarkers in current practice, which are undergoing scrutiny before they can be available for clinical use, and their impact on clinical outcomes.
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Affiliation(s)
- Ravi Dhingra
- Division of Cardiovascular Medicine, University of Wisconsin-Madison, 600 Highland Avenue, E5/582C, MC 5710, Madison, WI 53792.
| | - Ramachandran S Vasan
- Division of Cardiovascular Medicine, University of Wisconsin-Madison, 600 Highland Avenue, E5/582C, MC 5710, Madison, WI 53792
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Xie X, Wu SP, Tsai MJ, Tsai S. The Role of COUP-TFII in Striated Muscle Development and Disease. Curr Top Dev Biol 2017; 125:375-403. [PMID: 28527579 DOI: 10.1016/bs.ctdb.2016.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Skeletal and cardiac muscles are the only striated muscles in the body. Although sharing many structural and functional similarities, skeletal and cardiac muscles have intrinsic differences in terms of physiology and regenerative potential. While skeletal muscle possesses a robust regenerative response, the mammalian heart has limited repair capacity after birth. In this review, we provide an updated view regarding chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII) function in vertebrate myogenesis, with particular emphasis on the skeletal and cardiac muscles. We also highlight the new insights of COUP-TFII hyperactivity underlying striated muscle dysfunction. Lastly, we discuss the challenges and strategies in translating COUP-TFII action for clinical intervention.
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Affiliation(s)
- Xin Xie
- Baylor College of Medicine, Houston, TX, United States
| | - San-Pin Wu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC, United States
| | - Ming-Jer Tsai
- Baylor College of Medicine, Houston, TX, United States; Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States.
| | - Sophia Tsai
- Baylor College of Medicine, Houston, TX, United States; Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States.
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43
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Necela BM, Axenfeld BC, Serie DJ, Kachergus JM, Perez EA, Thompson EA, Norton N. The antineoplastic drug, trastuzumab, dysregulates metabolism in iPSC-derived cardiomyocytes. Clin Transl Med 2017; 6:5. [PMID: 28101782 PMCID: PMC5243239 DOI: 10.1186/s40169-016-0133-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/21/2016] [Indexed: 01/14/2023] Open
Abstract
Background The targeted ERBB2 therapy, trastuzumab, has had a tremendous impact on management of patients with HER2+ breast cancer, leading to development and increased use of further HER2 targeted therapies. The major clinical side effect is cardiotoxicity but the mechanism is largely unknown. On the basis that gene expression is known to be altered in multiple models of heart failure, we examined differential gene expression of iPSC-derived cardiomyocytes treated at day 11 with the ERBB2 targeted monoclonal antibody, trastuzumab for 48 h and the small molecule tyrosine kinase inhibitor of EGFR and ERBB2. Results Transcriptome sequencing was performed on four replicates from each group (48 h untreated, 48 h trastuzumab and 48 h lapatinib) and differential gene expression analyses were performed on each treatment group relative to untreated cardiomyocytes. 517 and 1358 genes were differentially expressed, p < 0.05, respectively in cardiomyocytes treated with trastuzumab and lapatinib. Gene ontology analyses revealed in cardiomyocytes treated with trastuzumab, significant down-regulation of genes involved in small molecule metabolism (p = 3.22 × 10−9) and cholesterol (p = 0.01) and sterol (p = 0.03) processing. We next measured glucose uptake and lactate production in iPSC-derived cardiomyocytes 13 days post-plating, treated with trastuzumab up to 96 h. We observed significantly decreased glucose uptake from the media of iPSC-derived cardiomyocytes treated with trastuzumab as early as 24 h (p = 0.001) and consistently up to 96 h (p = 0.03). Conclusions Our study suggests dysregulation of cardiac gene expression and metabolism as key elements of ERBB2 signaling that could potentially be early biomarkers of cardiotoxicity. Electronic supplementary material The online version of this article (doi:10.1186/s40169-016-0133-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brian M Necela
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Daniel J Serie
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | | - Edith A Perez
- Department of Hematology Oncology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Nadine Norton
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA.
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44
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Xu YZ, Chen CF, Chen B, Gao XF, Hua W, Cha YM, Dzeja PP. The Modulating Effects of Cardiac Resynchronization Therapy on Myocardial Metabolism in Heart Failure. PACING AND CLINICAL ELECTROPHYSIOLOGY: PACE 2016; 39:1404-1409. [PMID: 27807872 DOI: 10.1111/pace.12971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
Heart failure (HF) is associated with changes in cardiac substrate utilization and energy metabolism, including a decline in high-energy phosphate content, mitochondrial dysfunction, and phosphotransfer enzyme deficiency. A shift toward glucose metabolism was noted in the end stage of HF in animals, although HF in humans may not be associated with a shift toward predominant glucose utilization. Deficiencies of micronutrients are well-established causes of cardiomyopathy. Correction of these deficits can improve heart function. The genes governing the energy metabolism were predominantly underexpressed in nonischemic cardiomyopathy and hypertrophic cardiomyopathy but were overexpressed in ischemic cardiomyopathy. Cardiac resynchronization therapy (CRT) has been proven to increase cardiac efficiency without increasing myocardial oxygen consumption. Altered myocardial metabolism is normalized by CRT to improve ventricular function.
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Affiliation(s)
- Yi-Zhou Xu
- Department of Cardiology, Hangzhou First People's Hospital and Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - Chao-Feng Chen
- Department of Cardiology, Hangzhou First People's Hospital and Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - Bin Chen
- Department of Cardiology, Hangzhou First People's Hospital and Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - Xiao-Fei Gao
- Department of Cardiology, Hangzhou First People's Hospital and Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - Wei Hua
- The Cardiac Arrhythmia Center, Fu Wai Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong-Mei Cha
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota
| | - Petras P Dzeja
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota
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45
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Abstract
The health of the cardiovascular and pulmonary systems is inextricably linked to the renin-angiotensin system (RAS). Physiologically speaking, a balance between the vasodeleterious (Angiotensin-converting enzyme [ACE]/Angiotensin II [Ang II]/Ang II type 1 receptor [AT1R]) and vasoprotective (Angiotensin-converting enzyme 2 [ACE2]/Angiotensin-(1-7) [Ang-(1-7)]/Mas receptor [MasR]) components of the RAS is critical for cardiopulmonary homeostasis. Upregulation of the ACE/Ang II/AT1R axis shifts the system toward vasoconstriction, proliferation, hypertrophy, inflammation, and fibrosis, all factors that contribute to the development and progression of cardiopulmonary diseases. Conversely, stimulation of the vasoprotective ACE2/Ang-(1-7)/MasR axis produces a counter-regulatory response that promotes cardiovascular health. Current research is investigating novel strategies to augment actions of the vasoprotective RAS components, particularly ACE2, in order to treat various pathologies. Although multiple approaches to increase the activity of ACE2 have displayed beneficial effects against experimental disease models, the mechanisms behind its protective actions remain incompletely understood. Recent work demonstrating a non-catalytic role for ACE2 in amino acid transport in the gut has led us to speculate that the therapeutic effects of ACE2 can be mediated, in part, by its actions on the gastrointestinal tract and/or gut microbiome. This is consistent with emerging data which suggest that dysbiosis of the gut and lung microbiomes is associated with cardiopulmonary disease. This review highlights new developments in the protective actions of ACE2 against cardiopulmonary disorders, discusses innovative approaches to targeting ACE2 for therapy, and explores an evolving role for gut and lung microbiota in cardiopulmonary health.
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46
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Sweeney TE, Haynes WA, Vallania F, Ioannidis JP, Khatri P. Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res 2016; 45:e1. [PMID: 27634930 PMCID: PMC5224496 DOI: 10.1093/nar/gkw797] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 12/28/2022] Open
Abstract
Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Winston A Haynes
- Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Francesco Vallania
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John P Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA 94305, USA.,Meta-research Innovation Center at Stanford (METRICS), Stanford, CA 94305, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA .,Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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47
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Greco S, Zaccagnini G, Perfetti A, Fuschi P, Valaperta R, Voellenkle C, Castelvecchio S, Gaetano C, Finato N, Beltrami AP, Menicanti L, Martelli F. Long noncoding RNA dysregulation in ischemic heart failure. J Transl Med 2016; 14:183. [PMID: 27317124 PMCID: PMC4912721 DOI: 10.1186/s12967-016-0926-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/30/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are non-protein coding transcripts regulating a variety of physiological and pathological functions. However, their implication in heart failure is still largely unknown. The aim of this study is to identify and characterize lncRNAs deregulated in patients affected by ischemic heart failure. METHODS LncRNAs were profiled and validated in left ventricle biopsies of 18 patients affected by non end-stage dilated ischemic cardiomyopathy and 17 matched controls. Further validations were performed in left ventricle samples derived from explanted hearts of end-stage heart failure patients and in a mouse model of cardiac hypertrophy, obtained by transverse aortic constriction. Peripheral blood mononuclear cells of heart failure patients were also analyzed. LncRNA distribution in the heart was assessed by in situ hybridization. Function of the deregulated lncRNA was explored analyzing the expression of the neighbor mRNAs and by gene ontology analysis of the correlating coding transcripts. RESULTS Fourteen lncRNAs were significantly modulated in non end-stage heart failure patients, identifying a heart failure lncRNA signature. Nine of these lncRNAs (CDKN2B-AS1/ANRIL, EGOT, H19, HOTAIR, LOC285194/TUSC7, RMRP, RNY5, SOX2-OT and SRA1) were also confirmed in end-stage failing hearts. Intriguingly, among the conserved lncRNAs, h19, rmrp and hotair were also induced in a mouse model of heart hypertrophy. CDKN2B-AS1/ANRIL, HOTAIR and LOC285194/TUSC7 showed similar modulation in peripheral blood mononuclear cells and heart tissue, suggesting a potential role as disease biomarkers. Interestingly, RMRP displayed a ubiquitous nuclear distribution, while H19 RNA was more abundant in blood vessels and was both cytoplasmic and nuclear. Gene ontology analysis of the mRNAs displaying a significant correlation in expression with heart failure lncRNAs identified numerous pathways and functions involved in heart failure progression. CONCLUSIONS These data strongly suggest lncRNA implication in the molecular mechanisms underpinning HF.
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Affiliation(s)
- Simona Greco
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
| | - Germana Zaccagnini
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
| | - Alessandra Perfetti
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
| | - Paola Fuschi
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
| | - Rea Valaperta
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
| | - Christine Voellenkle
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
| | | | | | - Nicoletta Finato
- />Istituto di Anatomia Patologica Universitaria, Azienda Ospedaliero Universitaria “S. Maria della Misericordia”, Udine, Italy
| | - Antonio Paolo Beltrami
- />Istituto di Anatomia Patologica Universitaria, Azienda Ospedaliero Universitaria “S. Maria della Misericordia”, Udine, Italy
| | - Lorenzo Menicanti
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
| | - Fabio Martelli
- />IRCCS Policlinico San Donato, Via Morandi, 30, 20097 San Donato Milanese, Milan, Italy
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48
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Mercurio V, Pirozzi F, Lazzarini E, Marone G, Rizzo P, Agnetti G, Tocchetti CG, Ghigo A, Ameri P. Models of Heart Failure Based on the Cardiotoxicity of Anticancer Drugs. J Card Fail 2016; 22:449-58. [PMID: 27103426 DOI: 10.1016/j.cardfail.2016.04.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/12/2016] [Accepted: 04/13/2016] [Indexed: 12/13/2022]
Abstract
Heart failure (HF) is a complication of oncological treatments that may have dramatic clinical impact. It may acutely worsen a patient's condition or it may present with delayed onset, even years after treatment, when cancer has been cured or is in stable remission. Several studies have addressed the mechanisms of cancer therapy-related HF and some have led to the definition of disease models that hold valid for other and more common types of HF. Here, we review these models of HF based on the cardiotoxicity of antineoplastic drugs and classify them in cardiomyocyte-intrinsic, paracrine, or potentially secondary to effects on cardiac progenitor cells. The first group includes HF resulting from the combination of oxidative stress, mitochondrial dysfunction, and activation of the DNA damage response, which is typically caused by anthracyclines, and HF resulting from deranged myocardial energetics, such as that triggered by anthracyclines and sunitinib. Blockade of the neuregulin-1/ErbB4/ErbB2, vascular endothelial growth factor/vascular endothelial growth factor receptor and platelet-derived growth factor /platelet-derived growth factor receptor pathways by trastuzumab, sorafenib and sunitinib is proposed as paradigm of cancer therapy-related HF associated with alterations of myocardial paracrine pathways. Finally, anthracyclines and trastuzumab are also presented as examples of antitumor agents that induce HF by affecting the cardiac progenitor cell population.
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Affiliation(s)
- Valentina Mercurio
- Division of Internal Medicine, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Flora Pirozzi
- Division of Internal Medicine, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Edoardo Lazzarini
- Laboratory of Cardiovascular Biology, Department of Internal Medicine, University of Genova, Genova, Italy
| | - Giancarlo Marone
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Paola Rizzo
- Department of Morphology, Surgery and Experimental Medicine and Laboratory for Technologies of Advanced Therapies, University of Ferrara, Ferrara, Italy
| | - Giulio Agnetti
- Johns Hopkins University, Cardiology, Baltimore, Maryland; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Carlo G Tocchetti
- Division of Internal Medicine, Department of Translational Medical Sciences, Federico II University, Naples, Italy.
| | - Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Pietro Ameri
- Laboratory of Cardiovascular Biology, Department of Internal Medicine, University of Genova, Genova, Italy
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49
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Kazmi N, Gaunt TR. Diagnosis of Coronary Heart Diseases Using Gene Expression Profiling; Stable Coronary Artery Disease, Cardiac Ischemia with and without Myocardial Necrosis. PLoS One 2016; 11:e0149475. [PMID: 26930047 PMCID: PMC4773227 DOI: 10.1371/journal.pone.0149475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/31/2016] [Indexed: 01/08/2023] Open
Abstract
Cardiovascular disease (including coronary artery disease and myocardial infarction) is one of the leading causes of death in Europe, and is influenced by both environmental and genetic factors. With the recent advances in genomic tools and technologies there is potential to predict and diagnose heart disease using molecular data from analysis of blood cells. We analyzed gene expression data from blood samples taken from normal people (n = 21), non-significant coronary artery disease (n = 93), patients with unstable angina (n = 16), stable coronary artery disease (n = 14) and myocardial infarction (MI; n = 207). We used a feature selection approach to identify a set of gene expression variables which successfully differentiate different cardiovascular diseases. The initial features were discovered by fitting a linear model for each probe set across all arrays of normal individuals and patients with myocardial infarction. Three different feature optimisation algorithms were devised which identified two discriminating sets of genes, one using MI and normal controls (total genes = 6) and another one using MI and unstable angina patients (total genes = 7). In all our classification approaches we used a non-parametric k-nearest neighbour (KNN) classification method (k = 3). The results proved the diagnostic robustness of the final feature sets in discriminating patients with myocardial infarction from healthy controls. Interestingly it also showed efficacy in discriminating myocardial infarction patients from patients with clinical symptoms of cardiac ischemia but no myocardial necrosis or stable coronary artery disease, despite the influence of batch effects and different microarray gene chips and platforms.
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Affiliation(s)
- Nabila Kazmi
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, BS8 2BN, Bristol, United Kingdom
- * E-mail:
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, BS8 2BN, Bristol, United Kingdom
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50
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Kim EH, Galchev VI, Kim JY, Misek SA, Stevenson TK, Campbell MD, Pagani FD, Day SM, Johnson TC, Washburn JG, Vikstrom KL, Michele DE, Misek DE, Westfall MV. Differential protein expression and basal lamina remodeling in human heart failure. Proteomics Clin Appl 2016; 10:585-96. [PMID: 26756417 DOI: 10.1002/prca.201500099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/27/2015] [Accepted: 01/05/2016] [Indexed: 12/17/2022]
Abstract
PURPOSE A goal of this study was to identify and investigate previously unrecognized components of the remodeling process in the progression to heart failure by comparing protein expression in ischemic failing (F) and nonfailing (NF) human hearts. EXPERIMENTAL DESIGN Protein expression differences were investigated using multidimensional protein identification and validated by Western analysis. This approach detected basal lamina (BL) remodeling, and further studies analyzed samples for evidence of structural BL remodeling. A rat model of pressure overload (PO) was studied to determine whether nonischemic stressors also produce BL remodeling and impact cellular adhesion. RESULTS Differential protein expression of collagen IV, laminin α2, and nidogen-1 indicated BL remodeling develops in F versus NF hearts Periodic disruption of cardiac myocyte BL accompanied this process in F, but not NF heart. The rat PO myocardium also developed BL remodeling and compromised myocyte adhesion compared to sham controls. CONCLUSIONS AND CLINICAL RELEVANCE Differential protein expression and evidence of structural and functional BL alterations develop during heart failure. The compromised adhesion associated with this remodeling indicates a high potential for dysfunctional cellular integrity and tethering in failing myocytes. Therapeutically targeting BL remodeling could slow or prevent the progression of heart disease.
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Affiliation(s)
- Evelyn H Kim
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Sean A Misek
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Tamara K Stevenson
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Matthew D Campbell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Francis D Pagani
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Sharlene M Day
- Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - T Craig Johnson
- DNA Sequencing and Microarray Facility, University of Michigan, Ann Arbor, MI, USA
| | - Joseph G Washburn
- DNA Sequencing and Microarray Facility, University of Michigan, Ann Arbor, MI, USA
| | - Karen L Vikstrom
- Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Michele
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.,Cardiovascular Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - David E Misek
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Margaret V Westfall
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
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