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Liu J, Sun Z, Hong Y, Zhao Y, Wang S, Liu B, Zheng Y. Screening of immune-related biological markers for aneurysmal subarachnoid hemorrhage based on machine learning approaches. Biochem Biophys Rep 2023; 36:101564. [PMID: 38024864 PMCID: PMC10656213 DOI: 10.1016/j.bbrep.2023.101564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Background Aneurysmal subarachnoid hemorrhage (aSAH) is a common hemorrhagic condition frequently encountered in the emergency department, which is characterized by high mortality and disability rates. However, the precise molecular mechanisms underlying the rupture of an aneurysm are still not fully understood. The primary objective of this study is to elucidate the fundamental molecular mechanisms underlying aSAH and provide novel therapeutic targets for the treatment of aSAH. Methods The gene expression matrix of aSAH was downloaded from the Gene Expression Omnibus (GEO) database. In this study, we employed weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis (DEGs) screening to identify crucial modules and genes associated with aSAH. Furthermore, the evaluation of immune cell infiltration was conducted through the utilization of the single-sample gene set enrichment analysis (ssGSEA) technique and the CIBERSORT algorithm. The study utilized Gene Set Variation Analysis (GSVA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) to investigate and comprehend the fundamental biological pathways and mechanisms. Results Using WGCNA, six gene co-expression modules were constructed. Among the identified modules, the yellow module, which encompasses 184 genes, demonstrated the most significant correlation with aSAH. Consequently, it was determined to be the central module responsible for governing the pathogenesis of aSAH. Additionally, the application of WGCNA, LASSO regression, and multiple factor logistic regression analysis revealed ARHGAP26 and SLMAP as the key genes associated with aSAH. Furthermore, the diagnostic efficacy of these pivotal genes in aSAH was confirmed through the use of receiver operating characteristic (ROC) curve analysis, validating their discriminative potential. Moreover, the utilization of GO and KEGG pathway analysis revealed a significant enrichment of inflammation-related signaling in aSAH. Conclusion The genes ARHGAP26 and SLMAP were identified as significant predictors of aSAH. Accordingly, these genes demonstrate significant potential to function as novel biological markers and therapeutic targets for aSAH.
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Affiliation(s)
- Jing Liu
- Department of Emergency,Zhujiang Hospital,Southern Medical University, China
| | | | - Yiyu Hong
- Department of Emergency,Zhujiang Hospital,Southern Medical University, China
| | - Yibo Zhao
- Department of Emergency,Zhujiang Hospital,Southern Medical University, China
| | - Shuo Wang
- Department of Emergency,Zhujiang Hospital,Southern Medical University, China
| | - Bin Liu
- Department of Emergency,Zhujiang Hospital,Southern Medical University, China
| | - Yantao Zheng
- Department of Emergency,Zhujiang Hospital,Southern Medical University, China
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Singh P, Zhou L, Shah DA, Cejas RB, Crossman DK, Jouni M, Magdy T, Wang X, Sharafeldin N, Hageman L, McKenna DE, Horvath S, Armenian SH, Balis FM, Hawkins DS, Keller FG, Hudson MM, Neglia JP, Ritchey AK, Ginsberg JP, Landier W, Burridge PW, Bhatia S. Identification of novel hypermethylated or hypomethylated CpG sites and genes associated with anthracycline-induced cardiomyopathy. Sci Rep 2023; 13:12683. [PMID: 37542143 PMCID: PMC10403495 DOI: 10.1038/s41598-023-39357-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/24/2023] [Indexed: 08/06/2023] Open
Abstract
Anthracycline-induced cardiomyopathy is a leading cause of late morbidity in childhood cancer survivors. Aberrant DNA methylation plays a role in de novo cardiovascular disease. Epigenetic processes could play a role in anthracycline-induced cardiomyopathy but remain unstudied. We sought to examine if genome-wide differential methylation at 'CpG' sites in peripheral blood DNA is associated with anthracycline-induced cardiomyopathy. This report used participants from a matched case-control study; 52 non-Hispanic White, anthracycline-exposed childhood cancer survivors with cardiomyopathy were matched 1:1 with 52 survivors with no cardiomyopathy. Paired ChAMP (Chip Analysis Methylation Pipeline) with integrated reference-based deconvolution of adult peripheral blood DNA methylation was used to analyze data from Illumina HumanMethylation EPIC BeadChip arrays. An epigenome-wide association study (EWAS) was performed, and the model was adjusted for GrimAge, sex, interaction terms of age at enrollment, chest radiation, age at diagnosis squared, and cardiovascular risk factors (CVRFs: diabetes, hypertension, dyslipidemia). Prioritized genes were functionally validated by gene knockout in human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) using CRISPR/Cas9 technology. DNA-methylation EPIC array analyses identified 32 differentially methylated probes (DMP: 15 hyper-methylated and 17 hypo-methylated probes) that overlap with 23 genes and 9 intergenic regions. Three hundred and fifty-four differential methylated regions (DMRs) were also identified. Several of these genes are associated with cardiac dysfunction. Knockout of genes EXO6CB, FCHSD2, NIPAL2, and SYNPO2 in hiPSC-CMs increased sensitivity to doxorubicin. In addition, EWAS analysis identified hypo-methylation of probe 'cg15939386' in gene RORA to be significantly associated with anthracycline-induced cardiomyopathy. In this genome-wide DNA methylation profile study, we observed significant differences in DNA methylation at the CpG level between anthracycline-exposed childhood cancer survivors with and without cardiomyopathy, implicating differential DNA methylation of certain genes could play a role in pathogenesis of anthracycline-induced cardiomyopathy.
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Affiliation(s)
- Purnima Singh
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Liting Zhou
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Disheet A Shah
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Romina B Cejas
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mariam Jouni
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Tarek Magdy
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
- Department of Pathology and Translational Pathobiology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| | - Xuexia Wang
- Department of Biostatistics, Florida International University, Miami, FL, USA
| | - Noha Sharafeldin
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lindsey Hageman
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donald E McKenna
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Saro H Armenian
- Department of Population Sciences, City of Hope, Duarte, CA, USA
| | - Frank M Balis
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Frank G Keller
- Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | | | | | - A Kim Ritchey
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | - Wendy Landier
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA.
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Fang P, Ye Z, Li R, She D, Zong G, Zhang L, Xue Y, Zhang K. Glucagon-Like Peptide-1 Receptor Agonist Protects Against Diabetic Cardiomyopathy by Modulating microRNA-29b-3p/SLMAP. Drug Des Devel Ther 2023; 17:791-806. [PMID: 36936522 PMCID: PMC10019346 DOI: 10.2147/dddt.s400249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
Purpose Our aims were to investigate the pathogenesis of diabetic cardiomyopathy (DCM) and to explore the protective effect of glucagon-like peptide-1 receptor agonist (GLP-1RA) on DCM. Methods After 12 weeks of treatment with exenatide-loaded microspheres, a long-acting GLP-1RA, in DCM mice, cardiac structure and function were evaluated by plasma B-type natriuretic peptide (BNP), echocardiography, H&E, oil red and Sirius staining. The expression of glucagon-like peptide-1 receptor in mouse heart tissue was determined by immunofluorescence staining. The label-free proteomic analysis of cardiac proteins was conducted among control, DCM and DM+GLP-1RA groups. Then, quantitative real-time PCR, Western blotting and dual-luciferase reporter assay were performed to verify the regulation of target protein by the upstream microRNA (miRNA). Results GLP-1RA treatment obviously improved serum BNP, myocardial fibrosis, lipid deposition of the myocardium and echocardiography parameters in DCM mice. Sarcolemmal membrane-associated protein (SLMAP) was one of 61 differentially expressed cardiac proteins found in three groups by proteomic analysis. Up-regulation of microRNA-29b-3p (miR-29b-3p) and down-regulation of SLMAP were found in the ventricular myocardium of GLP-1RA-treated DCM mice. SLMAP was a target of miR-29b-3p, while GLP-1RA regulated SLMAP expression through miR-29b-3p. Furthermore, inhibition of glucagon-like peptide-1 receptor (GLP-1R) in cardiomyocytes reversed the effects of GLP-1RA on miR-29b/SLMAP. Conclusion SLMAP may play roles in the pathogenesis of DCM and may be a target of GLP-1RA in protecting against DCM. After binding to myocardial GLP-1R, GLP-1RA can regulate the expression of myocardial SLMAP through miR-29b-3p.
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Affiliation(s)
- Ping Fang
- Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Zhengqin Ye
- Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Ran Li
- Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Dunmin She
- Department of Endocrinology, Northern Jiangsu People’s Hospital Affiliated to Yangzhou University, Yangzhou, Jiangsu, 225001, People’s Republic of China
| | - Guannan Zong
- Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Liya Zhang
- Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People’s Republic of China
| | - Ying Xue
- Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People’s Republic of China
- Correspondence: Ying Xue; Keqin Zhang, Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, No. 389, Xincun Road, Shanghai, 200065, People’s Republic of China, Tel +86-21-66111061, Email ;
| | - Keqin Zhang
- Department of Endocrinology and Metabolism, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People’s Republic of China
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Sallam M, Mysara M, Benotmane MA, Tamarat R, Santos SCR, Crijns APG, Spoor D, Van Nieuwerburgh F, Deforce D, Baatout S, Guns PJ, Aerts A, Ramadan R. DNA Methylation Alterations in Fractionally Irradiated Rats and Breast Cancer Patients Receiving Radiotherapy. Int J Mol Sci 2022; 23:16214. [PMID: 36555856 PMCID: PMC9783664 DOI: 10.3390/ijms232416214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Radiation-Induced CardioVascular Disease (RICVD) is an important concern in thoracic radiotherapy with complex underlying pathophysiology. Recently, we proposed DNA methylation as a possible mechanism contributing to RICVD. The current study investigates DNA methylation in heart-irradiated rats and radiotherapy-treated breast cancer (BC) patients. Rats received fractionated whole heart X-irradiation (0, 0.92, 6.9 and 27.6 Gy total doses) and blood was collected after 1.5, 3, 7 and 12 months. Global and gene-specific methylation of the samples were evaluated; and gene expression of selected differentially methylated regions (DMRs) was validated in rat and BC patient blood. In rats receiving an absorbed dose of 27.6 Gy, DNA methylation alterations were detected up to 7 months with differential expression of cardiac-relevant DMRs. Of those, SLMAP showed increased expression at 1.5 months, which correlated with hypomethylation. Furthermore, E2F6 inversely correlated with a decreased global longitudinal strain. In BC patients, E2F6 and SLMAP exhibited differential expression directly and 6 months after radiotherapy, respectively. This study describes a systemic radiation fingerprint at the DNA methylation level, elucidating a possible association of DNA methylation to RICVD pathophysiology, to be validated in future mechanistic studies.
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Affiliation(s)
- Magy Sallam
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium; (M.S.); (M.M.); (M.A.B.); (S.B.); (A.A.)
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Mohamed Mysara
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium; (M.S.); (M.M.); (M.A.B.); (S.B.); (A.A.)
| | - Mohammed Abderrafi Benotmane
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium; (M.S.); (M.M.); (M.A.B.); (S.B.); (A.A.)
| | - Radia Tamarat
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PRP-HOM, SRBE, LR2I, 92260 Fontenay-aux-Roses, France;
| | - Susana Constantino Rosa Santos
- Centro Cardiovascular da Universidade de Lisboa (CCUL@RISE), Lisbon School of Medicine of the Universidade de Lisboa, 1649-028 Lisbon, Portugal;
| | - Anne P. G. Crijns
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (A.P.G.C.); (D.S.)
| | - Daan Spoor
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (A.P.G.C.); (D.S.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (F.V.N.); (D.D.)
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (F.V.N.); (D.D.)
| | - Sarah Baatout
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium; (M.S.); (M.M.); (M.A.B.); (S.B.); (A.A.)
- Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Pieter-Jan Guns
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium;
| | - An Aerts
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium; (M.S.); (M.M.); (M.A.B.); (S.B.); (A.A.)
| | - Raghda Ramadan
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium; (M.S.); (M.M.); (M.A.B.); (S.B.); (A.A.)
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Nader M. The SLMAP/Striatin complex: An emerging regulator of normal and abnormal cardiac excitation-contraction coupling. Eur J Pharmacol 2019; 858:172491. [PMID: 31233748 DOI: 10.1016/j.ejphar.2019.172491] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/01/2022]
Abstract
The excitation-contraction (E-C) module involves a harmonized correspondence between the sarcolemma and the sarcoplasmic reticulum. This is provided by membrane proteins, which primarily shape the caveolae, the T-tubule/Sarcoplasmic reticulum (TT/SR) junction, and the intercalated discs (ICDs). Distortion of either one of these structures impairs myocardial contraction, and subsequently translates into cardiac failure. Thus, detailed studies on the molecular cues of the E-C module are becoming increasingly necessary to pharmacologically eradicate cardiac failure Herein we reviewed the organization of caveolae, TT/SR junctions, and the ICDs in the heart, with special attention to the Sarcolemma Membrane Associated Protein (SLMAP) and striatin (STRN) in cardiac membranes biology and cardiomyocyte contraction. We emphasized on their in vivo and in vitro signaling in cardiac function/dysfunction. SLMAP is a cardiac membrane protein that plays an important role in E-C coupling and the adrenergic response of the heart. Similarly, STRN is a dynamic protein that is also involved in cardiac E-C coupling and ICD-related cardiomyopathies. Both SLMAP and STRN are linked to cardiac conditions, including heart failure, and their role in cardiomyocyte function was elucidated in our laboratory. They interact together in a protein complex that holds therapeutic potentials for cardiac dysfunction. This review is the first of its kind to conceptualize the role of the SLMAP/STRN complex in cardiac function and failure. It provides in depth information on the signaling of these two proteins and projects their interaction as a novel therapeutic target for cardiac failure.
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Affiliation(s)
- Moni Nader
- Department of Physiological Sciences, College of Medicine, Alfaisal University, Riyadh, 11533, P.O. Box 50927, Saudi Arabia; Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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