Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy
IntroductionHeart failure (HF) is a complex clinical syndrome leading to high morbidity. In this study, we aimed to identify the gene expression and protein signature of HF main causes, namely dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM).MethodsOmics data were accessed through GEO...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-02-01
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| Series: | Frontiers in Cardiovascular Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcvm.2023.1115623/full |
| _version_ | 1828034680160518144 |
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| author | Konstantina Portokallidou Konstantina Portokallidou Nikolas Dovrolis Nikolas Dovrolis Georgia Ragia Georgia Ragia Natalia Atzemian Natalia Atzemian George Kolios George Kolios Vangelis G. Manolopoulos Vangelis G. Manolopoulos Vangelis G. Manolopoulos |
| author_facet | Konstantina Portokallidou Konstantina Portokallidou Nikolas Dovrolis Nikolas Dovrolis Georgia Ragia Georgia Ragia Natalia Atzemian Natalia Atzemian George Kolios George Kolios Vangelis G. Manolopoulos Vangelis G. Manolopoulos Vangelis G. Manolopoulos |
| author_sort | Konstantina Portokallidou |
| collection | DOAJ |
| description | IntroductionHeart failure (HF) is a complex clinical syndrome leading to high morbidity. In this study, we aimed to identify the gene expression and protein signature of HF main causes, namely dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM).MethodsOmics data were accessed through GEO repository for transcriptomic and PRIDE repository for proteomic datasets. Sets of differentially expressed genes and proteins comprising DCM (DiSig) and ICM (IsSig) signatures were analyzed by a multilayered bioinformatics approach. Enrichment analysis via the Gene Ontology was performed through the Metascape platform to explore biological pathways. Protein-protein interaction networks were analyzed via STRING db and Network Analyst.ResultsIntersection of transcriptomic and proteomic analysis showed 10 differentially expressed genes/proteins in DiSig (AEBP1, CA3, HBA2, HBB, HSPA2, MYH6, SERPINA3, SOD3, THBS4, UCHL1) and 15 differentially expressed genes/proteins in IsSig (AEBP1, APOA1, BGN, CA3, CFH, COL14A1, HBA2, HBB, HSPA2, LTBP2, LUM, MFAP4, SOD3, THBS4, UCHL1). Common and distinct biological pathways between DiSig and IsSig were retrieved, allowing for their molecular characterization. Extracellular matrix organization, cellular response to stress and transforming growth factor-beta were common between two subphenotypes. Muscle tissue development was dysregulated solely in DiSig, while immune cells activation and migration in IsSig.DiscussionOur bioinformatics approach sheds light on the molecular background of HF etiopathology showing molecular similarities as well as distinct expression differences between DCM and ICM. DiSig and IsSig encompass an array of “cross-validated” genes at both transcriptomic and proteomic level, which can serve as novel pharmacological targets and possible diagnostic biomarkers. |
| first_indexed | 2024-04-10T15:36:25Z |
| format | Article |
| id | doaj.art-33ca60d130854fb7a83b48f909045145 |
| institution | Directory Open Access Journal |
| issn | 2297-055X |
| language | English |
| last_indexed | 2024-04-10T15:36:25Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Cardiovascular Medicine |
| spelling | doaj.art-33ca60d130854fb7a83b48f9090451452023-02-13T05:02:10ZengFrontiers Media S.A.Frontiers in Cardiovascular Medicine2297-055X2023-02-011010.3389/fcvm.2023.11156231115623Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathyKonstantina Portokallidou0Konstantina Portokallidou1Nikolas Dovrolis2Nikolas Dovrolis3Georgia Ragia4Georgia Ragia5Natalia Atzemian6Natalia Atzemian7George Kolios8George Kolios9Vangelis G. Manolopoulos10Vangelis G. Manolopoulos11Vangelis G. Manolopoulos12Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, GreeceIndividualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, GreeceLaboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, GreeceIndividualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, GreeceLaboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, GreeceIndividualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, GreeceLaboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, GreeceIndividualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, GreeceLaboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, GreeceIndividualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, GreeceLaboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, GreeceIndividualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, GreeceClinical Pharmacology Unit, Academic General Hospital of Alexandroupolis, Alexandroupolis, GreeceIntroductionHeart failure (HF) is a complex clinical syndrome leading to high morbidity. In this study, we aimed to identify the gene expression and protein signature of HF main causes, namely dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM).MethodsOmics data were accessed through GEO repository for transcriptomic and PRIDE repository for proteomic datasets. Sets of differentially expressed genes and proteins comprising DCM (DiSig) and ICM (IsSig) signatures were analyzed by a multilayered bioinformatics approach. Enrichment analysis via the Gene Ontology was performed through the Metascape platform to explore biological pathways. Protein-protein interaction networks were analyzed via STRING db and Network Analyst.ResultsIntersection of transcriptomic and proteomic analysis showed 10 differentially expressed genes/proteins in DiSig (AEBP1, CA3, HBA2, HBB, HSPA2, MYH6, SERPINA3, SOD3, THBS4, UCHL1) and 15 differentially expressed genes/proteins in IsSig (AEBP1, APOA1, BGN, CA3, CFH, COL14A1, HBA2, HBB, HSPA2, LTBP2, LUM, MFAP4, SOD3, THBS4, UCHL1). Common and distinct biological pathways between DiSig and IsSig were retrieved, allowing for their molecular characterization. Extracellular matrix organization, cellular response to stress and transforming growth factor-beta were common between two subphenotypes. Muscle tissue development was dysregulated solely in DiSig, while immune cells activation and migration in IsSig.DiscussionOur bioinformatics approach sheds light on the molecular background of HF etiopathology showing molecular similarities as well as distinct expression differences between DCM and ICM. DiSig and IsSig encompass an array of “cross-validated” genes at both transcriptomic and proteomic level, which can serve as novel pharmacological targets and possible diagnostic biomarkers.https://www.frontiersin.org/articles/10.3389/fcvm.2023.1115623/fullheart failuredilated cardiomyopathyischemic cardiomyopathyprecision medicineproteomicstranscriptomics |
| spellingShingle | Konstantina Portokallidou Konstantina Portokallidou Nikolas Dovrolis Nikolas Dovrolis Georgia Ragia Georgia Ragia Natalia Atzemian Natalia Atzemian George Kolios George Kolios Vangelis G. Manolopoulos Vangelis G. Manolopoulos Vangelis G. Manolopoulos Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy Frontiers in Cardiovascular Medicine heart failure dilated cardiomyopathy ischemic cardiomyopathy precision medicine proteomics transcriptomics |
| title | Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy |
| title_full | Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy |
| title_fullStr | Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy |
| title_full_unstemmed | Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy |
| title_short | Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy |
| title_sort | multi omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy |
| topic | heart failure dilated cardiomyopathy ischemic cardiomyopathy precision medicine proteomics transcriptomics |
| url | https://www.frontiersin.org/articles/10.3389/fcvm.2023.1115623/full |
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