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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research. Sci Rep 2024; 14:7471. [PMID: 38553458 PMCID: PMC10980734 DOI: 10.1038/s41598-024-56562-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in CVD research. Caenorhabditis elegans, a nematode species, has emerged as a prominent experimental organism widely utilized in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilization for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signaling pathway, the FoxO signaling pathway, the MAPK signaling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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Affiliation(s)
- Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, India.
| | - Anjali Priya
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait.
| | | | - Alok Kumar Singh
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, India
| | - Payal Mago
- Shaheed Rajguru College of Applied Science for Women, University of Delhi, New Delhi, India
- Campus of Open Learning, University of Delhi, New Delhi, India
| | - Chirashree Ghosh
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. Conserved Cardiovascular Network: Bioinformatics Insights into Genes and Pathways for Establishing Caenorhabditis elegans as an Animal Model for Cardiovascular Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.24.573256. [PMID: 38234826 PMCID: PMC10793405 DOI: 10.1101/2023.12.24.573256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in cardiovascular disease (CVD) research. Caenorhabditis elegans , a nematode species, has emerged as a prominent experimental organism widely utilised in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilisation for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signalling pathway, the FoxO signalling pathway, the MAPK signalling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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Anjos M, Fontes-Oliveira M, Costa VM, Santos M, Ferreira R. An update of the molecular mechanisms underlying doxorubicin plus trastuzumab induced cardiotoxicity. Life Sci 2021; 280:119760. [PMID: 34166713 DOI: 10.1016/j.lfs.2021.119760] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/24/2022]
Abstract
Cardiotoxicity is a major side effect of the chemotherapeutic drug doxorubicin (Dox), which is further exacerbated when it is combined with trastuzumab, a standard care approach for Human Epidermal growth factor Receptor-type 2 (HER2) positive cancer patients. However, the molecular mechanisms of the underlying cardiotoxicity of this combination are still mostly elusive. Increased oxidative stress, impaired energetic substrate uses and topoisomerase IIB inhibition are among the biological processes proposed to explain Dox-induced cardiomyocyte dysfunction. Since cardiomyocytes express HER2, trastuzumab can also damage these cells by interfering with neuroregulin-1 signaling and mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K)/Akt and focal adhesion kinase (FAK)-dependent pathways. Nevertheless, Dox and trastuzumab target other cardiac cell types, such as endothelial cells, fibroblasts, cardiac progenitor cells and leukocytes, which can contribute to the clinical cardiotoxicity observed. This review aims to summarize the current knowledge on the cardiac signaling pathways modulated by these two antineoplastic drugs highly used in the management of breast cancer, not only focusing on cardiomyocytes but also to broaden the knowledge of the potential impact on other cells found in the heart.
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Affiliation(s)
- Miguel Anjos
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | | | - Vera M Costa
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mário Santos
- Cardiology Department, Centro Hospitalar Universitário do Porto, Porto, Portugal; UMIB, Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal
| | - Rita Ferreira
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal.
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Haidar MN, Islam MB, Chowdhury UN, Rahman MR, Huq F, Quinn JMW, Moni MA. Network-based computational approach to identify genetic links between cardiomyopathy and its risk factors. IET Syst Biol 2020; 14:75-84. [PMID: 32196466 PMCID: PMC8687405 DOI: 10.1049/iet-syb.2019.0074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/23/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Cardiomyopathy (CMP) is a group of myocardial diseases that progressively impair cardiac function. The mechanisms underlying CMP development are poorly understood, but lifestyle factors are clearly implicated as risk factors. This study aimed to identify molecular biomarkers involved in inflammatory CMP development and progression using a systems biology approach. The authors analysed microarray gene expression datasets from CMP and tissues affected by risk factors including smoking, ageing factors, high body fat, clinical depression status, insulin resistance, high dietary red meat intake, chronic alcohol consumption, obesity, high-calorie diet and high-fat diet. The authors identified differentially expressed genes (DEGs) from each dataset and compared those from CMP and risk factor datasets to identify common DEGs. Gene set enrichment analyses identified metabolic and signalling pathways, including MAPK, RAS signalling and cardiomyopathy pathways. Protein-protein interaction (PPI) network analysis identified protein subnetworks and ten hub proteins (CDK2, ATM, CDT1, NCOR2, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E and HIST1H4L). Five transcription factors (FOXC1, GATA2, FOXL1, YY1, CREB1) and five miRNAs were also identified in CMP. Thus the authors' approach reveals candidate biomarkers that may enhance understanding of mechanisms underlying CMP and their link to risk factors. Such biomarkers may also be useful to develop new therapeutics for CMP.
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Affiliation(s)
- Md Nasim Haidar
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj 6751, Bangladesh
| | - Fazlul Huq
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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Tamargo J, Caballero R, Delpón E. New drugs in preclinical and early stage clinical development in the treatment of heart failure. Expert Opin Investig Drugs 2018; 28:51-71. [DOI: 10.1080/13543784.2019.1551357] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Juan Tamargo
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense, CIBERCV, Madrid,
Spain
| | - Ricardo Caballero
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense, CIBERCV, Madrid,
Spain
| | - Eva Delpón
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense, CIBERCV, Madrid,
Spain
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