Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression
BackgroundCoronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and i...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1369311/full |
| _version_ | 1797242994273812480 |
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| author | Zhen Zhang Hao Jin Xu Zhang Mei Bai Kexin Zheng Jing Tian Bin Deng Lingling Mao Pengcheng Qiu Bo Huang Bo Huang |
| author_facet | Zhen Zhang Hao Jin Xu Zhang Mei Bai Kexin Zheng Jing Tian Bin Deng Lingling Mao Pengcheng Qiu Bo Huang Bo Huang |
| author_sort | Zhen Zhang |
| collection | DOAJ |
| description | BackgroundCoronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and increased mortality when affected by COVID-19. Despite this connection, the molecular intricacies linking COVID-19, influenza, and HIV remain unclear. Our research endeavors to elucidate the shared pathways and molecular markers in individuals with HIV concurrently infected with COVID-19 and influenza. Furthermore, we aim to identify potential medications that may prove beneficial in managing these three interconnected illnesses.MethodsSequencing data for COVID-19 (GSE157103), influenza (GSE185576), and HIV (GSE195434) were retrieved from the GEO database. Commonly expressed differentially expressed genes (DEGs) were identified across the three datasets, followed by immune infiltration analysis and diagnostic ROC analysis on the DEGs. Functional enrichment analysis was performed using GO/KEGG and Gene Set Enrichment Analysis (GSEA). Hub genes were screened through a Protein-Protein Interaction networks (PPIs) analysis among DEGs. Analysis of miRNAs, transcription factors, drug chemicals, diseases, and RNA-binding proteins was conducted based on the identified hub genes. Finally, quantitative PCR (qPCR) expression verification was undertaken for selected hub genes.ResultsThe analysis of the three datasets revealed a total of 22 shared DEGs, with the majority exhibiting an area under the curve value exceeding 0.7. Functional enrichment analysis with GO/KEGG and GSEA primarily highlighted signaling pathways associated with ribosomes and tumors. The ten identified hub genes included IFI44L, IFI44, RSAD2, ISG15, IFIT3, OAS1, EIF2AK2, IFI27, OASL, and EPSTI1. Additionally, five crucial miRNAs (hsa-miR-8060, hsa-miR-6890-5p, hsa-miR-5003-3p, hsa-miR-6893-3p, and hsa-miR-6069), five essential transcription factors (CREB1, CEBPB, EGR1, EP300, and IRF1), and the top ten significant drug chemicals (estradiol, progesterone, tretinoin, calcitriol, fluorouracil, methotrexate, lipopolysaccharide, valproic acid, silicon dioxide, cyclosporine) were identified.ConclusionThis research provides valuable insights into shared molecular targets, signaling pathways, drug chemicals, and potential biomarkers for individuals facing the complex intersection of COVID-19, influenza, and HIV. These findings hold promise for enhancing the precision of diagnosis and treatment for individuals with HIV co-infected with COVID-19 and influenza. |
| first_indexed | 2024-04-24T18:48:03Z |
| format | Article |
| id | doaj.art-031dc7948ca84c9a83f3216f0f06db80 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-24T18:48:03Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-031dc7948ca84c9a83f3216f0f06db802024-03-27T04:34:58ZengFrontiers Media S.A.Frontiers in Immunology1664-32242024-03-011510.3389/fimmu.2024.13693111369311Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expressionZhen Zhang0Hao Jin1Xu Zhang2Mei Bai3Kexin Zheng4Jing Tian5Bin Deng6Lingling Mao7Pengcheng Qiu8Bo Huang9Bo Huang10Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, ChinaMicrobiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, ChinaMicrobiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, ChinaMicrobiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, ChinaMicrobiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, ChinaDepartment of Immunology, School of Basic Medical Science, Jinzhou Medical University, Jinzhou, Liaoning, ChinaLaboratory Department, Jinzhou Central Hospital, Jinzhou, Liaoning, ChinaInstitute for Prevention and Control of Infection and Infectious Diseases, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, ChinaThoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, ChinaThoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, ChinaThoracic Surgery Department, Yingkou Central Hospital, Yingkou, Liaoning, ChinaBackgroundCoronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and increased mortality when affected by COVID-19. Despite this connection, the molecular intricacies linking COVID-19, influenza, and HIV remain unclear. Our research endeavors to elucidate the shared pathways and molecular markers in individuals with HIV concurrently infected with COVID-19 and influenza. Furthermore, we aim to identify potential medications that may prove beneficial in managing these three interconnected illnesses.MethodsSequencing data for COVID-19 (GSE157103), influenza (GSE185576), and HIV (GSE195434) were retrieved from the GEO database. Commonly expressed differentially expressed genes (DEGs) were identified across the three datasets, followed by immune infiltration analysis and diagnostic ROC analysis on the DEGs. Functional enrichment analysis was performed using GO/KEGG and Gene Set Enrichment Analysis (GSEA). Hub genes were screened through a Protein-Protein Interaction networks (PPIs) analysis among DEGs. Analysis of miRNAs, transcription factors, drug chemicals, diseases, and RNA-binding proteins was conducted based on the identified hub genes. Finally, quantitative PCR (qPCR) expression verification was undertaken for selected hub genes.ResultsThe analysis of the three datasets revealed a total of 22 shared DEGs, with the majority exhibiting an area under the curve value exceeding 0.7. Functional enrichment analysis with GO/KEGG and GSEA primarily highlighted signaling pathways associated with ribosomes and tumors. The ten identified hub genes included IFI44L, IFI44, RSAD2, ISG15, IFIT3, OAS1, EIF2AK2, IFI27, OASL, and EPSTI1. Additionally, five crucial miRNAs (hsa-miR-8060, hsa-miR-6890-5p, hsa-miR-5003-3p, hsa-miR-6893-3p, and hsa-miR-6069), five essential transcription factors (CREB1, CEBPB, EGR1, EP300, and IRF1), and the top ten significant drug chemicals (estradiol, progesterone, tretinoin, calcitriol, fluorouracil, methotrexate, lipopolysaccharide, valproic acid, silicon dioxide, cyclosporine) were identified.ConclusionThis research provides valuable insights into shared molecular targets, signaling pathways, drug chemicals, and potential biomarkers for individuals facing the complex intersection of COVID-19, influenza, and HIV. These findings hold promise for enhancing the precision of diagnosis and treatment for individuals with HIV co-infected with COVID-19 and influenza.https://www.frontiersin.org/articles/10.3389/fimmu.2024.1369311/fullCOVID-19influenzaHIVdifferentially expressed genesimmune infiltrationhub genes |
| spellingShingle | Zhen Zhang Hao Jin Xu Zhang Mei Bai Kexin Zheng Jing Tian Bin Deng Lingling Mao Pengcheng Qiu Bo Huang Bo Huang Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression Frontiers in Immunology COVID-19 influenza HIV differentially expressed genes immune infiltration hub genes |
| title | Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression |
| title_full | Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression |
| title_fullStr | Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression |
| title_full_unstemmed | Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression |
| title_short | Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression |
| title_sort | bioinformatics and system biology approach to identify the influences among covid 19 influenza and hiv on the regulation of gene expression |
| topic | COVID-19 influenza HIV differentially expressed genes immune infiltration hub genes |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1369311/full |
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