Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients
Abstract This study aimed to identify significant gene expression profiles of the human lung epithelial cells caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We performed a comparative genomic analysis to show genomic observations between SARS-CoV and SARS-CoV-2. A...
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description | Abstract
This study aimed to identify significant gene expression profiles of the human lung epithelial cells caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We performed a comparative genomic analysis to show genomic observations between SARS-CoV and SARS-CoV-2. A phylogenetic tree has been carried for genomic analysis that confirmed the genomic variance between SARS-CoV and SARS-CoV-2. Transcriptomic analyses have been performed for SARS-CoV-2 infection responses and pulmonary arterial hypertension (PAH) patients’ lungs as a number of patients have been identified who faced PAH after being diagnosed with coronavirus disease 2019 (COVID-19). Gene expression profiling showed significant expression levels for SARS-CoV-2 infection responses to human lung epithelial cells and PAH lungs as well. Differentially expressed genes identification and integration showed concordant genes (SAA2, S100A9, S100A8, SAA1, S100A12 and EDN1) for both SARS-CoV-2 and PAH samples, including S100A9 and S100A8 genes that showed significant interaction in the protein–protein interactions network. Extensive analyses of gene ontology and signaling pathways identification provided evidence of inflammatory responses regarding SARS-CoV-2 infections. The altered signaling and ontology pathways that have emerged from this research may influence the development of effective drugs, especially for the people with preexisting conditions. Identification of regulatory biomolecules revealed the presence of active promoter gene of SARS-CoV-2 in Transferrin-micro Ribonucleic acid (TF-miRNA) co-regulatory network. Predictive drug analyses provided concordant drug compounds that are associated with SARS-CoV-2 infection responses and PAH lung samples, and these compounds showed significant immune response against the RNA viruses like SARS-CoV-2, which is beneficial in therapeutic development in the COVID-19 pandemic. |
doi_str_mv | 10.1093/bib/bbab026 |
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This study aimed to identify significant gene expression profiles of the human lung epithelial cells caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We performed a comparative genomic analysis to show genomic observations between SARS-CoV and SARS-CoV-2. A phylogenetic tree has been carried for genomic analysis that confirmed the genomic variance between SARS-CoV and SARS-CoV-2. Transcriptomic analyses have been performed for SARS-CoV-2 infection responses and pulmonary arterial hypertension (PAH) patients’ lungs as a number of patients have been identified who faced PAH after being diagnosed with coronavirus disease 2019 (COVID-19). Gene expression profiling showed significant expression levels for SARS-CoV-2 infection responses to human lung epithelial cells and PAH lungs as well. Differentially expressed genes identification and integration showed concordant genes (SAA2, S100A9, S100A8, SAA1, S100A12 and EDN1) for both SARS-CoV-2 and PAH samples, including S100A9 and S100A8 genes that showed significant interaction in the protein–protein interactions network. Extensive analyses of gene ontology and signaling pathways identification provided evidence of inflammatory responses regarding SARS-CoV-2 infections. The altered signaling and ontology pathways that have emerged from this research may influence the development of effective drugs, especially for the people with preexisting conditions. Identification of regulatory biomolecules revealed the presence of active promoter gene of SARS-CoV-2 in Transferrin-micro Ribonucleic acid (TF-miRNA) co-regulatory network. Predictive drug analyses provided concordant drug compounds that are associated with SARS-CoV-2 infection responses and PAH lung samples, and these compounds showed significant immune response against the RNA viruses like SARS-CoV-2, which is beneficial in therapeutic development in the COVID-19 pandemic.</description><identifier>ISSN: 1467-5463</identifier><identifier>EISSN: 1477-4054</identifier><identifier>DOI: 10.1093/bib/bbab026</identifier><identifier>PMID: 33611340</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Algorithms ; Biomarkers ; Biomarkers - metabolism ; Biomolecules ; Case Study ; Coronaviruses ; COVID-19 ; COVID-19 - complications ; COVID-19 - metabolism ; COVID-19 - virology ; Drug development ; Epithelial cells ; Epithelium ; Gene expression ; Gene Ontology ; Genes ; Genomic analysis ; Humans ; Hypertension ; Hypertension, Pulmonary - complications ; Hypertension, Pulmonary - metabolism ; Immune response ; Immunosuppressive agents ; Infections ; Inflammation ; Information Storage and Retrieval ; Lungs ; MicroRNAs - metabolism ; miRNA ; Ontology ; Pandemics ; Phylogeny ; Protein interaction ; Protein Interaction Maps ; Proteins ; Pulmonary hypertension ; Respiratory diseases ; Ribonucleic acid ; RNA ; RNA viruses ; SARS-CoV-2 - isolation & purification ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Signal transduction ; Signaling ; Transcription Factors - metabolism ; Transcriptomics ; Transferrin ; Transferrins ; Viral diseases ; Viruses</subject><ispartof>Briefings in bioinformatics, 2021-03, Vol.22 (2), p.1451-1465</ispartof><rights>The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.</rights><rights>The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c468t-4c1ba9610a7828b957ac02e35e7941a8bea4f56a408019cd8b77ae19b87a38373</citedby><cites>FETCH-LOGICAL-c468t-4c1ba9610a7828b957ac02e35e7941a8bea4f56a408019cd8b77ae19b87a38373</cites><orcidid>0000-0002-4034-9819 ; 0000-0003-0756-1006</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7929374/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7929374/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bib/bbab026$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33611340$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Taz, Tasnimul Alam</creatorcontrib><creatorcontrib>Ahmed, Kawsar</creatorcontrib><creatorcontrib>Paul, Bikash Kumar</creatorcontrib><creatorcontrib>Al-Zahrani, Fahad Ahmed</creatorcontrib><creatorcontrib>Mahmud, S M Hasan</creatorcontrib><creatorcontrib>Moni, Mohammad Ali</creatorcontrib><title>Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients</title><title>Briefings in bioinformatics</title><addtitle>Brief Bioinform</addtitle><description>Abstract
This study aimed to identify significant gene expression profiles of the human lung epithelial cells caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We performed a comparative genomic analysis to show genomic observations between SARS-CoV and SARS-CoV-2. A phylogenetic tree has been carried for genomic analysis that confirmed the genomic variance between SARS-CoV and SARS-CoV-2. Transcriptomic analyses have been performed for SARS-CoV-2 infection responses and pulmonary arterial hypertension (PAH) patients’ lungs as a number of patients have been identified who faced PAH after being diagnosed with coronavirus disease 2019 (COVID-19). Gene expression profiling showed significant expression levels for SARS-CoV-2 infection responses to human lung epithelial cells and PAH lungs as well. Differentially expressed genes identification and integration showed concordant genes (SAA2, S100A9, S100A8, SAA1, S100A12 and EDN1) for both SARS-CoV-2 and PAH samples, including S100A9 and S100A8 genes that showed significant interaction in the protein–protein interactions network. Extensive analyses of gene ontology and signaling pathways identification provided evidence of inflammatory responses regarding SARS-CoV-2 infections. The altered signaling and ontology pathways that have emerged from this research may influence the development of effective drugs, especially for the people with preexisting conditions. Identification of regulatory biomolecules revealed the presence of active promoter gene of SARS-CoV-2 in Transferrin-micro Ribonucleic acid (TF-miRNA) co-regulatory network. Predictive drug analyses provided concordant drug compounds that are associated with SARS-CoV-2 infection responses and PAH lung samples, and these compounds showed significant immune response against the RNA viruses like SARS-CoV-2, which is beneficial in therapeutic development in the COVID-19 pandemic.</description><subject>Algorithms</subject><subject>Biomarkers</subject><subject>Biomarkers - metabolism</subject><subject>Biomolecules</subject><subject>Case Study</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>COVID-19 - complications</subject><subject>COVID-19 - metabolism</subject><subject>COVID-19 - virology</subject><subject>Drug development</subject><subject>Epithelial cells</subject><subject>Epithelium</subject><subject>Gene expression</subject><subject>Gene Ontology</subject><subject>Genes</subject><subject>Genomic analysis</subject><subject>Humans</subject><subject>Hypertension</subject><subject>Hypertension, Pulmonary - complications</subject><subject>Hypertension, Pulmonary - metabolism</subject><subject>Immune response</subject><subject>Immunosuppressive agents</subject><subject>Infections</subject><subject>Inflammation</subject><subject>Information Storage and Retrieval</subject><subject>Lungs</subject><subject>MicroRNAs - metabolism</subject><subject>miRNA</subject><subject>Ontology</subject><subject>Pandemics</subject><subject>Phylogeny</subject><subject>Protein interaction</subject><subject>Protein Interaction Maps</subject><subject>Proteins</subject><subject>Pulmonary hypertension</subject><subject>Respiratory diseases</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA viruses</subject><subject>SARS-CoV-2 - isolation & purification</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Signal transduction</subject><subject>Signaling</subject><subject>Transcription Factors - metabolism</subject><subject>Transcriptomics</subject><subject>Transferrin</subject><subject>Transferrins</subject><subject>Viral diseases</subject><subject>Viruses</subject><issn>1467-5463</issn><issn>1477-4054</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kU9LHTEUxUOpqLWuui-BQjdlNJlkJslGkEf_CIJQq9twk5fpi85MxiTT9n2FfmrzeK-im65y4f5yzrkchN5RckKJYqfGm1NjwJC6fYUOKRei4qThrzdzK6qGt-wAvUnpjpCaCEn30QFjLaWMk0P092Lpxuw7byH7MOLQYePDAPHexYRhXOIJ8uo3rBPuQsR55fD1-ffrahFuqxr7sXN28y-VDWQ8wL3DNgxT7_747F0qBJ7mfggjxDWGmF300OPVenJlHtPGshj4kiG9RXsd9Mkd794jdPPl84_Ft-ry6uvF4vyysryVueKWGlAtJSBkLY1qBFhSO9Y4oTgFaRzwrmmBE0mosktphABHlZECmGSCHaGzre40m8EtbfGO0Osp-nL2Wgfw-uVm9Cv9M_zSQtWKCV4EPuwEYniYXcr6LsxxLJl13dRKtaIRtFCftpSNIaXouicHSvSmOF2K07viCv3-eagn9l9TBfi4BcI8_VfpETuipU0</recordid><startdate>20210322</startdate><enddate>20210322</enddate><creator>Taz, Tasnimul Alam</creator><creator>Ahmed, Kawsar</creator><creator>Paul, Bikash Kumar</creator><creator>Al-Zahrani, Fahad Ahmed</creator><creator>Mahmud, S M Hasan</creator><creator>Moni, Mohammad Ali</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SC</scope><scope>8FD</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-4034-9819</orcidid><orcidid>https://orcid.org/0000-0003-0756-1006</orcidid></search><sort><creationdate>20210322</creationdate><title>Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients</title><author>Taz, Tasnimul Alam ; Ahmed, Kawsar ; Paul, Bikash Kumar ; Al-Zahrani, Fahad Ahmed ; Mahmud, S M Hasan ; Moni, Mohammad Ali</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c468t-4c1ba9610a7828b957ac02e35e7941a8bea4f56a408019cd8b77ae19b87a38373</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Algorithms</topic><topic>Biomarkers</topic><topic>Biomarkers - metabolism</topic><topic>Biomolecules</topic><topic>Case Study</topic><topic>Coronaviruses</topic><topic>COVID-19</topic><topic>COVID-19 - complications</topic><topic>COVID-19 - metabolism</topic><topic>COVID-19 - virology</topic><topic>Drug development</topic><topic>Epithelial cells</topic><topic>Epithelium</topic><topic>Gene expression</topic><topic>Gene Ontology</topic><topic>Genes</topic><topic>Genomic analysis</topic><topic>Humans</topic><topic>Hypertension</topic><topic>Hypertension, Pulmonary - complications</topic><topic>Hypertension, Pulmonary - metabolism</topic><topic>Immune response</topic><topic>Immunosuppressive agents</topic><topic>Infections</topic><topic>Inflammation</topic><topic>Information Storage and Retrieval</topic><topic>Lungs</topic><topic>MicroRNAs - metabolism</topic><topic>miRNA</topic><topic>Ontology</topic><topic>Pandemics</topic><topic>Phylogeny</topic><topic>Protein interaction</topic><topic>Protein Interaction Maps</topic><topic>Proteins</topic><topic>Pulmonary hypertension</topic><topic>Respiratory diseases</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA viruses</topic><topic>SARS-CoV-2 - isolation & purification</topic><topic>Severe acute respiratory syndrome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Signal transduction</topic><topic>Signaling</topic><topic>Transcription Factors - metabolism</topic><topic>Transcriptomics</topic><topic>Transferrin</topic><topic>Transferrins</topic><topic>Viral diseases</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Taz, Tasnimul Alam</creatorcontrib><creatorcontrib>Ahmed, Kawsar</creatorcontrib><creatorcontrib>Paul, Bikash Kumar</creatorcontrib><creatorcontrib>Al-Zahrani, Fahad Ahmed</creatorcontrib><creatorcontrib>Mahmud, S M Hasan</creatorcontrib><creatorcontrib>Moni, Mohammad Ali</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Briefings in bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Taz, Tasnimul Alam</au><au>Ahmed, Kawsar</au><au>Paul, Bikash Kumar</au><au>Al-Zahrani, Fahad Ahmed</au><au>Mahmud, S M Hasan</au><au>Moni, Mohammad Ali</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients</atitle><jtitle>Briefings in bioinformatics</jtitle><addtitle>Brief Bioinform</addtitle><date>2021-03-22</date><risdate>2021</risdate><volume>22</volume><issue>2</issue><spage>1451</spage><epage>1465</epage><pages>1451-1465</pages><issn>1467-5463</issn><eissn>1477-4054</eissn><abstract>Abstract
This study aimed to identify significant gene expression profiles of the human lung epithelial cells caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. We performed a comparative genomic analysis to show genomic observations between SARS-CoV and SARS-CoV-2. A phylogenetic tree has been carried for genomic analysis that confirmed the genomic variance between SARS-CoV and SARS-CoV-2. Transcriptomic analyses have been performed for SARS-CoV-2 infection responses and pulmonary arterial hypertension (PAH) patients’ lungs as a number of patients have been identified who faced PAH after being diagnosed with coronavirus disease 2019 (COVID-19). Gene expression profiling showed significant expression levels for SARS-CoV-2 infection responses to human lung epithelial cells and PAH lungs as well. Differentially expressed genes identification and integration showed concordant genes (SAA2, S100A9, S100A8, SAA1, S100A12 and EDN1) for both SARS-CoV-2 and PAH samples, including S100A9 and S100A8 genes that showed significant interaction in the protein–protein interactions network. Extensive analyses of gene ontology and signaling pathways identification provided evidence of inflammatory responses regarding SARS-CoV-2 infections. The altered signaling and ontology pathways that have emerged from this research may influence the development of effective drugs, especially for the people with preexisting conditions. Identification of regulatory biomolecules revealed the presence of active promoter gene of SARS-CoV-2 in Transferrin-micro Ribonucleic acid (TF-miRNA) co-regulatory network. Predictive drug analyses provided concordant drug compounds that are associated with SARS-CoV-2 infection responses and PAH lung samples, and these compounds showed significant immune response against the RNA viruses like SARS-CoV-2, which is beneficial in therapeutic development in the COVID-19 pandemic.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>33611340</pmid><doi>10.1093/bib/bbab026</doi><tpages>15</tpages><orcidid>https://orcid.org/0000-0002-4034-9819</orcidid><orcidid>https://orcid.org/0000-0003-0756-1006</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Algorithms Biomarkers Biomarkers - metabolism Biomolecules Case Study Coronaviruses COVID-19 COVID-19 - complications COVID-19 - metabolism COVID-19 - virology Drug development Epithelial cells Epithelium Gene expression Gene Ontology Genes Genomic analysis Humans Hypertension Hypertension, Pulmonary - complications Hypertension, Pulmonary - metabolism Immune response Immunosuppressive agents Infections Inflammation Information Storage and Retrieval Lungs MicroRNAs - metabolism miRNA Ontology Pandemics Phylogeny Protein interaction Protein Interaction Maps Proteins Pulmonary hypertension Respiratory diseases Ribonucleic acid RNA RNA viruses SARS-CoV-2 - isolation & purification Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Signal transduction Signaling Transcription Factors - metabolism Transcriptomics Transferrin Transferrins Viral diseases Viruses |
title | Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients |
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