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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Veröffentlicht in:Briefings in bioinformatics 2021-03, Vol.22 (2), p.1451-1465
Hauptverfasser: Taz, Tasnimul Alam, Ahmed, Kawsar, Paul, Bikash Kumar, Al-Zahrani, Fahad Ahmed, Mahmud, S M Hasan, Moni, Mohammad Ali
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container_issue 2
container_start_page 1451
container_title Briefings in bioinformatics
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creator Taz, Tasnimul Alam
Ahmed, Kawsar
Paul, Bikash Kumar
Al-Zahrani, Fahad Ahmed
Mahmud, S M Hasan
Moni, Mohammad Ali
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.
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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 &amp; 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. 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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. 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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. 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source Oxford University Press Open Access
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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