Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis
The SARS-CoV-2 is one of the most infectious and deadly coronaviruses, which has gripped the world, causing the COVID-19 pandemic. Despite the numerous studies being conducted on this virus, many uncertainties are with the disease. This is exacerbated by the speedy mutations acquired by the viral st...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Informatics in Medicine Unlocked |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S235291482200123X |
| _version_ | 1828262387268976640 |
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| author | Lavanya C Aajnaa Upadhyaya Arpita Guha Neogi Vidya Niranjan |
| author_facet | Lavanya C Aajnaa Upadhyaya Arpita Guha Neogi Vidya Niranjan |
| author_sort | Lavanya C |
| collection | DOAJ |
| description | The SARS-CoV-2 is one of the most infectious and deadly coronaviruses, which has gripped the world, causing the COVID-19 pandemic. Despite the numerous studies being conducted on this virus, many uncertainties are with the disease. This is exacerbated by the speedy mutations acquired by the viral strain, which enables the disease to present itself differently in different people, introducing new factors of uncertainty. This study aims at the identification of regulatory pathways across two cell lines, namely, the peripheral blood mononuclear cell line (PBMC) and the normal human bronchial epithelial (NHBE) cell line. Both the above-mentioned cell lines were considered because they support viral replication. Furthermore, the NHBE cell line captures vital changes in the lungs, which are the main organs affected by the COVID-19 patients, and the PBMC cell line is closely linked to the body's immune system. RNA-Seq analysis, differential gene expression and gene set enrichment analysis for pathway identification were followed. Pathway analysis throws light upon the various systems affected in the body due to the COVID-19. Gene regulatory networks associated with the significant pathways were also designed. These networks aid in identifying various gene targets, along with their interactions. Studying the functionality of the pathways and the gene interactions associated with them, aided by long COVID studies, will provide immense clarity about the current COVID-19 scenario. In the long term, this will help in the design of therapeutic approaches against the SARS-CoV-2 and can also contribute to drug repurposing studies. Ultimately, this study identifies and analyses the relationship of various undiscovered or lesser explored pathways in the human body to the SARS-CoV-2 and establish a clearer picture of the association to help streamline further studies and approaches. |
| first_indexed | 2024-04-13T03:53:25Z |
| format | Article |
| id | doaj.art-9ee910a375e64747b39f3bcce378ae43 |
| institution | Directory Open Access Journal |
| issn | 2352-9148 |
| language | English |
| last_indexed | 2024-04-13T03:53:25Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Informatics in Medicine Unlocked |
| spelling | doaj.art-9ee910a375e64747b39f3bcce378ae432022-12-22T03:03:42ZengElsevierInformatics in Medicine Unlocked2352-91482022-01-0131100979Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysisLavanya C0Aajnaa Upadhyaya1Arpita Guha Neogi2Vidya Niranjan3Department of Biotechnology, R. V. College of Engineering, Bengaluru, IndiaDepartment of Biotechnology, R. V. College of Engineering, Bengaluru, IndiaDepartment of Biotechnology, R. V. College of Engineering, Bengaluru, IndiaCorresponding author. Department of Biotechnology, RV College of Engineering, RV Vidyaniketan Post, Mysore Road, Bengaluru, 560059, India.; Department of Biotechnology, R. V. College of Engineering, Bengaluru, IndiaThe SARS-CoV-2 is one of the most infectious and deadly coronaviruses, which has gripped the world, causing the COVID-19 pandemic. Despite the numerous studies being conducted on this virus, many uncertainties are with the disease. This is exacerbated by the speedy mutations acquired by the viral strain, which enables the disease to present itself differently in different people, introducing new factors of uncertainty. This study aims at the identification of regulatory pathways across two cell lines, namely, the peripheral blood mononuclear cell line (PBMC) and the normal human bronchial epithelial (NHBE) cell line. Both the above-mentioned cell lines were considered because they support viral replication. Furthermore, the NHBE cell line captures vital changes in the lungs, which are the main organs affected by the COVID-19 patients, and the PBMC cell line is closely linked to the body's immune system. RNA-Seq analysis, differential gene expression and gene set enrichment analysis for pathway identification were followed. Pathway analysis throws light upon the various systems affected in the body due to the COVID-19. Gene regulatory networks associated with the significant pathways were also designed. These networks aid in identifying various gene targets, along with their interactions. Studying the functionality of the pathways and the gene interactions associated with them, aided by long COVID studies, will provide immense clarity about the current COVID-19 scenario. In the long term, this will help in the design of therapeutic approaches against the SARS-CoV-2 and can also contribute to drug repurposing studies. Ultimately, this study identifies and analyses the relationship of various undiscovered or lesser explored pathways in the human body to the SARS-CoV-2 and establish a clearer picture of the association to help streamline further studies and approaches.http://www.sciencedirect.com/science/article/pii/S235291482200123XGene regulatory networksNeurodegenerative disordersDifferential gene expressionPathway analysisDrug repurposing |
| spellingShingle | Lavanya C Aajnaa Upadhyaya Arpita Guha Neogi Vidya Niranjan Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis Informatics in Medicine Unlocked Gene regulatory networks Neurodegenerative disorders Differential gene expression Pathway analysis Drug repurposing |
| title | Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis |
| title_full | Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis |
| title_fullStr | Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis |
| title_full_unstemmed | Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis |
| title_short | Identification of novel regulatory pathways across normal human bronchial epithelial cell lines (NHBEs) and peripheral blood mononuclear cell lines (PBMCs) in COVID-19 patients using transcriptome analysis |
| title_sort | identification of novel regulatory pathways across normal human bronchial epithelial cell lines nhbes and peripheral blood mononuclear cell lines pbmcs in covid 19 patients using transcriptome analysis |
| topic | Gene regulatory networks Neurodegenerative disorders Differential gene expression Pathway analysis Drug repurposing |
| url | http://www.sciencedirect.com/science/article/pii/S235291482200123X |
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