TY - JOUR
T1 - Identification of shared biological features in four different lung cell lines infected with SARS-CoV-2 virus through RNA-seq analysis
AU - Zhang, Xiaoxi
AU - Ahn, Seungjun
AU - Qiu, Peihua
AU - Datta, Somnath
N1 - Publisher Copyright:
Copyright © 2023 Zhang, Ahn, Qiu and Datta.
PY - 2023
Y1 - 2023
N2 - The COVID-19 pandemic caused by SARS-CoV-2 has resulted in millions of confirmed cases and deaths worldwide. Understanding the biological mechanisms of SARS-CoV-2 infection is crucial for the development of effective therapies. This study conducts differential expression (DE) analysis, pathway analysis, and differential network (DN) analysis on RNA-seq data of four lung cell lines, NHBE, A549, A549.ACE2, and Calu3, to identify their common and unique biological features in response to SARS-CoV-2 infection. DE analysis shows that cell line A549.ACE2 has the highest number of DE genes, while cell line NHBE has the lowest. Among the DE genes identified for the four cell lines, 12 genes are overlapped, associated with various health conditions. The most significant signaling pathways varied among the four cell lines. Only one pathway, “cytokine-cytokine receptor interaction”, is found to be significant among all four cell lines and is related to inflammation and immune response. The DN analysis reveals considerable variation in the differential connectivity of the most significant pathway shared among the four lung cell lines. These findings help to elucidate the mechanisms of SARS-CoV-2 infection and potential therapeutic targets.
AB - The COVID-19 pandemic caused by SARS-CoV-2 has resulted in millions of confirmed cases and deaths worldwide. Understanding the biological mechanisms of SARS-CoV-2 infection is crucial for the development of effective therapies. This study conducts differential expression (DE) analysis, pathway analysis, and differential network (DN) analysis on RNA-seq data of four lung cell lines, NHBE, A549, A549.ACE2, and Calu3, to identify their common and unique biological features in response to SARS-CoV-2 infection. DE analysis shows that cell line A549.ACE2 has the highest number of DE genes, while cell line NHBE has the lowest. Among the DE genes identified for the four cell lines, 12 genes are overlapped, associated with various health conditions. The most significant signaling pathways varied among the four cell lines. Only one pathway, “cytokine-cytokine receptor interaction”, is found to be significant among all four cell lines and is related to inflammation and immune response. The DN analysis reveals considerable variation in the differential connectivity of the most significant pathway shared among the four lung cell lines. These findings help to elucidate the mechanisms of SARS-CoV-2 infection and potential therapeutic targets.
KW - COVID-19
KW - RNA-seq
KW - SARS-CoV-2
KW - differential expression analysis
KW - differential network analysis
KW - lung cell lines
KW - pathway analysis
UR - http://www.scopus.com/inward/record.url?scp=85169679710&partnerID=8YFLogxK
U2 - 10.3389/fgene.2023.1235927
DO - 10.3389/fgene.2023.1235927
M3 - Article
AN - SCOPUS:85169679710
SN - 1664-8021
VL - 14
JO - Frontiers in Genetics
JF - Frontiers in Genetics
M1 - 1235927
ER -