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对感染野生型SARS-CoV-2及其E基因缺失12个碱基对变体的人肺上皮细胞进行的比较转录组分析。

Comparative transcriptomic analyzes of human lung epithelial cells infected with wild-type SARS-CoV-2 and its variant with a 12-bp missing in the E gene.

作者信息

Sun Yi-Sheng, Sun Hao, Zhu Han-Ping, Li Gao-Lei, Xu Fang, Lu Hang-Jing, Tang An, Wu Bei-Bei, Li Yu-Dong, Yao Ping-Ping, Jiang Jian-Min

机构信息

Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.

Department of Biological Engineering, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.

出版信息

Front Microbiol. 2023 Jan 9;13:1079764. doi: 10.3389/fmicb.2022.1079764. eCollection 2022.

DOI:10.3389/fmicb.2022.1079764
PMID:36699595
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9868179/
Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that caused a global outbreak of coronavirus disease 2019 (COVID-19) pandemic. To elucidate the mechanism of SARS-CoV-2 replication and immunogenicity, we performed a comparative transcriptome profile of mRNA and long non-coding RNAs (lncRNAs) in human lung epithelial cells infected with the SARS-CoV-2 wild-type strain (8X) and the variant with a 12-bp deletion in the E gene (F8). In total, 3,966 differentially expressed genes (DEGs) and 110 differentially expressed lncRNA (DE-lncRNA) candidates were identified. Of these, 94 DEGs and 32 DE-lncRNAs were found between samples infected with F8 and 8X. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzes revealed that pathways such as the TNF signaling pathway and viral protein interaction with cytokine and cytokine receptor were involved. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to the immune response, which might explain the different replication and immunogenicity properties of the 8X and F8 strains. These results provide a useful resource for studying the pathogenesis of SARS-CoV-2 variants.

摘要

严重急性呼吸综合征冠状病毒2（SARS-CoV-2）是一种新型冠状病毒，它引发了2019冠状病毒病（COVID-19）的全球大流行。为了阐明SARS-CoV-2复制和免疫原性的机制，我们对感染了SARS-CoV-2野生型毒株（8X）和E基因有12个碱基对缺失的变体（F8）的人肺上皮细胞中的mRNA和长链非编码RNA（lncRNA）进行了比较转录组分析。总共鉴定出3966个差异表达基因（DEG）和110个差异表达lncRNA（DE-lncRNA）候选物。其中，在感染F8和8X的样本之间发现了94个DEG和32个DE-lncRNA。基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析表明，TNF信号通路以及病毒蛋白与细胞因子和细胞因子受体的相互作用等途径参与其中。此外，我们构建了一个lncRNA-蛋白质编码基因共表达相互作用网络。对共表达基因的KEGG分析表明，这些差异表达的lncRNA在与免疫反应相关的途径中富集，这可能解释了8X和F8毒株不同的复制和免疫原性特性。这些结果为研究SARS-CoV-2变体的发病机制提供了有用的资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/d4574fc18337/fmicb-13-1079764-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/8bd1fb831d09/fmicb-13-1079764-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/7c5eef6e5c53/fmicb-13-1079764-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/0d263e45b1b5/fmicb-13-1079764-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/47a769e2a746/fmicb-13-1079764-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/9b99b9956c9b/fmicb-13-1079764-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/31874b6c4b9e/fmicb-13-1079764-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/d4574fc18337/fmicb-13-1079764-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/8bd1fb831d09/fmicb-13-1079764-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/7c5eef6e5c53/fmicb-13-1079764-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/0d263e45b1b5/fmicb-13-1079764-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/47a769e2a746/fmicb-13-1079764-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/9b99b9956c9b/fmicb-13-1079764-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/31874b6c4b9e/fmicb-13-1079764-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e8f5/9868179/d4574fc18337/fmicb-13-1079764-g007.jpg

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