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Evasion of antiviral innate immunity by SARS-CoV-2 NSP1 is exerted through H3K9 di-methylation

ABSTRACT: The pathogen causing the current COVID-19 pandemic, the severe acute respiratory syndrome coronavirus (SARS-CoV-2), evades the innate immune machinery through the independent action of several viral proteins, including the nonstructural protein 1 (NSP1). NSP1 has multiple functions, but the relative contribution of NSP1-mediated translational repression, ribosome-proximate degradation of host mRNA, or other molecular mechanisms to viral immune evasion remains unclear. Here we combined several genome wide approaches, including RNA-seq, ribosome footprinting, and ChIP-seq to find that NSP1 predominantly affects transcription of immune-related genes. NSP1 expression in A549 cells induced Histone 3 Lysine 9 (H3K9) methylation of antiviral gene loci, leading to specific suppression of type I and type III interferon pathways. Treatment with the G9a/GLP H3K9 methyltransferase inhibitor UNC0638 reverses this suppression of antiviral genes and blocks viral replication after SARS-CoV2 infection of A549 cells. Our results call attention to epigenetic reprogramming induced by SARS-CoV2 and highlight the importance to identify innate factors regulating histone modification of gene loci targeted by SARS-CoV-2, with possible relevance to the understanding and therapy of other immunomodulatory diseases.

ORGANISM(S): Homo sapiens

PROVIDER: GSE208116 | GEO | 2023/07/12

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study are to monitor the evolution pattern of SARS-CoV2 in depending host cells by viral transcriptome sequencing analysis of Vero, A549, Caco2, and HRT18 cells infected with SARS-CoV2. Methods: SARS-CoV-2 isolate was passaged 4 time on Vero cells and used to extract RNA for the high-throughput sequencing. The 8×104 PFU of SARS-CoV2 stocks passaged on vero cells were inoculated to the monolayer of A549, CaCO2, and HRT-18 cell lines in 75T flask for 1hour at 37℃ in a 5% CO2 incubator with gentle shaking of 15 minutes interval. After that, the infected cells were washed two times with DPBS and incubated with the fresh maintenance medium for 3 days. The virus inoculation was performed in triplicate for each cell lines. In case of the first passage, the infected cell pellets were resuspended to 250µl with fresh medium, to extract RNA for the high-throughput sequencing. The cultured cell supernatant of the virus-infected A549, CaCO2, and HRT18 cells was centrifuged at 3,000g for 10min to use for the next passage, and stored at -80℃. The serial passage of SARS-CoV-2 on A549, CaCO2, and HRT18 cell lines were continued to passage 12 and the cultured cell supernatant of the infected cells in passage 12 was centrifuged at 3,000g for 10 min, and used to extract RNA for the high-throughput sequencing. The RNA samples were sequenced with illumine TruSeq Strand Total RNA LT kit and illumine NovaSeq6000 plaform form Macrogen, Inc (Seoul, Korea) for high throughput sequencing. The raw reads were trimmed with BBDuk and mapped the isolate SARS-CoV-2/human/KOR/KCDC03-NCCP43326/2020 (Genebank accession number. MW466791) with Bowtie 2 using Geneious program 2021.2.2 Result: Using SNP analysis workflow, our result showed the sequence variations pattern of SARS-CoV2 depending on host cell (A549, CaCO2, and HRT18 cell lines) and it was confirmed that a relatively large number of SNPs were commonly observed in spike protein. Some SNPs affect amino acid changes, and a common pattern of amino acid changes was observed the genomic sequence of SARS-CoV2 passaged in A549, CaCO2 and HRT18 cells. Conclusion: In this study, we tried to monitor the SARS-CoV-2 (GenBank accession No. MW466791 in 2020, Korea) evolution pattern in different host cells using high throughput sequencing analysis, and compare the selected mutations by each host cells with natural mutations found in currently circulating SARS-CoV-2 variants.

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Evasion of antiviral innate immunity by SARS-CoV-2 NSP1 is exerted through H3K9 di-methylation

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