Ribosome-Profiling Reveals Restricted Post Transcriptional Expression of Antiviral Cytokines and Transcription Factors during SARS-CoV-2 Infection

Abstract

The global COVID-19 pandemic caused by SARS-CoV-2 has resulted in over 2.2 million deaths. Disease outcomes range from asymptomatic to severe with, so far, minimal genotypic change to the virus so understanding the host response is paramount. Transcriptomics has become incredibly important in understanding host-pathogen interactions; however, post-transcriptional regulation plays an important role in infection and immunity through translation and mRNA stability, allowing tight control over potent host responses by both the host and the invading virus. Here, we apply ribosome profiling to assess post-transcriptional regulation of host genes during SARS-CoV-2 infection of a human lung epithelial cell line (Calu-3). We have identified numerous transcription factors (JUN, ZBTB20, ATF3, HIVEP2 and EGR1) as well as select antiviral cytokine genes, namely IFNB1, IFNL1,2 and 3, IL-6 and CCL5, that are restricted at the post-transcriptional level by SARS-CoV-2 infection and discuss the impact this would have on the host response to infection. This early phase restriction of antiviral transcripts in the lungs may allow high viral load and consequent immune dysregulation typically seen in SARS-CoV-2 infection.

Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression

“…This inhibition of host mRNA nuclear export has been found to reduce synthesis of interferon-stimulated genes 114 , and mutations in nsp1β which ablate this activity lead to reduced viral load and increased neutralising antibody titres in pigs 115 . These findings suggest that nsp1β-mediated nuclear export inhibition may be responsible for the translational repression seen in our host differential gene expression analyses, which, analogously to conclusions drawn for SARS-CoV-2 [109,110] , may be a key mechanism by which PRRSV evades the host response to infection.…”

“…Global analysis of the host response to PRRSV infection at 12 hpi reveals that many of the observed changes in transcript abundance are offset at the translational level, indicating that changes in translation efficiency of host mRNAs may play a dominant role in the response to infection. This phenomenon of host transcriptional responses being counteracted by opposing changes in TE has also been observed in response to SARS-CoV-2 infection, where it was attributed to inhibition of mRNA export from the nucleus, preventing translation 109,110 . This activity is known to be associated with coronavirus nsp1, which inhibits nuclear export by interacting with the nuclear export factor NXF1 in SARS-CoV or the nuclear pore complex component Nup93 in SARS-CoV-2 [111,112] .…”

SARS-CoV-2 Infected Pediatric Cerebral Cortical Neurons: Transcriptomic Analysis and Potential Role of Toll-like Receptors in Pathogenesis

“…JUN and FOS were downregulated, as found also in a transcriptomic analysis of nasopharyngeal swabs of SARS-CoV-2 positive compared to negative subjects [ 67 ]. Interestingly, JUN transcript was restricted at post transcriptional level by SARS-CoV-2 [ 68 ], also due to its short half-life [ 69 ]. However, looking at the transcription factors activated by MAPK in KEGG, we found the upregulation of ATF4 , reported to be activated by TLR4 pro-inflammatory signaling [ 70 ].…”

A Structurally Conserved RNA Element within SARS-CoV-2 ORF1a RNA and S mRNA Regulates Translation in Response to Viral S Protein-Induced Signaling in Human Lung Cells

“…Subsequently, four structural proteins, spike (S), envelope (E), membrane (M), and nucleocapsid (N), as well as several other accessory proteins, are produced from a nested set of subgenomic mRNAs transcribed from the 3′ one-third of the genome ( 1 ). Importantly, SARS-CoV-2 has successfully adopted a multipronged strategy to repress cellular translation, which results in robust downregulation of retinoic acid-inducible gene 1 (RIG-1), a cytosolic pattern recognition receptor that plays a key role in type-1 interferon (IFN1) response ( 2 – 5 ). This severely compromises IFN-dependent immune responses that would be the host’s first line of defense against the virus.…”

“…This severely compromises IFN-dependent immune responses that would be the host’s first line of defense against the virus. Mechanisms of translation suppression utilized by SARS-CoV-2 include (i) binding of the viral NSP1 protein to the mRNA entry channel of the host 40S ribosomal subunit ( 2 , 3 ); (ii) impairment of the translation of cellular transcripts encoding cytokines and other factors involved in innate immune responses ( 4 , 5 ); and (iii) accelerated degradation of cytosolic cellular mRNAs, preventing newly transcribed host mRNAs from accessing ribosomes ( 4 ). Apart from direct inhibition of translation of host proteins as mentioned above, NSP8 and NSP9 of SARS-CoV-2 disrupt protein trafficking through targeting the 7SL RNA component of the signal recognition particle (SRP) ( 2 ).…”