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The lysine demethylase LSD1 controls the balance between inflammatory and antiviral responses against coronaviruses

ABSTRACT: Innate responses to coronavirus are highly cell-specific and remain to date incompletely understood. Tissue-resident macrophages, which are infected by SARS-CoV2 in patients but inconsistently in vitro, exert critical but conflicting effects by secreting both anti-viral type I Interferons and tissue-damaging inflammatory cytokines. Steroids, the only class of host-targeting drugs approved for Covid19, indiscriminately suppress both responses, possibly impairing viral clearance. Here we set up in vitro culture systems with the prototypical murine coronavirus MHV that allow to separately investigate cell-intrinsic and -extrinsic proinflammatory and antiviral activities. We then studied the role of the lysine-demethylase LSD1, previously implicated in innate responses in cancer. We show that the NF-κB-dependent inflammatory response is selectively inhibited by ablating LSD1 with negligible impact on antiviral interferon response. LSD1 ablation additionally unleashed an interferon-independent antiviral response and blocked viral egress through the lysosomal pathway. A cell-intrinsic antiviral and anti-inflammatory activity of LSD1 inhibition was confirmed on in vitro and a recently developed aerosolized in vivo model of human SARS-COV2 infection. These results show that LSD1 controls innate responses against coronaviruses at multiple levels and provide a mechanistic rationale for repurposing LSD1 inhibitors, a class of drugs extensively studied in oncology, for Covid-19 treatment.

ORGANISM(S): Mus musculus

PROVIDER: GSE169399 | GEO | 2023/06/24

REPOSITORIES: GEO

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Project description:The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. Small non-coding RNAs (sncRNAs) are known to play important roles in almost all biological processes. In the context of viral infections, sncRNAs have been shown to regulate the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK‐RNA‐seq, a modified next‐generation sequencing (NGS), we recently found that nasopharyngeal swabs (NPS) samples from SARS-CoV-2 positive and negative subjects show a significant difference in sncRNA profiles. There are about 166 SARS-CoV- 2-impacted sncRNAs. Among them, tRFs are the most significantly affected and almost all impacted tRFs are derived from the 5’-end of tRNAs (tRF5). Using a modified qRT-PCR, which was recently developed to specifically quantify tRF5s by isolating the tRF signals from its corresponding parent tRNA signals, we validated that tRF5s derived from tRNA GluCTC (tRF5-GluCTC), LysCTT (tRF5-LysCTT), ValCAC (tRF5-ValCAC), CysGCA (tRF5-CysGCA) and GlnCTG (tRF5-GlnCTG) are enhanced in NPS samples of SARS-CoV2 patients and SARS-CoV2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several sncRNAs derived from the virus (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3’-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs.

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The lysine demethylase LSD1 controls the balance between inflammatory and antiviral responses against coronaviruses

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