Research Article
Elimination of Aicardi–Goutières syndrome protein SAMHD1 activates cellular innate immunity and suppresses SARS-CoV-2 replication

https://doi.org/10.1016/j.jbc.2022.101635Get rights and content
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The lack of antiviral innate immune responses during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is characterized by limited production of interferons (IFNs). One protein associated with Aicardi–Goutières syndrome, SAMHD1, has been shown to negatively regulate the IFN-1 signaling pathway. However, it is unclear whether elevated IFN signaling associated with genetic loss of SAMHD1 would affect SARS-CoV-2 replication. In this study, we established in vitro tissue culture model systems for SARS-CoV-2 and human coronavirus OC43 infections in which SAMHD1 protein expression was absent as a result of CRISPR–Cas9 gene KO or lentiviral viral protein X–mediated proteosomal degradation. We show that both SARS-CoV-2 and human coronavirus OC43 replications were suppressed in SAMHD1 KO 293T and differentiated THP-1 macrophage cell lines. Similarly, when SAMHD1 was degraded by virus-like particles in primary monocyte-derived macrophages, we observed lower levels of SARS-CoV-2 RNA. The loss of SAMHD1 in 293T and differentiated THP-1 cells resulted in upregulated gene expression of IFNs and innate immunity signaling proteins from several pathways, with STAT1 mRNA being the most prominently elevated ones. Furthermore, SARS-CoV-2 replication was significantly increased in both SAMHD1 WT and KO cells when expression and phosphorylation of STAT1 were downregulated by JAK inhibitor baricitinib, which over-rode the activated antiviral innate immunity in the KO cells. This further validates baricitinib as a treatment of SARS-CoV-2–infected patients primarily at the postviral clearance stage. Overall, our tissue culture model systems demonstrated that the elevated innate immune response and IFN activation upon genetic loss of SAMHD1 effectively suppresses SARS-CoV-2 replication.

Keywords

SAMHD1
SARS-CoV-2
innate immunity
JAK pathway
Stat1

Abbreviations

ACE2
angiotensin-converting enzyme 2
AGS
Aicardi–Goutières syndrome
ARHGEF5
Rho guanine nucleotide exchange factor 5
cDNA
complementary DNA
COVID-19
coronavirus disease 2019
DMEM
Dulbecco's modified Eagle's medium
FBS
fetal bovine serum
FDA
US Food and Drug Administration
HCoV-OC43
human coronavirus OC43
IFN
interferon
IRF3
IFN regulatory factor 3
ISG
IFN-stimulated gene
JAK
Janus kinase
MDM
monocyte-derived macrophage
MOI
multiplicity of infection
NSP
nonstructural protein
pSTAT1
phosphorylated form of STAT1
qRT–PCR
quantitative RT–PCR
SAMHD1
sterile alpha motif and histidine–aspartate domain–containing protein 1
SARS-CoV-2
severe acute respiratory syndrome coronavirus 2
STAT1
signal transducer and activator of transcription 1
VLP
virus-like particle
Vpx
viral protein X

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These authors contributed equally to this work.