Blocking of doublecortin-like kinase 1-regulated SARS-CoV-2 replication cycle restores cell signaling network

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can lead to fatal outcomes for subgroups of patients with pre-existing co-morbidities. We previously reported a significant association between high expression levels of a cancer stem cell protein, doublecortin-like kinase 1 (DCLK1), in the lungs and macrophages of SARS-CoV-2-infected patients and the severity of coronavirus disease 2019 (COVID-19). Herein, we demonstrate a pivotal role of DCLK1 in the viral replication cycle and the dysregulation of cell signaling that contributes to SARS-CoV-2 pathology. Through CRISPR/Cas9-mediated DCLK1 knockout and inhibition of its kinase using a small molecule kinase inhibitor of DCLK1 (DCLK1-IN-1), we effectively blocked the viral replication-transcription processes. Furthermore, DCLK1 inhibition reversed the virus-induced positive and/or negative modulation of the cellular interactome and signaling pathways. We observed a decrease in the phosphorylation of a serine/arginine-rich region in the nucleocapsid protein, which regulates viral replication and packaging, upon treatment with DCLK1-IN-1. In a murine model of COVID-19, intranasal inoculation of SARS-CoV-2 induced severe lung pathology accompanied by increased DCLK1 expression, high titers of viral genomic and subgenomic RNAs, and elevated levels of inflammatory cytokines (interleukin-6 and tumor necrosis factor alpha). Remarkably, treatment of infected mice with DCLK1-IN-1 reduced viral RNAs, downregulated inflammatory cytokines, restored normal cell signaling pathways, and improved lung pathology. In conclusion, our findings underscore the crucial role of DCLK1 in SARS-CoV-2 pathology and suggest it as a promising target for therapeutic intervention.

Automated summary

The study reveals the crucial role of DCLK1 in SARS-CoV-2 pathology, showing that inhibition of DCLK1 can effectively block viral replication and transcription processes and reverse virus-induced dysregulation of cell signaling pathways. Furthermore, treatment with DCLK1-IN-1 reduces viral RNA levels, downregulates inflammatory cytokines, restores normal cell signaling pathways, and improves lung pathology.