Transcriptomics-driven antiviral drug screening identifies ATF6 as a homeostatic regulator of ER stress and innate immunity.

introductionSARS-CoV-2 caused a global pandemic with widespread devastation on health system and many other aspects. Traditional drug development strategies have primarily focused on single targets in either the virus or host cells. While these strategies can significantly inhibit viral replication at the cellular level, the clinical efficacy remains difficult to guarantee, and many host-targeting drugs are associated with relatively high toxicity and side effects. Therefore, to prepare for the possible future viral pandemics, there remains an urgent need for effective therapeutic strategies that are comprehensive and easy to administer.

objectivesThe main objective of this study is to identify the optimal antiviral transcriptomic response of host cells based on the "dynamic virus-host interaction", conduct large-scale drug screening, and discover pan-transcriptomic responses or pan-targets capable of inhibiting viral replication through the integrated analysis of pharmacologically active compounds.

methodsWe used deep RNA sequencing techniques to study gene expression changes of host cells (Huh7 and Vero-E6) along with viral replication dynamics upon SARS-CoV-2 infection. The imbalanced host genes serve as the SARS-CoV-2 expression signatures for computational screening of the compounds with anti-viral potential, following the concept of Connectivity Map (cMap). Furthermore, the gene perturbation signatures of effective compounds were integrated via bioinformatics approaches, and combined with techniques such as CRISPR-Cas9 and Western Blot (WB) to elucidate the targets and mechanisms underlying viral replication inhibition.

resultsThis study found that acute activation of host innate immunity pathway plays an essential role to suppress SARS-CoV-2 replication, and a variety of compounds with pharmacological activity against SARS-CoV-2 were successfully identified. Further transcriptomic comparison revealed the endoplasmic reticulum (ER) stress as the key machinery underneath the efficacy difference. Mechanistically, ATF6, an ER stress regulator, promotes viral replication by tempering PERK/IRE1-driven rapid activation of NF-κB and innate immunity (e.g., IL-1α, TNF-α).

conclusionThis work positions ER stress modulation, particularly ATF6 targeting, as a strategy to balance antiviral defense and inflammatory toxicity, offering a roadmap for pan-coronavirus therapeutics. With these results, we established a paradigm for transcriptomic signature-based drug screening system for future treatment development of virus pandemics.