MEK1/2 inhibitor ATR-002 reshapes host transcriptome and modulates immune regulatory genes in SARS-CoV-2 infection

Abstract

Introduction: SARS-CoV-2 portrays a public health threat because severe progression of infections can lead to hospitalization. Severity is often characterized by a systemic inflammatory response in later stages, along with disbalance in cytokine production, multi-organ failure, or acute respiratory distress syndrome (ARDS). As severe infections can be challenging due to limited treatment windows for direct-acting antivirals, host-targets, e.g., the Raf/MEK/ERK signaling cascade, came into focus. Specifically, MEK1/2 has been suggested as a target for antiviral and anti-inflammatory therapy. A recent phase II clinical trial showed the efficacy of the MEK1/2 inhibitor zapnometinib (ZMN/ATR-002) in hospitalized COVID-19 patients. The anti-inflammatory action of ATR-002 was only studied on some candidate cytokines.

Methods: To generate a comprehensive overview of transcriptional effects on immune regulatory genes, we performed a transcriptome analysis of SARS-CoV-2-infected Calu-3 cells in the presence or absence of ATR-002.

Results: Gene expression data revealed significant upregulation of innate immune-response-related genes, e.g., cytokines (CXCL10 and CCL5), which are associated with severe cases of COVID-19, or ISGs (MX1 and OASL) induced by the infection. ATR-002 could reverse this effect in the infection. To exclude the possibility that regulated immune-response-related genes are not affected by the reduced viral load upon inhibitor treatment, but by the pathway interference itself, MEK1/2 inhibition in a non-infectious scenario was tested. Lowered immune regulatory gene expression was traced back to impaired viral replication, as shown by different genes affected in the non-infected contrast. However, some target genes (EGR1, IFNL1, and NLRP1), which could be connected to transcriptional regulation via the Raf/MEK/ERK axis, proved to be involved in the modulation of innate immunity. Especially NLRP1 expression was newly identified as a target of MEK1/2 inhibition, which links Raf/MEK/ERK signaling to caspase-1 activity and the subsequent processing of IL-1β, a major driver of hyperinflammation. MEK1/2-inhibition-mediated regulation of other targets, such as EGR1, may exert additional immune regulatory processes, influencing inflammation in SARS-CoV-2 infections.

Discussion: With our analysis of transcriptional regulation after SARS-CoV-2 infection and the potential influence of ATR-002, we were able to identify ERK1/2-dependent gene expression and candidate genes (EGR1, IFNL1, and NLRP1), which could be involved in the regulation of innate immune-response-related processes.

Keywords: MEK; SARS-CoV-2; immune response; inhibitor; transcriptome; virus.