Human RNase 2 is essential for macrophage response to viral RNA and enerates tRNA-derived small RNAs by selective cleavage at tRNA anticodon loops and CCA ends

RNase 2 is the most abundant human RNase A member in macrophages, and its expression is activated upon virus exposure. Here, we explored the protein role by co-transcriptomics of wild-type (WT) and RNase 2-knock-out (KO) macrophages in absence/presence of a virus-derived single-stranded RNA (ssRNA40). Results revealed that RNase 2 is key for maintaining cell homeostasis. RNase 2 deletion induced the expression of stress-response markers and abolished the antiviral response. In contrast, the up-regulated genes in WT macrophages participate in pro-inflammatory response through TLR8-dependent pathways and antiviral immunity, with activation of MAPK and JAK-STAT pathways. We identified five top tRNA-derived small RNAs (tDRs) in response to ssRNA40 in presence of RNase 2, showing preferential cleavage at CA and uridine rich regions of anticodon loops. Another conserved target in all RNase2-generated 3’tDRs was found at the CCA end, releasing truncated 3’-CC. Among tDRs unique for WT exposed to ssRNA40, tRNA-LysTTT 3’-half stands out with the highest significant sequence coverage difference. Last, the immune response profile of RNase 2-KO cells is mostly recovered by addition of tRNA-LysTTT digestion products generated in vitro by recombinant RNase 2, suggesting an activation mechanism mediated by tDRs. Results highlight the essential role of RNase 2 selective tRNA cleavage in antiviral response and inflammation.