Selective cleavage of ncRNA and antiviral activity by RNase2/EDN in THP1-induced macrophages

Abstract

RNase2 is the member of the RNaseA family most abundant in macrophages. Here, we knocked out RNase2 in THP-1 cells and analysed the response to Respiratory Syncytial Virus (RSV). RSV induced RNase2 expression, which significantly enhanced cell survival. Next, by cP-RNAseq sequencing, which amplifies the cyclic-phosphate endonuclease products, we analysed the ncRNA population. Among the ncRNAs accumulated in WT vs KO cells, we found mostly tRNA-derived fragments (tRFs) and second miRNAs. Differential sequence coverage identified tRFs from only few parental tRNAs, revealing a predominant cleavage at anticodon and d-loops at U/C (B1) and A (B2) sites. Selective tRNA cleavage was confirmed in vitro using the recombinant protein. Likewise, only few miRNAs were significantly more abundant in WT vs RNase2-KO cells. Complementarily, by screening of a tRF & tiRNA array, we identified an enriched population associated to RNase2 expression and RSV exposure. The results confirm the protein antiviral action and provide the first evidence of its cleavage selectivity on ncRNAs. Graphical abstract

Reconstructed Genome-Scale Metabolic Model Characterizes Adaptive Metabolic Flux Changes in Peripheral Blood Mononuclear Cells in Severe COVID-19 Patients

“…Additionally, some key up-regulated genes are related to SARS-CoV-2 infection ( Table S1 ). For example, ribonuclease A family member 2 (RNASE2) exhibits anti-viral capacity [ 32 ]; the up-regulation of thioredoxin domain containing 5 (TXNDC5) is induced by hypoxia [ 33 ]; marginal zone B and B1 cell-specific protein (MZB1) is involved in humoral immunity up-regulation in lung regional lymph nodes of severe COVID-19 patients [ 34 ]; lactotransferrin (LTF) displays anti-inflammatory capacity, and competes for binding receptors with SARS-CoV-2 [ 35 ]. Such intense activation of immune-related genes is the major response of severe patients to SARS-CoV-2 infection.…”

Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines

“…ANG cleavage is mainly discussed here, but other concomitant pathways have been described. For instance, Dicer cleaves tRNAs into miR-like fragments (tRFs) [63] , [64] and another Dicer- and ANG-independent pathways have been reported [2] , [7] , [65] . These multiple and overlapping tRNA cleavage pathways create an impressive number of tRNA-derived small RNAs, thus appealing for more detailed characterization.…”

Role of the Ribonuclease ONCONASE in miRNA Biogenesis and tRNA Processing: Focus on Cancer and Viral Infections

“…RNases play a key role in immune defense, since it is well known their engagement in the protection of cells and organisms from microbes, especially viruses. Interestingly, Boix and coworkers recently found that RNase2 exerts its antiviral activity, in a cell line of human macrophages, by cleaving tRNAs and other ncRNA species [ 60 , 155 ].…”