Contribution of host an viral small non-coding RNAs to SARS-CoV lung pathology. Mus musculus

Severe acute respiratory syndrome coronavirus (SARS-CoV) causes lethal disease in humans, with viral E protein promoting the exacerbated inflammatory response. By deep sequencing RNAs from the lungs of infected mice, we have addressed the relevance of small, non-coding RNAs in SARS-CoV pathology. Host microRNAs (miRNAs) expressed during infection by a virulent virus encoding the E protein were significantly enriched for cytokine-mediated inflammatory pathways when compared with attenuated SARS-CoV-∆E, suggesting contribution of miRNAs to E protein-induced inflammation. The discovery of three 18-22 nt small viral RNAs (svRNAs) derived from the nsp3 and N genomic regions of SARS-CoV in mouse lung and cell cultures is also described. Depletion of these svRNAs significantly reduced viral titers and genomic RNA levels, indicating their positive contribution to virus growth. Remarkably, svRNA-N antagomirs significantly reduced in vivo lung pathology and pro-inflammatory cytokine expression, indicating that svRNAs contribute to SARS-CoV pathogenesis and highlighting the potential of these antagomirs as antivirals. Overall design: Strand-specific, single-end, reads were generated for detecting smallRNAs (18 nts or more) in lungs (mouse). Three or four replicates were prepared per sample type.

严重急性呼吸综合征冠状病毒（SARS-CoV）可引发人类致死性疾病，其病毒E蛋白可加剧炎症反应。本研究通过对感染小鼠的肺部RNA进行深度测序，探究了小型非编码RNA在SARS-CoV致病过程中的相关作用。相较于缺失E蛋白的减毒毒株SARS-CoV-∆E，编码E蛋白的强毒毒株感染过程中宿主表达的微小RNA（microRNAs, miRNAs）显著富集于细胞因子介导的炎症通路，提示miRNAs参与了E蛋白诱导的炎症反应。本研究同时报道了在小鼠肺部及细胞培养物中，从SARS-CoV的nsp3与N基因组区域衍生出的3种长度为18-22 nt的病毒小型RNA（small viral RNAs, svRNAs）。敲除这些svRNAs可显著降低病毒滴度与基因组RNA水平，表明其对病毒增殖具有正向促进作用。值得注意的是，svRNA-N拮抗寡核苷酸（antagomirs）可显著降低体内肺部病理损伤与促炎细胞因子的表达，表明svRNAs参与了SARS-CoV的致病过程，并凸显了这类拮抗寡核苷酸作为抗病毒药物的潜力。整体实验设计：本研究采用链特异性单端测序技术获取读段，以检测小鼠肺部的小型RNA（长度≥18 nt）；每种样本类型设置3至4次生物学重复。