IsomiRome analysis reveals dysregulation of 5’ isomiRs during SARS-CoV-2 infection

Annotated canonical miRNAs (anomiRs) are critical regulators of COVID-19 pathogenesis. Their 5' isomiR counterparts, which harbor a shifted 5' end and an altered seed region relative to cognate anomiRs, represent an essential yet understudied component of the miRNAome. Herein, we performed an integrative analysis to investigate the expression and regulation of 5' isomiRs in SARS-CoV-2-infected human lung cells. Using Argonaute (AGO) immunoprecipitated small-RNA sequencing data, we established a repertoire of AGO-loaded 5' isomiRome encompassing 826 5' isomiRs from SARS-CoV-2-infected lung cells. A total of 54 5' isomiRs were differentially expressed, with the majority showing dysregulation 24 h after SARS-CoV-2 infection. Compared to anomiRs, 5' isomiRs were preferentially induced at 24 h post SARS-CoV-2 infection, including six 5' isomiRs derived from miR-4485 precursor. By focusing on a 5' isomiR of miR-4485-3p exhibiting one nucleotide downstream shift of the 5' end (miR-4485-3p|+1), we demonstrated that miR-4485-3p|+ 1 overexpression significantly repressed genes involved in cellular processes relating to cell cycle, cytoplasmic translation, and carbohydrate derivative metabolic process. Importantly, transcriptome integration further revealed that these cellular processes repressed by miR-4485-3p|+ 1 overexpression were strongly downregulated at 24 h following SARS-CoV-2 infection. Moreover, 26 out of 43 (60.5 %) hub genes co-repressed by miR-4485-3p|+ 1 and SARS-CoV-2 infection in these three cellular processes have reported association with COVID-19 in the literature. Taken together, our findings reveal the repertoire and temporal dynamics of AGO-loaded 5' isomiRs in SARS-CoV-2-infected lung cells and identify miR-4485-3p|+ 1 as a potential regulator of host pathways relevant to COVID-19 pathogenesis.