Dataset Information

RNA-seq profiling following a 5’ isomiR transfection

ABSTRACT: Annotated canonical miRNAs (anomiRs) are critical regulators of COVID-19 pathogenesis. 5’ isomiRs, which exhibit a shifted 5’ end and distinct seed region compared to their cognate anomiRs, represent an essential component of the miRNAome. However, little is known about their repertoire and expression dynamics following SARS-CoV-2 infection. 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 hours after SARS-CoV-2 infection. Compared to anomiRs, 5’ isomiRs were preferentially induced at 24 hours 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 hours 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 expression alterations of AGO-loaded 5’ isomiRs in SARS-CoV-2-infected lung cells. The identified regulatory effects of miR-4485-3p|+1 highlight potential roles of 5’ isomiRs in COVID-19 pathogenesis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE309153 | GEO | 2025/12/02

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:The lack of available biomarkers for diagnosing and predicting different stages of coronavirus disease 2019 (COVID-19) is currently one of the main challenges that clinicians are facing. Recent evidence indicates that the plasma levels of specific miRNAs may be significantly modified in COVID-19 patients. Large-scale deep sequencing analysis of small RNA expression was performed on plasma samples from 40 patients hospitalized for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (between March and May 2020) (median 13.50 [IQR 9–24] days since symptoms initiation) and 21 healthy noninfected individuals. Patients were categorized as hospitalized not requiring oxygen therapy (n = 6), hospitalized requiring low-flow oxygen (n = 23), and hospitalized requiring high-flow oxygen support (n = 11). A total of 1218 different micro(mi)RNAs were identified. When compared with healthy noninfected donors, SARS-CoV-2 infected patients showed significantly (fold change [FC] >1.2 and adjusted p [padj] <0.05) altered expression of 190 miRNAs. The top 10 differentially expressed (DE) miRNAs were miR-122-5p, let-7b-5p, miR-146a-5p, miR-342-3p, miR-146b-5p, miR-629-5p, miR-24-3p, miR-12136, let-7a-5p, and miR-191-5p, which displayed FC and padj values ranging from 153 to 5 and 2.51 × 10-32 to 2.21 × 10-21, respectively, which unequivocally diagnosed SARS-CoV-2 infection. No differences in blood cell counts and biochemical plasma parameters, including interleukin 6, ferritin and D-dimer, were observed between COVID-19 patients on high-flow oxygen therapy, low-flow oxygen therapy, or not requiring oxygen therapy. Notably, 31 significantly deregulated miRNAs were found when patients on high- and low-flow oxygen therapy were compared. Similarly, 6 DE miRNAs were identified between patients on high flow and those not requiring oxygen therapy. SARS-CoV-2 infection generates a specific miRNA signature in hospitalized patients. Furthermore, specific miRNA profiles are associated with COVID-19 prognosis in severe patients.

Dataset Information

RNA-seq profiling following a 5’ isomiR transfection

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets