miRCOVID-19: Potential Targets of Human miRNAs in SARS-CoV-2 for RNA-Based Drug Discovery.
Tanvir Alam,Leonard Lipovich +1 more
Reads0
Chats0
TLDR
In this article, the authors presented miRCOVID-19, a computational meta-analysis framework identifying the predicted binding sites of human microRNAs along the SARS-CoV-2 RNA genome.Abstract:
Sense-antisense interactions of long and short RNAs in human cells are integral to post-transcriptional gene regulation, in particular that of mRNAs by microRNAs. Many viruses, including severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 (the causative agent of coronavirus disease 2019, COVID-19), have RNA genomes, and interactions between host and viral RNAs, while known to be functional in other viral diseases, have not yet been investigated in COVID-19. To remedy this gap in knowledge, we present miRCOVID-19, a computational meta-analysis framework identifying the predicted binding sites of human microRNAs along the SARS-CoV-2 RNA genome. To highlight the potential relevance of SARS-CoV-2-genome-complementary miRNAs to COVID-19 pathogenesis, we assessed their expression in COVID-19-relevant tissues using public transcriptome data. miRCOVID-19 identified 14 high-confidence mature miRNAs that are highly likely to interact with the SARS-CoV-2 genome and are expressed in diverse respiratory epithelial and immune cell types that are relevant to COVID-19 pathogenesis. As a proof of principle, we have shown that human miR-122, a previously known co-factor of another RNA virus, the hepatitis C virus (HCV) whose genome it binds as a prerequisite for pathogenesis, was predicted to also bind the SARS-CoV-2 RNA genome with high affinity, suggesting the perspective of repurposing anti-HCV RNA-based drugs, such as Miravirsen, to treat COVID-19. Our study is the first to identify all high-confidence binding sites of human miRNAs in the SARS-CoV-2 genome using multiple tools. Our work directly facilitates experimental validation of the reported targets, which would accelerate RNA-based drug discovery for COVID-19 and has the potential to provide new avenues for treating symptomatic COVID-19, and block SARS-CoV-2 replication, in humans.read more
Citations
More filters
Journal ArticleDOI
Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection.
Juliana Mara Serpeloni,Quirino Alves de Lima Neto,Léia Carolina Lucio,Anelisa Ramão,Jaqueline Carvalho de Oliveira,Daniela Fiori Gradia,Danielle Malheiros,Adriano Ferrasa,Rafael D. Marchi,David Livingstone Alves Figueiredo,Wilson A. Silva,Enilze Maria de Souza Fonseca Ribeiro,Ilce Mara de Syllos Cólus,Luciane R. Cavalli +13 more
TL;DR: In this paper, the authors highlight the interaction of SARS-CoV-2 virus and host genomes, reporting the current studies on the sequence analysis of isolates and host genome from diverse world populations.
Journal ArticleDOI
Therapeutic Significance of microRNA-Mediated Regulation of PARP-1 in SARS-CoV-2 Infection.
TL;DR: In this paper, microRNA/PARP-1 axis and its therapeutic potential for COVID-19 pathologies are discussed. But, the authors do not discuss the potential of microRNAs in this context.
Journal ArticleDOI
In vitro induction of interleukin-8 by SARS-CoV-2 Spike protein is inhibited in bronchial epithelial IB3-1 cells by a miR-93-5p agomiR.
Jessica Gasparello,Elisabetta D'Aversa,Giulia Breveglieri,Monica Borgatti,Alessia Finotti,Roberto Gambari +5 more
TL;DR: In this article, the authors showed that the release of key proteins of the COVID-19 "cytokine storm" can be inhibited by mimicking the biological activity of microRNAs.
Journal ArticleDOI
Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An in Silico Analysis
TL;DR: In this paper, the functional role and mechanism of transcriptional regulation of deregulated genes in COVID-19 patients were investigated and it was observed that 66 lncRNA and 5491 protein coding gene (PCG) were deregulated in more than one experimental condition.
Journal ArticleDOI
Nucleic Acid-Based COVID-19 Therapy Targeting Cytokine Storms: Strategies to Quell the Storm
Mai Abdel Haleem Abusalah,M. Khalifa,Mohammad A. I. Al-Hatamleh,Mu'taman Jarrar,Rohimah Mohamud,Y.Y. Chan +5 more
TL;DR: This work is an up-to-date review aimed to comprehensively discuss the current nucleic acid-based therapeutics against COVID-19 and their mechanisms of action, taking into consideration the emerging SARS-CoV-2 variants of concern, as well as providing potential future directions.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
miRBase: annotating high confidence microRNAs using deep sequencing data.
Ana Kozomara,Sam Griffiths-Jones +1 more
TL;DR: An update of the miRBase database is described, including the collation and use of deep sequencing data sets to assign levels of confidence to miR base entries, and a high confidence subset of miR Base entries are provided, based on the pattern of mapped reads.
Journal ArticleDOI
miRBase: integrating microRNA annotation and deep-sequencing data
Ana Kozomara,Sam Griffiths-Jones +1 more
TL;DR: This work has mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings, which can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature micro RNAs, and allow us to revisit previous annotations.
Journal ArticleDOI
Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals.
Alba Grifoni,Daniela Weiskopf,Sydney I. Ramirez,Sydney I. Ramirez,Jose Mateus,Jennifer M. Dan,Jennifer M. Dan,Carolyn Rydyznski Moderbacher,Stephen A. Rawlings,Aaron Sutherland,Lakshmanane Premkumar,Ramesh Jadi,Daniel Marrama,Aravinda M. de Silva,April Frazier,Aaron F. Carlin,Jason A. Greenbaum,Bjoern Peters,Bjoern Peters,Florian Krammer,Davey M. Smith,Shane Crotty,Shane Crotty,Alessandro Sette,Alessandro Sette +24 more
TL;DR: Using HLA class I and II predicted peptide ‘megapools’, circulating SARS-CoV-2−specific CD8+ and CD4+ T cells were identified in ∼70% and 100% of COVID-19 convalescent patients, respectively, suggesting cross-reactive T cell recognition between circulating ‘common cold’ coronaviruses and SARS.