1
|
Arman K, Dalloul Z, Bozgeyik E. Emerging role of microRNAs and long non-coding RNAs in COVID-19 with implications to therapeutics. Gene 2023; 861:147232. [PMID: 36736508 PMCID: PMC9892334 DOI: 10.1016/j.gene.2023.147232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection which is commonly known as COVID-19 (COronaVIrus Disease 2019) has creeped into the human population taking tolls of life and causing tremendous economic crisis. It is indeed crucial to gain knowledge about their characteristics and interactions with human host cells. It has been shown that the majority of our genome consists of non-coding RNAs. Non-coding RNAs including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs) display significant roles in regulating gene expression in almost all cancers and viral diseases. It is intriguing that miRNAs and lncRNAs remarkably regulate the function and expression of major immune components of SARS-CoV-2. MiRNAs act via RNA interference mechanism in which they bind to the complementary sequences of the viral RNA strand, inducing the formation of silencing complex that eventually degrades or inhibits the viral RNA and viral protein expression. LncRNAs have been extensively shown to regulate gene expression in cytokine storm and thus emerges as a critical target for COVID-19 treatment. These lncRNAs also act as competing endogenous RNAs (ceRNAs) by sponging miRNAs and thus affecting the expression of downstream targets during SARS-CoV-2 infection. In this review, we extensively discuss the role of miRNAs and lncRNAs, describe their mechanism of action and their different interacting human targets cells during SARS-CoV-2 infection. Finally, we discuss possible ways how an interference with their molecular function could be exploited for new therapies against SARS-CoV-2.
Collapse
Affiliation(s)
- Kaifee Arman
- Institut de recherches cliniques de Montréal, Montréal, QC H2W 1R7, Canada.
| | - Zeinab Dalloul
- Institut de recherches cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Esra Bozgeyik
- Department of Medical Services and Techniques, Vocational School of Health Services, Adiyaman University, Adiyaman, Turkey
| |
Collapse
|
2
|
Jiang S, Chen J, Li X, Ren W, Li F, Wang T, Li C, Dong Z, Tian X, Zhang L, Wang L, Lu C, Chi J, Feng L, Yan M. Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection. BMC Genomics 2022; 23:486. [PMID: 35787252 PMCID: PMC9251034 DOI: 10.1186/s12864-022-08722-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are pivotal regulators involved in the pathogenic mechanism of multiple coronaviruses. Porcine deltacoronavirus (PDCoV) has evolved multiple strategies to escape the innate immune response of host cells, but whether ncRNAs are involved in this process during PDCoV infection is still unknown. Results In this study, the expression profiles of miRNAs, lncRNAs and mRNAs in IPEC-J2 cells infected with PDCoV at 0, 12 and 24 hours postinfection (hpi) were identified through small RNA and RNA sequencing. The differentially expressed miRNAs (DEmiRNAs), lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were screened from the comparison group of IPEC-J2 cells at 0 and 12 hpi as well as the comparison group of IPEC-J2 cells at 12 and 24 hpi. The target genes of these DEncRNAs were predicted. The bioinformatics analysis of the target genes revealed multiple significantly enriched functions and pathways. Among them, the genes that were associated with innate immunity were specifically screened. The expression of innate immunity-related ncRNAs and mRNAs was validated by RT–qPCR. Competing endogenous RNA (ceRNA) regulatory networks among innate immunity-related ncRNAs and their target mRNAs were established. Moreover, we found that the replication of PDCoV was significantly inhibited by two innate immunity-related miRNAs, ssc-miR-30c-3p and ssc-miR-374b-3p, in IPEC-J2 cells. Conclusions This study provides a data platform to conduct studies of the pathogenic mechanism of PDCoV from a new perspective and will be helpful for further elucidation of the functional role of ncRNAs involved in PDCoV escaping the innate immune response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08722-2.
Collapse
Affiliation(s)
- Shan Jiang
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Jianfei Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiuli Li
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Weike Ren
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Fengxiang Li
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Ting Wang
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Cheng Li
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Zhimin Dong
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Xiangxue Tian
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Li Zhang
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Lili Wang
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Chao Lu
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Jingjing Chi
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Minghua Yan
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China. .,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China.
| |
Collapse
|
3
|
Jin XH, Zhang YF, Yuan YX, Han L, Zhang GP, Hu H. Isolation, characterization and transcriptome analysis of porcine deltacoronavirus strain HNZK-02 from Henan Province, China. Mol Immunol 2021; 134:86-99. [PMID: 33740580 DOI: 10.1016/j.molimm.2021.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/26/2020] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
Porcine deltacoronavirus (PDCoV), an emerging porcine enteropathogenic coronavirus, causes acute watery diarrhea and vomiting in piglets. Here, we isolated a strain of PDCoV from intestinal content of a piglet with severe watery diarrhea on a farm located in Henan Province, named PDCoV strain HNZK-02. Subsequently, the complete genomes of cell-cultured PDCoV HNZK-02 passage 5 and 15 were sequenced and analyzed. There was a continuous 3-nucleotide deletion and 7 amino acid changes in S genes when compared with the other reported PDCoVs. RNA sequencing (RNA-seq)-based transcriptome analysis was used to quantitatively identify differentially expressed genes after PDCoV infection in ST cells. In total, 523 differentially expressed genes (DEGs) were identified, including 62 upregulated genes and 457 downregulated genes. The 62 upregulated genes were associated with TNF signaling pathway, cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, IL-17 signaling, chemokine signaling pathway and NF-κB signaling pathway. The significant expressing changed genes, including three antiviral genes (Mx1, OASL, OAS1) and three inflammatory chemokine related genes (CCL5, CXCL8, CXCL10) were further validated using quantitative real-time RT-PCR (qRT-PCR) assay. It showed the consistent expression patterns of the candidate genes with those from RNA-seq. Our results demonstrated that PDCoV infection activates NF-κB signaling pathway and leads to the expression of inflammatory factors, which may be related to TLRs but TLR2 is not a critical factor.In general, these results can help us to confirm the molecular regulation mechanism and also provide us a comprehensive resource of PDCoV infection.
Collapse
Affiliation(s)
- Xiao-Hui Jin
- The College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Yun-Fei Zhang
- The College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Yi-Xin Yuan
- The College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Li Han
- Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, 450002, PR China
| | - Gai-Ping Zhang
- The College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Hui Hu
- The College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, PR China; Key Laboratory for Animal-derived Food Safety of Henan Province, Zhengzhou, 450002, PR China.
| |
Collapse
|
4
|
Maranon DG, Anderson JR, Maranon AG, Wilusz J. The interface between coronaviruses and host cell RNA biology: Novel potential insights for future therapeutic intervention. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1614. [PMID: 32638509 PMCID: PMC7361139 DOI: 10.1002/wrna.1614] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022]
Abstract
Coronaviruses, including SARS-Cov-2, are RNA-based pathogens that interface with a large variety of RNA-related cellular processes during infection. These processes include capping, polyadenylation, localization, RNA stability, translation, and regulation by RNA binding proteins or noncoding RNA effectors. The goal of this article is to provide an in-depth perspective on the current state of knowledge of how various coronaviruses interact with, usurp, and/or avoid aspects of these cellular RNA biology machineries. A thorough understanding of how coronaviruses interact with RNA-related posttranscriptional processes in the cell should allow for new insights into aspects of viral pathogenesis as well as identify new potential avenues for the development of anti-coronaviral therapeutics. This article is categorized under: RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- David G Maranon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Abril G Maranon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|