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Molinero M, Perez-Pons M, González J, Barbé F, de Gonzalo-Calvo D. Decoding viral and host microRNA signatures in airway-derived biosamples: Insights for biomarker discovery in viral respiratory infections. Biomed Pharmacother 2024; 177:116984. [PMID: 38908203 DOI: 10.1016/j.biopha.2024.116984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024] Open
Abstract
The global public health crisis caused by the COVID-19 pandemic has intensified the global concern regarding viral respiratory tract infections. Despite their considerable impact on health, society and the economy, effective management of these conditions remains a significant challenge. Integrating high-throughput analyses is pivotal for early detection, prognostication of adverse outcomes, elucidating pathogenetic pathways and developing therapeutic approaches. In recent years, microRNAs (miRNAs), a subset of small noncoding RNAs (ncRNAs), have emerged as promising tools for molecular phenotyping. Current evidence suggests that miRNAs could serve as innovative biological markers, aiding in informed medical decision-making. The cost-effective quantification of miRNAs in standardized samples using techniques routinely employed in clinical laboratories has become feasible. In this context, samples obtained from the airways represent a valuable source of information due to their direct exposure to the infectious agent and host response within the respiratory tract. This review explores viral and host miRNA profiling in airway-derived biosamples as a source of molecular information to guide patient management, with a specific emphasis on SARS-CoV-2 infection.
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Affiliation(s)
- Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
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2
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Aghajani Mir M. Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105613. [PMID: 38844190 DOI: 10.1016/j.meegid.2024.105613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Babol University of Medical Sciences, Babol, Iran.
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3
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Zhang Y, Zhan L, Jiang X, Tang X. Comprehensive review for non-coding RNAs: From mechanisms to therapeutic applications. Biochem Pharmacol 2024; 224:116218. [PMID: 38643906 DOI: 10.1016/j.bcp.2024.116218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
Non-coding RNAs (ncRNAs) are an assorted collection of transcripts that are not translated into proteins. Since their discovery, ncRNAs have gained prominence as crucial regulators of various biological functions across diverse cell types and tissues, and their abnormal functioning has been implicated in disease. Notably, extensive research has focused on the relationship between microRNAs (miRNAs) and human cancers, although other types of ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as significant contributors to human disease. In this review, we provide a comprehensive summary of our current knowledge regarding the roles of miRNAs, lncRNAs, and circRNAs in cancer and other major human diseases, particularly cancer, cardiovascular, neurological, and infectious diseases. Moreover, we discuss the potential utilization of ncRNAs as disease biomarkers and as targets for therapeutic interventions.
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Affiliation(s)
- YanJun Zhang
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, Jiangsu, 223005, China
| | - Lijuan Zhan
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, Jiangsu, 223005, China
| | - Xue Jiang
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, Jiangsu, 223005, China.
| | - Xiaozhu Tang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Chen B, Cao G, Chen Y, Zhang T, Zhou G, Yang X. Reduced cold tolerance of viral-infected leafhoppers attenuates viral persistent epidemics. mBio 2024; 15:e0321123. [PMID: 38564693 PMCID: PMC11077983 DOI: 10.1128/mbio.03211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Most arthropod-borne viruses produce intermittent epidemics in infected plants. However, the underlying mechanisms of these epidemics are unclear. Here, we demonstrated that rice stripe mosaic virus (RSMV), a viral pathogen, significantly increases the mortality of its overwintering vector, the leafhopper species Recilia dorsalis. Cold-stress assays indicated that RSMV reduces the cold tolerance of leafhoppers, a process associated with the downregulation of leafhopper cuticular protein genes. An RSMV-derived small RNA (vsiR-t00355379) was found to facilitate the downregulation of a leafhopper endocuticle gene that is mainly expressed in the abdomen (named RdABD-5) and is conserved across dipteran species. The downregulation of RdABD-5 expression in R. dorsalis resulted in fewer and thinner endocuticle lamellae, leading to decreased cold tolerance. This effect was correlated with a reduced incidence rate of RSMV in early-planted rice plants. These findings contribute to our understanding of the mechanism by which viral pathogens reduce cold tolerance in arthropod vectors and suggest an approach to managing the fluctuating prevalence of arboviruses. IMPORTANCE Increasing arthropod vector dispersal rates have increased the susceptibility of crop to epidemic viral diseases. However, the incidence of some viral diseases fluctuates annually. In this study, we demonstrated that a rice virus reduces the cold tolerance of its leafhopper vector, Recilia dorsalis. This effect is linked to the virus-derived small RNA-mediated downregulation of a gene encoding a leafhopper abdominal endocuticle protein. Consequently, the altered structural composition of the abdominal endocuticle reduces the overwinter survival of leafhoppers, resulting in a lower incidence of RSMV infection in early-planted rice plants. Our findings illustrate the important roles of RNA interference in virus-vector insect-environment interactions and help explain the annual fluctuations of viral disease epidemics in rice fields.
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Affiliation(s)
- Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Gehui Cao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yulu Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
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5
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Cecere G. Epigenetic and gene regulatory functions of small RNAs. C R Biol 2024; 346:75-77. [PMID: 38113091 DOI: 10.5802/crbiol.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 12/21/2023]
Abstract
In this review article, I summarize the intervention I made during the "Hommage à François Gros" held at the Institut Pasteur in Paris on the 25th of April, 2023. I discuss how the discovery of the existence of an RNA intermediate between genetic information and protein translation has changed our perspective on the role of RNA in gene regulation in these past years. I also discuss new emerging paradigms, highlighting the role of RNA in heritable information similar to the well-known DNA function.
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Driedonks TA, Nyberg LH, Conte A, Ma Z, Pekosz A, Duban E, Tonevitsky A, Sültmann H, Turchinovich A, Witwer KW. Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs. Heliyon 2024; 10:e24570. [PMID: 38314306 PMCID: PMC10837498 DOI: 10.1016/j.heliyon.2024.e24570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/06/2024] Open
Abstract
RNA viruses have been shown to express various short RNAs, some of which have regulatory roles during replication, transcription, and translation of viral genomes. However, short viral RNAs generated from SARS-CoV-1 and SARS-CoV-2 genomic RNAs remained largely unexplored, possibly due limitations of the widely used library preparation methods for small RNA deep sequencing and corresponding data processing. By analyzing publicly available small RNA sequencing datasets, we observed that human Calu-3 cells infected by SARS-CoV-1 or SARS-CoV-2 accumulate multiple previously unreported short viral RNAs. In addition, we verified the presence of the five most abundant SARS-CoV-2 short viral RNAs in SARS-CoV-2-infected human lung adenocarcinoma cells by quantitative PCR. Interestingly, the copy number of the observed SARS-CoV-2 short viral RNAs dramatically exceeded the expression of previously reported viral microRNAs in the same cells. We hypothesize that the reported SARS-CoV-2 short viral RNAs could serve as biomarkers for early infection stages due to their high abundance. Furthermore, unlike SARS-CoV-1, the SARS-CoV-2 infection induced significant (Benjamini-Hochberg-corrected p-value <0.05) deregulation of Y-RNA, transfer RNA, vault RNA, as well as more than 300 endogenous short RNAs that aligned predominantly to human protein-coding and long noncoding RNA transcripts. In particular, more than 20-fold upregulation of reads derived from Y-RNA (and several transfer RNAs) have been documented in RNA-seq datasets from SARS-CoV-2 infected cells. Finally, a significant proportion of short RNAs derived from full-length viral genomes also aligned to various human genome (hg38) sequences, suggesting opportunities to investigate regulatory roles of short viral RNAs during infection. Further characterization of the small RNA landscape of both viral and host genomes is clearly warranted to improve our understanding of molecular events related to infection and to design more efficient strategies for therapeutic interventions as well as early diagnosis.
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Affiliation(s)
- Tom A.P. Driedonks
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lyle H. Nyberg
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Zexu Ma
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Heidelberg Biolabs GmbH, Heidelberg, Germany
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Heidelberg University, Heidelberg/Mannheim, Germany
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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7
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Tucker EJ, Wong SW, Marri S, Ali S, Fedele AO, Michael MZ, Rojas-Canales D, Li JY, Lim CK, Gleadle JM. SARS-CoV-2 produces a microRNA CoV2-miR-O8 in patients with COVID-19 infection. iScience 2024; 27:108719. [PMID: 38226175 PMCID: PMC10788221 DOI: 10.1016/j.isci.2023.108719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Many viruses produce microRNAs (miRNAs), termed viral miRNAs (v-miRNAs), with the capacity to target host gene expression. Bioinformatic and cell culture studies suggest that SARS-CoV-2 can also generate v-miRNAs. This patient-based study defines the SARS-CoV-2 encoded small RNAs present in nasopharyngeal swabs of patients with COVID-19 infection using small RNA-seq. A specific conserved sequence (CoV2-miR-O8) is defined that is not expressed in other coronaviruses but is preserved in all SARS-CoV-2 variants. CoV2-miR-O8 is highly represented in nasopharyngeal samples from patients with COVID-19 infection, is detected by RT-PCR assays in patients, has features consistent with Dicer and Drosha generation as well as interaction with Argonaute and targets specific human microRNAs.
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Affiliation(s)
- Elise J. Tucker
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Soon Wei Wong
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Shashikanth Marri
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Saira Ali
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Anthony O. Fedele
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
| | - Michael Z. Michael
- College of Medicine and Public Health, Flinders University, SA, Australia
- Department of Gastroenterology, Flinders Medical Centre, SA, Australia
| | - Darling Rojas-Canales
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Jordan Y. Li
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
| | - Chuan Kok Lim
- Infectious Diseases Laboratories, SA Pathology, SA, Australia
| | - Jonathan M. Gleadle
- Department of Renal Medicine, Flinders Medical Centre, SA, Australia
- College of Medicine and Public Health, Flinders University, SA, Australia
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8
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Mihaescu G, Chifiriuc MC, Filip R, Bleotu C, Ditu LM, Constantin M, Cristian RE, Grigore R, Bertesteanu SV, Bertesteanu G, Vrancianu CO. Role of interferons in the antiviral battle: from virus-host crosstalk to prophylactic and therapeutic potential in SARS-CoV-2 infection. Front Immunol 2024; 14:1273604. [PMID: 38288121 PMCID: PMC10822962 DOI: 10.3389/fimmu.2023.1273604] [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: 08/06/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Mammalians sense antigenic messages from infectious agents that penetrate the respiratory and digestive epithelium, as well as signals from damaged host cells through membrane and cytosolic receptors. The transduction of these signals triggers a personalized response, depending on the nature of the stimulus and the host's genetics, physiological condition, and comorbidities. Interferons (IFNs) are the primary effectors of the innate immune response, and their synthesis is activated in most cells within a few hours after pathogen invasion. IFNs are primarily synthesized in infected cells, but their anti-infective effect is extended to the neighboring cells by autocrine and paracrine action. The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in 2019 was a stark reminder of the potential threat posed by newly emerging viruses. This pandemic has also triggered an overwhelming influx of research studies aiming to unveil the mechanisms of protective versus pathogenic host immune responses induced by SARS-CoV-2. The purpose of this review is to describe the role of IFNs as vital players in the battle against SARS-CoV-2 infection. We will briefly characterize and classify IFNs, present the inductors of IFN synthesis, their sensors, and signaling pathways, and then discuss the role of IFNs in controlling the evolution of SARS-CoV-2 infection and its clinical outcome. Finally, we will present the perspectives and controversies regarding the prophylactic and therapeutic potential of IFNs in SARS-CoV-2 infection.
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Affiliation(s)
- Grigore Mihaescu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Department of Life, Medical and Agricultural Sciences, Biological Sciences Section, Academy of Romanian Scientists, Bucharest, Romania
| | - Roxana Filip
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, Suceava, Romania
- Microbiology Department, Suceava Emergency County Hospital, Suceava, Romania
| | - Coralia Bleotu
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Cellular and Molecular Pathology Department, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Lia Mara Ditu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Marian Constantin
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Institute of Biology of Romanian Academy, Bucharest, Romania
| | - Roxana-Elena Cristian
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Raluca Grigore
- ENT Department, University of Medicine and Pharmacy Carol Davila and Coltea Clinical Hospital, Bucharest, Romania
| | - Serban Vifor Bertesteanu
- ENT Department, University of Medicine and Pharmacy Carol Davila and Coltea Clinical Hospital, Bucharest, Romania
| | - Gloria Bertesteanu
- ENT Department, University of Medicine and Pharmacy Carol Davila and Coltea Clinical Hospital, Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- DANUBIUS Department, National Institute of Research and Development for Biological Sciences, Bucharest, Romania
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Wang H, Dong Y, Xu Q, Wang M, Li S, Ji Y. MicroRNA750-3p Targets Processing of Precursor 7 to Suppress Rice Black-Streaked Dwarf Virus Propagation in Vector Laodelphax striatellus. Viruses 2024; 16:97. [PMID: 38257797 PMCID: PMC10820416 DOI: 10.3390/v16010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs, which, as members of the RNA interference pathway, play a pivotal role in antiviral infection. Almost 80% of plant viruses are transmitted by insect vectors; however, little is known about the interaction of the miRNAs of insect vectors with plant viruses. Here, we took rice black-streaked dwarf virus (RBSDV), a devastating virus to rice production in eastern Asia, and the small brown planthopper, (SBPH, Laodelphax striatellus) as a model to investigate the role of microRNA750-3p (miR750-3p) in regulating viral transmission. Our results showed that Ls-miR750-3p was downregulated in RBSDV-infected SBPH and predominately expressed in the midgut of SBPH. Injection with miR750-3p agomir significantly reduced viral accumulation, and the injection with the miR750-3p inhibitor, antagomir-750-3p, dramatically promoted the viral accumulation in SBPH, as detected using RT-qPCR and Western blotting. The processing of precursor 7 (POP7), a subunit of RNase P and RNase MRP, was screened, identified, and verified using a dual luciferase reporter assay as one target of miR750-3p. Knockdown of POP7 notably increased RBSDV viral propagation in SBPH and then increased the viral transmission rate by SBPH. Taken together, our data indicate that miR750-3p targets POP7 to suppress RBSDV infection in its insect vector. These results enriched the role of POP7 in modulating virus infection in host insects and shared new insight into the function of miRNAs in plant virus and insect vector interaction.
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Affiliation(s)
| | | | | | | | | | - Yinghua Ji
- Institute of Plant Protection, Key Laboratory of Food Quality and Safety of Jiangsu Province, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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10
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Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
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Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
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11
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Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023; 15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023] Open
Abstract
Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.
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Affiliation(s)
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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12
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Naeli P, Zhang X, Snell PH, Chatterjee S, Kamran M, Ladak RJ, Orr N, Duchaine T, Sonenberg N, Jafarnejad SM. The SARS-CoV-2 protein NSP2 enhances microRNA-mediated translational repression. J Cell Sci 2023; 136:jcs261286. [PMID: 37732428 PMCID: PMC10617620 DOI: 10.1242/jcs.261286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
Viruses use microRNAs (miRNAs) to impair the host antiviral response and facilitate viral infection by expressing their own miRNAs or co-opting cellular miRNAs. miRNAs inhibit translation initiation of their target mRNAs by recruiting the GIGYF2-4EHP (or EIF4E2) translation repressor complex to the mRNA 5'-cap structure. We recently reported that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-encoded non-structural protein 2 (NSP2) interacts with GIGYF2. This interaction is critical for blocking translation of the Ifnb1 mRNA that encodes the cytokine interferon β, and thereby impairs the host antiviral response. However, it is not known whether NSP2 also affects miRNA-mediated silencing. Here, we demonstrate the pervasive augmentation of miRNA-mediated translational repression of cellular mRNAs by NSP2. We show that NSP2 interacts with argonaute 2 (AGO2), the core component of the miRNA-induced silencing complex (miRISC), via GIGYF2 and enhances the translational repression mediated by natural miRNA-binding sites in the 3' untranslated region of cellular mRNAs. Our data reveal an additional layer of the complex mechanism by which SARS-CoV-2 and likely other coronaviruses manipulate the host gene expression program by co-opting the host miRNA-mediated silencing machinery.
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Affiliation(s)
- Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Xu Zhang
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Patric Harris Snell
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Susanta Chatterjee
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Muhammad Kamran
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Reese Jalal Ladak
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Nick Orr
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Thomas Duchaine
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, H3A 1A3, Canada
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
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13
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Moatar AI, Chis AR, Romanescu M, Ciordas PD, Nitusca D, Marian C, Oancea C, Sirbu IO. Plasma miR-195-5p predicts the severity of Covid-19 in hospitalized patients. Sci Rep 2023; 13:13806. [PMID: 37612439 PMCID: PMC10447562 DOI: 10.1038/s41598-023-40754-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Predicting the clinical course of Covid-19 is a challenging task, given the multi-systemic character of the disease and the paucity of minimally invasive biomarkers of disease severity. Here, we evaluated the early (first two days post-admission) level of circulating hsa-miR-195-5p (miR-195, a known responder to viral infections and SARS-CoV-2 interactor) in Covid-19 patients and assessed its potential as a biomarker of disease severity. We show that plasma miR-195 correlates with several clinical and paraclinical parameters, and is an excellent discriminator between the severe and mild forms of the disease. Our Gene Ontology analysis of miR-195 targets differentially expressed in Covid-19 indicates a strong impact on cardiac mitochondria homeostasis, suggesting a possible role in long Covid and chronic fatigue syndrome (CFS) syndromes.
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Affiliation(s)
- Alexandra Ioana Moatar
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
- Doctoral School, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
| | - Aimee Rodica Chis
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
- Center for Complex Network Science, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
| | - Mirabela Romanescu
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
- Doctoral School, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
| | - Paula-Diana Ciordas
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
- Doctoral School, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
| | - Diana Nitusca
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
- Doctoral School, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
- Center for Complex Network Science, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania
| | - Cristian Oancea
- Department of Infectious Diseases, Discipline of Pulmonology, University of Medicine and Pharmacy "Victor Babes", E. Murgu Square no.2, 300041, Timisoara, Romania
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases, "Victor Babes" University of Medicine and Pharmacy Timisoara, E. Murgu Square 2, 300041, Timisoara, Romania
| | - Ioan-Ovidiu Sirbu
- Department of Biochemistry and Pharmacology, Discipline of Biochemistry, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania.
- Center for Complex Network Science, University of Medicine and Pharmacy "Victor Babes", E Murgu Square no.2, 300041, Timisoara, Romania.
- Timisoara Institute of Complex Systems, 18 Vasile Lucaciu Str, 300044, Timisoara, Romania.
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14
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Lopez-Orozco J, Fayad N, Khan JQ, Felix-Lopez A, Elaish M, Rohamare M, Sharma M, Falzarano D, Pelletier J, Wilson J, Hobman TC, Kumar A. The RNA Interference Effector Protein Argonaute 2 Functions as a Restriction Factor Against SARS-CoV-2. J Mol Biol 2023; 435:168170. [PMID: 37271493 PMCID: PMC10238125 DOI: 10.1016/j.jmb.2023.168170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Argonaute 2 (Ago2) is a key component of the RNA interference (RNAi) pathway, a gene-regulatory system that is present in most eukaryotes. Ago2 uses microRNAs (miRNAs) and small interfering RNAs (siRNAs) for targeting to homologous mRNAs which are then degraded or translationally suppressed. In plants and invertebrates, the RNAi pathway has well-described roles in antiviral defense, but its function in limiting viral infections in mammalian cells is less well understood. Here, we examined the role of Ago2 in replication of the betacoronavirus SARS-CoV-2, the etiologic agent of COVID-19. Microscopic analyses of infected cells revealed that a pool of Ago2 closely associates with viral replication sites and gene ablation studies showed that loss of Ago2 resulted in over 1,000-fold increase in peak viral titers. Replication of the alphacoronavirus 229E was also significantly increased in cells lacking Ago2. The antiviral activity of Ago2 was dependent on both its ability to bind small RNAs and its endonuclease function. Interestingly, in cells lacking Dicer, an upstream component of the RNAi pathway, viral replication was the same as in parental cells. This suggests that the antiviral activity of Ago2 is independent of Dicer processed miRNAs. Deep sequencing of infected cells by other groups identified several SARS-CoV-2-derived small RNAs that bind to Ago2. A mutant virus lacking the most abundant ORF7A-derived viral miRNA was found to be significantly less sensitive to Ago2-mediated restriction. This combined with our findings that endonuclease and small RNA-binding functions of Ago2 are required for its antiviral function, suggests that Ago2-small viral RNA complexes target nascent viral RNA produced at replication sites for cleavage. Further studies are required to elucidate the processing mechanism of the viral small RNAs that are used by Ago2 to limit coronavirus replication.
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Affiliation(s)
- Joaquin Lopez-Orozco
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
| | - Nawell Fayad
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
| | - Juveriya Qamar Khan
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Alberto Felix-Lopez
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
| | - Mohamed Elaish
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
| | - Megha Rohamare
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Maansi Sharma
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Canada; Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Joyce Wilson
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Tom C Hobman
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada; Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada.
| | - Anil Kumar
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada.
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15
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Rojas-Cruz AF, Bermúdez-Santana CI. Computational Prediction of RNA-RNA Interactions between Small RNA Tracks from Betacoronavirus Nonstructural Protein 3 and Neurotrophin Genes during Infection of an Epithelial Lung Cancer Cell Line: Potential Role of Novel Small Regulatory RNA. Viruses 2023; 15:1647. [PMID: 37631989 PMCID: PMC10458423 DOI: 10.3390/v15081647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Whether RNA-RNA interactions of cytoplasmic RNA viruses, such as Betacoronavirus, might end in the biogenesis of putative virus-derived small RNAs as miRNA-like molecules has been controversial. Even more, whether RNA-RNA interactions of wild animal viruses may act as virus-derived small RNAs is unknown. Here, we address these issues in four ways. First, we use conserved RNA structures undergoing negative selection in the genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 circulating in different bat species, intermediate animals, and human hosts. Second, a systematic literature review was conducted to identify Betacoronavirus-targeting hsa-miRNAs involved in lung cell infection. Third, we employed sophisticated long-range RNA-RNA interactions to refine the seed sequence homology of hsa-miRNAs with conserved RNA structures. Fourth, we used high-throughput RNA sequencing of a Betacoronavirus-infected epithelial lung cancer cell line (Calu-3) to validate the results. We proposed nine potential virus-derived small RNAs: two vsRNAs in SARS-CoV (Bats: SB-vsRNA-ORF1a-3p; SB-vsRNA-S-5p), one vsRNA in MERS-CoV (Bats: MB-vsRNA-ORF1b-3p), and six vsRNAs in SARS-CoV-2 (Bats: S2B-vsRNA-ORF1a-5p; intermediate animals: S2I-vsRNA-ORF1a-5p; and humans: S2H-vsRNA-ORF1a-5p, S2H-vsRNA-ORF1a-3p, S2H-vsRNA-ORF1b-3p, S2H-vsRNA-ORF3a-3p), mainly encoded by nonstructural protein 3. Notably, Betacoronavirus-derived small RNAs targeted 74 differentially expressed genes in infected human cells, of which 55 upregulate the molecular mechanisms underlying acute respiratory distress syndrome (ARDS), and the 19 downregulated genes might be implicated in neurotrophin signaling impairment. These results reveal a novel small RNA-based regulatory mechanism involved in neuropathogenesis that must be further studied to validate its therapeutic use.
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Affiliation(s)
- Alexis Felipe Rojas-Cruz
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
- Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Clara Isabel Bermúdez-Santana
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
- Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
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16
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Ruivinho C, Gama-Carvalho M. Small non-coding RNAs encoded by RNA viruses: old controversies and new lessons from the COVID-19 pandemic. Front Genet 2023; 14:1216890. [PMID: 37415603 PMCID: PMC10322155 DOI: 10.3389/fgene.2023.1216890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The recurring outbreaks caused by emerging RNA viruses have fostered an increased interest in the research of the mechanisms that regulate viral life cycles and the pathological outcomes associated with infections. Although interactions at the protein level are well-studied, interactions mediated by RNA molecules are less explored. RNA viruses can encode small non-coding RNAs molecules (sncRNAs), including viral miRNAs (v-miRNAs), that play important roles in modulating host immune responses and viral replication by targeting viral or host transcripts. Starting from the analysis of public databases compiling the known repertoire of viral ncRNA molecules and the evolution of publications and research interests on this topic in the wake of the COVID-19 pandemic, we provide an updated view on the current knowledge on viral sncRNAs, with a focus on v-miRNAs encoded by RNA viruses, and their mechanisms of action. We also discuss the potential of these molecules as diagnostic and prognostic biomarkers for viral infections and the development of antiviral therapies targeting v-miRNAs. This review emphasizes the importance of continued research efforts to characterize sncRNAs encoded by RNA viruses, identifies the most relevant pitfalls in the study of these molecules, and highlights the paradigm changes that have occurred in the last few years regarding their biogenesis, prevalence and functional relevance in the context of host-pathogen interactions.
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17
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Yao T, Foo C, Zheng G, Huang R, Li Q, Shen J, Wang Z. Insight into the mechanisms of coronaviruses evading host innate immunity. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166671. [PMID: 36858323 PMCID: PMC9968664 DOI: 10.1016/j.bbadis.2023.166671] [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: 06/19/2022] [Revised: 09/15/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023]
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) induced coronavirus disease 2019 (COVID-19) has recently caused a pandemic. Patients with COVID-19 presented with a wide spectrum of symptoms for the disease, from entirely asymptomatic disease to full-blown pneumonia and multiorgan failures. More evidence emerged, showing the production of interferons (IFNs) in the severe cases were significantly lower than their milder counterparts, suggesting linkage of COVID-19 to impaired innate immunity. This review presents a brief overview of how coronaviruses evade innate immunity, according to the current studies about SARS-CoV and middle-east respiratory syndrome-coronavirus (MERS-CoV). The coronaviruses manage to block, escape, or dampen the innate immune response by antagonizing double-stranded RNA (dsRNA) sensor, mitochondrial antiviral-signaling protein (MAVS) and stimulator of IFN genes (STING) pathways, epigenetic modification, posttranslational modifications, and host mRNA translation. We provide novel insights into a comprehensive therapy to combat SARS-CoV-2 infection.
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Affiliation(s)
- Tengteng Yao
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200025, China
| | - Chingchoon Foo
- Family Medicine Programme College of Medicine & Veterinary Medicine, The University of Edinburgh, EH89YL Edinburgh, United Kingdom
| | - Guopei Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200025, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200025, China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200025, China
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200025, China.
| | - Zhaoyang Wang
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200092, China.
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18
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Greco F, Lorefice E, Carissimi C, Laudadio I, Ciccosanti F, Di Rienzo M, Colavita F, Meschi S, Maggi F, Fimia GM, Fulci V. A microRNA Arising from the Negative Strand of SARS-CoV-2 Genome Targets FOS to Reduce AP-1 Activity. Noncoding RNA 2023; 9:33. [PMID: 37368333 DOI: 10.3390/ncrna9030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Virus-encoded microRNAs were first reported in the Epstein-Barr virus in 2004. Subsequently, a few hundred viral miRNAs have been identified, mainly in DNA viruses belonging to the herpesviridae family. To date, only 30 viral miRNAs encoded by RNA viruses are reported by miRBase. Since the outbreak of the SARS-CoV-2 pandemic, several studies have predicted and, in some cases, experimentally validated miRNAs originating from the positive strand of the SARS-CoV-2 genome. By integrating NGS data analysis and qRT-PCR approaches, we found that SARS-CoV-2 also encodes for a viral miRNA arising from the minus (antisense) strand of the viral genome, in the region encoding for ORF1ab, herein referred to as SARS-CoV-2-miR-AS1. Our data show that the expression of this microRNA increases in a time course analysis of SARS-CoV-2 infected cells. Furthermore, enoxacin treatment enhances the accumulation of the mature SARS-CoV-2-miR-AS1 in SARS-CoV-2 infected cells, arguing for a Dicer-dependent processing of this small RNA. In silico analysis suggests that SARS-CoV-2-miR-AS1 targets a set of genes which are translationally repressed during SARS-CoV-2 infection. We experimentally validated that SARS-CoV-2-miR-AS1 targets FOS, thus repressing the AP-1 transcription factor activity in human cells.
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Affiliation(s)
- Francesco Greco
- Dipartimento di Medicina Molecolare, Università di Roma "La Sapienza", 00161 Rome, Italy
| | - Elisa Lorefice
- Dipartimento di Medicina Molecolare, Università di Roma "La Sapienza", 00161 Rome, Italy
| | - Claudia Carissimi
- Dipartimento di Medicina Molecolare, Università di Roma "La Sapienza", 00161 Rome, Italy
| | - Ilaria Laudadio
- Dipartimento di Medicina Molecolare, Università di Roma "La Sapienza", 00161 Rome, Italy
| | - Fabiola Ciccosanti
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', 00149 Rome, Italy
| | - Martina Di Rienzo
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', 00149 Rome, Italy
| | - Francesca Colavita
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', 00149 Rome, Italy
| | - Silvia Meschi
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', 00149 Rome, Italy
| | - Fabrizio Maggi
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', 00149 Rome, Italy
| | - Gian Maria Fimia
- Dipartimento di Medicina Molecolare, Università di Roma "La Sapienza", 00161 Rome, Italy
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', 00149 Rome, Italy
| | - Valerio Fulci
- Dipartimento di Medicina Molecolare, Università di Roma "La Sapienza", 00161 Rome, Italy
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy
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19
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Fossat N, Lundsgaard EA, Costa R, Rivera-Rangel LR, Nielsen L, Mikkelsen LS, Ramirez S, Bukh J, Scheel TKH. Identification of the viral and cellular microRNA interactomes during SARS-CoV-2 infection. Cell Rep 2023; 42:112282. [PMID: 36961814 PMCID: PMC9995319 DOI: 10.1016/j.celrep.2023.112282] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 01/24/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has had a tremendous impact worldwide. Mapping virus-host interactions is critical to understand disease progression. MicroRNAs (miRNAs) are important RNA regulators, but their interaction with SARS-CoV-2 RNA was not experimentally investigated. Here, using Argonaute (AGO) cross-linking immunoprecipitation combined with RNA proximity ligation (CLEAR-CLIP), we provide unbiased mapping of SARS-CoV-2/miRNA interactions. We identified six main regions on the viral RNA bound primarily by one specific miRNA. Targeted mutagenesis and AGO1-3 knockdown demonstrated that these interactions are not critical for virus production. Moreover, we identified perturbed regulation of cellular miRNA interactions during infection, including non-compensated viral sequestration of the miR-15 family. Transcriptome analysis further showed that mRNAs targeted by this miRNA family are derepressed. This work delineates the interphase between miRNA regulation and SARS-CoV-2 infection and further contributes to deciphering the full molecular interactome of this virus.
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Affiliation(s)
- Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Emma A Lundsgaard
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rui Costa
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lizandro R Rivera-Rangel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Louise Nielsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lotte S Mikkelsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, 10065 NY, USA.
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20
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Saini S, Khurana S, Saini D, Rajput S, Thakur CJ, Singh J, Jaswal A, Kapoor Y, Kumar V, Saini A. In silico analysis of genomic landscape of SARS-CoV-2 and its variant of concerns (Delta and Omicron) reveals changes in the coding potential of miRNAs and their target genes. Gene X 2023; 853:147097. [PMID: 36470485 PMCID: PMC9721428 DOI: 10.1016/j.gene.2022.147097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
COVID-19 related morbidities and mortalities are still continued due to the emergence of new variants of SARS-CoV-2. In the last few years, viral miRNAs have been the centre of study to understand the disease pathophysiology. In this work, we aimed to predict the change in coding potential of the viral miRNAs in SARS-CoV-2's VOCs, Delta and Omicron compared to the Reference (Wuhan origin) strain using bioinformatics tools. After ab-intio based screening by the Vmir tool and validation, we retrieved 22, 6, and 6 pre-miRNAs for Reference, Delta, and Omicron. Most of the predicted unique pre-miRNAs of Delta and Omicron were found to be encoded from the terminal and origin of the genomic sequence, respectively. Mature miRNAs identified by MatureBayes from the unique pre-miRNAs were used for target identification using miRDB. A total of 1786, 216, and 143 high-confidence target genes were captured for GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The GO and KEGG pathways terms analysis revealed the involvement of Delta miRNAs targeted genes in the pathways such as Human cytomegalovirus infection, Breast cancer, Apoptosis, Neurotrophin signaling, and Axon guidance whereas the Sphingolipid signaling pathway was found for the Omicron. Furthermore, we focussed our analysis on target genes that were validated through GEO's (Gene Expression Omnibus) DEGs (Differentially Expressed Genes) dataset, in which FGL2, TNSF12, OGN, GDF11, and BMP11 target genes were found to be down-regulated by Reference miRNAs and YAE1 and RSU1 by Delta. Few genes were also observed to be validated among in up-regulated gene set of the GEO dataset, in which MMP14, TNFRSF21, SGMS1, and TMEM192 were related to Reference whereas ZEB2 was detected in all three strains. This study thus provides an in-silico based analysis that deciphered the unique pre-miRNAs in Delta and Omicron compared to Reference. However, the findings need future wet lab studies for validation.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India,Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India,Corresponding authors at: Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India (S. Saini)
| | - Savi Khurana
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Dikshant Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Saru Rajput
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Jeevisha Singh
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Akanksha Jaswal
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Yogesh Kapoor
- Department of Engineering and Technology, Shoolini University, Solan, Himachal Pradesh, India
| | - Varinder Kumar
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India,Corresponding authors at: Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India (S. Saini)
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21
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Meseguer S, Rubio MP, Lainez B, Pérez-Benavente B, Pérez-Moraga R, Romera-Giner S, García-García F, Martinez-Macias O, Cremades A, Iborra FJ, Candelas-Rivera O, Almazan F, Esplugues E. SARS-CoV-2-encoded small RNAs are able to repress the host expression of SERINC5 to facilitate viral replication. Front Microbiol 2023; 14:1066493. [PMID: 36876111 PMCID: PMC9978209 DOI: 10.3389/fmicb.2023.1066493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Serine incorporator protein 5 (SERINC5) is a key innate immunity factor that operates in the cell to restrict the infectivity of certain viruses. Different viruses have developed strategies to antagonize SERINC5 function but, how SERINC5 is controlled during viral infection is poorly understood. Here, we report that SERINC5 levels are reduced in COVID-19 patients during the infection by SARS-CoV-2 and, since no viral protein capable of repressing the expression of SERINC5 has been identified, we hypothesized that SARS-CoV-2 non-coding small viral RNAs (svRNAs) could be responsible for this repression. Two newly identified svRNAs with predicted binding sites in the 3'-untranslated region (3'-UTR) of the SERINC5 gene were characterized and we found that the expression of both svRNAs during the infection was not dependent on the miRNA pathway proteins Dicer and Argonaute-2. By using svRNAs mimic oligonucleotides, we demonstrated that both viral svRNAs can bind the 3'UTR of SERINC5 mRNA, reducing SERINC5 expression in vitro. Moreover, we found that an anti-svRNA treatment to Vero E6 cells before SARS-CoV-2 infection recovered the levels of SERINC5 and reduced the levels of N and S viral proteins. Finally, we showed that SERINC5 positively controls the levels of Mitochondrial Antiviral Signalling (MAVS) protein in Vero E6. These results highlight the therapeutic potential of targeting svRNAs based on their action on key proteins of the innate immune response during SARS-CoV-2 viral infection.
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Affiliation(s)
- Salvador Meseguer
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Mari-Paz Rubio
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Begoña Lainez
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Beatriz Pérez-Benavente
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Raúl Pérez-Moraga
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Sergio Romera-Giner
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Francisco García-García
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | | | | | - Francisco J Iborra
- Biological Noise and Cell Plasticity Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Associated Unit to Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
| | - Oscar Candelas-Rivera
- Molecular and Cellular Biology Department, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Fernando Almazan
- Molecular and Cellular Biology Department, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Enric Esplugues
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, United States
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22
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Diggins NL, Hancock MH. Viral miRNA regulation of host gene expression. Semin Cell Dev Biol 2022; 146:2-19. [PMID: 36463091 PMCID: PMC10101914 DOI: 10.1016/j.semcdb.2022.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Viruses have evolved a multitude of mechanisms to combat barriers to productive infection in the host cell. Virally-encoded miRNAs are one such means to regulate host gene expression in ways that benefit the virus lifecycle. miRNAs are small non-coding RNAs that regulate protein expression but do not trigger the adaptive immune response, making them powerful tools encoded by viruses to regulate cellular processes. Diverse viruses encode for miRNAs but little sequence homology exists between miRNAs of different viral species. Despite this, common cellular pathways are targeted for regulation, including apoptosis, immune evasion, cell growth and differentiation. Herein we will highlight the viruses that encode miRNAs and provide mechanistic insight into how viral miRNAs aid in lytic and latent infection by targeting common cellular processes. We also highlight how viral miRNAs can mimic host cell miRNAs as well as how viral miRNAs have evolved to regulate host miRNA expression. These studies dispel the myth that viral miRNAs are subtle regulators of gene expression, and highlight the critical importance of viral miRNAs to the virus lifecycle.
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Affiliation(s)
- Nicole L Diggins
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, USA
| | - Meaghan H Hancock
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, USA.
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23
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Liu Y, Rao J, Mi Y, Chen L, Feng L, Li Q, Geng J, Yang X, Zhan X, Ren L, Chen J, Zhang X. SARS-CoV-2 RNAs are processed into 22-nt vsRNAs in Vero cells. Front Immunol 2022; 13:1008084. [DOI: 10.3389/fimmu.2022.1008084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global pandemic, resulting in great fatalities around the world. Although the antiviral roles of RNA interference (RNAi) have been well studied in plants, nematodes and insects, the antiviral roles of RNAi in mammalians are still debating as RNAi effect is suspected to be suppressed by interferon (IFN) signaling pathways in most cell types. To determine the role of RNAi in mammalian resistance to SARS-CoV-2, we studied the profiling of host small RNAs and SARS-CoV-2 virus-derived small RNAs (vsRNAs) in the early infection stages of Vero cells, an IFN-deficient cell line. We found that host microRNAs (miRNAs) were dysregulated upon SARS-CoV-2 infection, resulting in downregulation of microRNAs playing antiviral functions and upregulation of microRNAs facilitating viral proliferations. Moreover, vsRNA peaked at 22 nt at negative strand but not the positive strand of SARS-CoV-2 and formed successive Dicer-spliced pattern at both strands. Similar characteristics of vsRNAs were observed in IFN-deficient cell lines infected with Sindbis and Zika viruses. Together, these findings indicate that host cell may deploy RNAi pathway to combat SARS-CoV-2 infection in IFN-deficient cells, informing the alternative antiviral strategies to be developed for patients or tissues with IFN deficiency.
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24
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Viral and Host Small RNA Response to SARS-CoV-2 Infection. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13040056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
After two years into the pandemic of the coronavirus disease 2019 (COVID-19), it remains unclear how the host RNA interference (RNAi) pathway and host miRNAs regulate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and impact the development of COVID-19. In this study, we profiled small RNAs in SARS-CoV-2-infected human ACE2-expressing HEK293T cells and observed dysregulated host small RNA groups, including specific host miRNAs that are altered in response to SARS-CoV-2 infection. By comparing dysregulated miRNAs in different SARS-CoV-2-infected samples, we identified miRNA-210-3p, miRNA-30-5p, and miR-146a/b as key host miRNAs that may be involved in SARS-CoV-2 infection. Furthermore, by comparing virally derived small RNAs (vsmRNAs) in different SARS-CoV-2-infected samples, we observed multiple hot spots in the viral genome that are prone to generating vsmRNAs, and their biogenesis can be dependent on the antiviral isoform of Dicer. Moreover, we investigated the biogenesis of a recently identified SARS-CoV-2 viral miRNA encoded by ORF7a and found that it is differentially expressed in different infected cell lines or in the same cell line with different viral doses. Our results demonstrate the involvement of both host small RNAs and vsmRNAs in SARS-CoV-2 infection and identify these small RNAs as potential targets for anti-COVID-19 therapeutic development.
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25
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Mustafin RN, Kazantseva AV, Kovas YV, Khusnutdinova EK. Role Of Retroelements In The Development Of COVID-19 Neurological Consequences. RUSSIAN OPEN MEDICAL JOURNAL 2022. [DOI: 10.15275/rusomj.2022.0313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Retroelements play a key role in brain functioning in humans and other animals, since they represent dynamic regulatory elements controlling the expression of specific neuron types. The activity of retroelements in the brain is impaired under the influence of SARS-CoV-2, penetrating the blood-brain barrier. We propose a new concept, according to which the neurological complications of COVID-19 and their long-term effects are caused by modified expression of retroelements in neurons due to viral effect. This effect is implemented in several ways: a direct effect of the virus on the promoter regions of retroelement-encoding genes, virus interaction with miRNAs causing silencing of transposons, and an effect of the viral RNA on the products of retroelement transcription. Aging-related physiological activation of retroelements in the elderly is responsible for more severe course of COVID-19. The associations of multiple sclerosis, Parkinson’s disease, Guillain-Barré syndrome, acute disseminated encephalomyelitis with coronavirus lesions also indicate the role of retroelements in such complications, because retroelements are involved in the mechanisms of the development of these diseases. According to meta-analyses, COVID-19-caused neurological complications ranged 36.4-73%. The neuropsychiatric consequences of COVID-19 are observed in patients over a long period after recovery, and their prevalence may exceed those during the acute phase of the disease. Even 12 months after recovery, unmotivated fatigue, headache, mental disorders, and neurocognitive impairment were observed in 82%, 60%, 26.2-45%, and 16.2-46.8% of patients, correspondingly. These manifestations are explained by the role of retroelements in the integration of SARS-CoV-2 into the human genome using their reverse transcriptase and endonuclease, which results in a long-term viral persistence. The research on the role of specific retroelements in these changes can become the basis for developing targeted therapy for neurological consequences of COVID-19 using miRNAs, since epigenetic changes in the functioning of the genome in neurons, affected by transposons, are reversible.
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Affiliation(s)
| | - Anastasiya V. Kazantseva
- Ufa Federal Research Center of the Russian Academy of Sciences; Bashkir State University, Ufa, Russia
| | - Yulia V. Kovas
- Bashkir State University, Ufa, Russia;University of London, London, Great Britain
| | - Elza K. Khusnutdinova
- Academy of Sciences of the Republic of Bashkortostan; Russian Academy of Education; Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia
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26
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Li W, Wang H, Zheng SJ. Roles of RNA Sensors in Host Innate Response to Influenza Virus and Coronavirus Infections. Int J Mol Sci 2022; 23:ijms23158285. [PMID: 35955436 PMCID: PMC9368391 DOI: 10.3390/ijms23158285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
Influenza virus and coronavirus are two important respiratory viruses, which often cause serious respiratory diseases in humans and animals after infection. In recent years, highly pathogenic avian influenza virus (HPAIV) and SARS-CoV-2 have become major pathogens causing respiratory diseases in humans. Thus, an in-depth understanding of the relationship between viral infection and host innate immunity is particularly important to the stipulation of effective control strategies. As the first line of defense against pathogens infection, innate immunity not only acts as a natural physiological barrier, but also eliminates pathogens through the production of interferon (IFN), the formation of inflammasomes, and the production of pro-inflammatory cytokines. In this process, the recognition of viral pathogen-associated molecular patterns (PAMPs) by host pattern recognition receptors (PRRs) is the initiation and the most important part of the innate immune response. In this review, we summarize the roles of RNA sensors in the host innate immune response to influenza virus and coronavirus infections in different species, with a particular focus on innate immune recognition of viral nucleic acids in host cells, which will help to develop an effective strategy for the control of respiratory infectious diseases.
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Affiliation(s)
- Wei Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hongnuan Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shijun J. Zheng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (W.L.); (H.W.)
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel./Fax: +86-10-62834681
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27
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Kannan A, Suomalainen M, Volle R, Bauer M, Amsler M, Trinh HV, Vavassori S, Schmid JP, Vilhena G, Marín-González A, Perez R, Franceschini A, von Mering C, Hemmi S, Greber UF. Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects. Viruses 2022; 14:v14071407. [PMID: 35891387 PMCID: PMC9322957 DOI: 10.3390/v14071407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023] Open
Abstract
Pathogen-associated molecular patterns, including cytoplasmic DNA and double-strand (ds)RNA trigger the induction of interferon (IFN) and antiviral states protecting cells and organisms from pathogens. Here we discovered that the transfection of human airway cell lines or non-transformed fibroblasts with 24mer dsRNA mimicking the cellular micro-RNA (miR)29b-1* gives strong anti-viral effects against human adenovirus type 5 (AdV-C5), influenza A virus X31 (H3N2), and SARS-CoV-2. These anti-viral effects required blunt-end complementary RNA strands and were not elicited by corresponding single-strand RNAs. dsRNA miR-29b-1* but not randomized miR-29b-1* mimics induced IFN-stimulated gene expression, and downregulated cell adhesion and cell cycle genes, as indicated by transcriptomics and IFN-I responsive Mx1-promoter activity assays. The inhibition of AdV-C5 infection with miR-29b-1* mimic depended on the IFN-alpha receptor 2 (IFNAR2) and the RNA-helicase retinoic acid-inducible gene I (RIG-I) but not cytoplasmic RNA sensors MDA5 and ZNFX1 or MyD88/TRIF adaptors. The antiviral effects of miR29b-1* were independent of a central AUAU-motif inducing dsRNA bending, as mimics with disrupted AUAU-motif were anti-viral in normal but not RIG-I knock-out (KO) or IFNAR2-KO cells. The screening of a library of scrambled short dsRNA sequences identified also anti-viral mimics functioning independently of RIG-I and IFNAR2, thus exemplifying the diverse anti-viral mechanisms of short blunt-end dsRNAs.
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Affiliation(s)
- Abhilash Kannan
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Neurimmune AG, Wagistrasse 18, 8952 Schlieren, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Romain Volle
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Marco Amsler
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Hung V. Trinh
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Genezen, 9900 Westpoint Dr, Suite 128, Indianapolis, IN 46256, USA
| | - Stefano Vavassori
- Division of Immunology, University Children’s Hospital Zürich, 8032 Zürich, Switzerland; (S.V.); (J.P.S.)
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children’s Hospital Zürich, 8032 Zürich, Switzerland; (S.V.); (J.P.S.)
- Faculty of Medicine, University of Zürich, 8006 Zürich, Switzerland
| | - Guilherme Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain; (G.V.); (R.P.)
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Alberto Marín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Cantoblanco, E-28049 Madrid, Spain;
| | - Ruben Perez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain; (G.V.); (R.P.)
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Andrea Franceschini
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Correspondence:
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