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Corell-Sierra J, Marquez-Molins J, Marqués MC, Hernandez-Azurdia AG, Montagud-Martínez R, Cebriá-Mendoza M, Cuevas JM, Albert E, Navarro D, Rodrigo G, Gómez G. SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity. NPJ Syst Biol Appl 2024; 10:41. [PMID: 38632240 PMCID: PMC11024147 DOI: 10.1038/s41540-024-00367-z] [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: 09/21/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.
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Affiliation(s)
- Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - María-Carmen Marqués
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | | | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, 46010, Valencia, Spain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Gustavo Gómez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
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Chowdhury S, Sais D, Donnelly S, Tran N. The knowns and unknowns of helminth-host miRNA cross-kingdom communication. Trends Parasitol 2024; 40:176-191. [PMID: 38151361 DOI: 10.1016/j.pt.2023.12.003] [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: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that oversee gene modulation. They are integral to cellular functions and can migrate between species, leading to cross-kingdom gene suppression. Recent breakthroughs in helminth genome studies have sparked curiosity about helminth RNA regulators and their ability to regulate genes across species. Growing data indicate that helminth miRNAs have a significant impact on the host's immune system. Specific miRNAs from helminth parasites can merge with the host's miRNA system, implying that parasites could exploit their host's regulatory machinery and function. This review highlights the role of cross-kingdom helminth-derived miRNAs in the interplay between host and parasite, exploring potential routes for their uptake, processing, and consequences in host interaction.
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Affiliation(s)
- Sumaiya Chowdhury
- The School of Life Sciences, University of Technology, Sydney, Australia; School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Dayna Sais
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Sheila Donnelly
- The School of Life Sciences, University of Technology, Sydney, Australia.
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia.
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3
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Delcher HA, DeMeis JD, Ghobar N, Godang NL, Knight SL, Alqudah SY, Nguyen KN, Watters BC, Borchert GM. SARS-Cov-2 small viral RNA suppresses gene expression via complementary binding to mRNA 3' UTR. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000790. [PMID: 38312351 PMCID: PMC10835431 DOI: 10.17912/micropub.biology.000790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/06/2024]
Abstract
SARS-CoV-2 (SC2) has been intensely studied since its emergence. However, the mechanisms of host immune dysregulation triggered by SC2 remain poorly understood. That said, it is well established that many prominent viral families encode microRNAs (miRNAs) or related small viral RNAs (svRNAs) capable of regulating human genes involved in immune function. Importantly, recent reports have shown that SC2 encodes its own svRNAs. In this study, we have identified 12 svRNAs expressed during SC2 infection and show that one of these svRNAs can regulate target gene expression via complementary binding to mRNA 3' untranslated regions (3'UTRs) much like human microRNAs.
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Affiliation(s)
- Haley A Delcher
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Jeffrey D DeMeis
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Nicole Ghobar
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Noel L Godang
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Sierra L Knight
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Shahem Y Alqudah
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Kevin N Nguyen
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Brianna C Watters
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
| | - Glen M Borchert
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL
- Department of Biology, College of Arts and Sciences, University of South Alabama, Mobile, AL
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4
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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.
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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
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Hashimoto R, Tamura T, Watanabe Y, Sakamoto A, Yasuhara N, Ito H, Nakano M, Fuse H, Ohta A, Noda T, Matsumura Y, Nagao M, Yamamoto T, Fukuhara T, Takayama K. Evaluation of Broad Anti-Coronavirus Activity of Autophagy-Related Compounds Using Human Airway Organoids. Mol Pharm 2023; 20:2276-2287. [PMID: 36946991 PMCID: PMC10041349 DOI: 10.1021/acs.molpharmaceut.3c00114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/23/2023]
Abstract
To deal with the broad spectrum of coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that threaten human health, it is essential to not only drugs develop that target viral proteins but also consider drugs that target host proteins/cellular processes to protect them from being hijacked for viral infection and replication. To this end, it has been reported that autophagy is deeply involved in coronavirus infection. In this study, we used airway organoids to screen a chemical library of autophagic modulators to identify compounds that could potentially be used to fight against infections by a broad range of coronaviruses. Among the 80 autophagy-related compounds tested, cycloheximide and thapsigargin reduced SARS-CoV-2 infection efficiency in a dose-dependent manner. Cycloheximide treatment reduced the infection efficiency of not only six SARS-CoV-2 variants but also human coronavirus (HCoV)-229E and HCoV-OC43. Cycloheximide treatment also reversed viral infection-induced innate immune responses. However, even low-dose (1 μM) cycloheximide treatment altered the expression profile of ribosomal RNAs; thus, side effects such as inhibition of protein synthesis in host cells must be considered. These results suggest that cycloheximide has broad-spectrum anti-coronavirus activity in vitro and warrants further investigation.
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Affiliation(s)
- Rina Hashimoto
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tomokazu Tamura
- Department
of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Yukio Watanabe
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Ayaka Sakamoto
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naoko Yasuhara
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hayato Ito
- Department
of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Masahiro Nakano
- Laboratory
of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- Laboratory
of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Hiromitsu Fuse
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akira Ohta
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takeshi Noda
- Laboratory
of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- Laboratory
of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Yasufumi Matsumura
- Department
of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Miki Nagao
- Department
of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Yamamoto
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
- Medical-risk
Avoidance based on iPS Cells Team, RIKEN
Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
- Institute
for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Takasuke Fukuhara
- Department
of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan
- Laboratory
of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan
- AMED-CREST, Japan Agency for
Medical Research and Development
(AMED), Tokyo 100-0004, Japan
| | - Kazuo Takayama
- Center
for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
- AMED-CREST, Japan Agency for
Medical Research and Development
(AMED), Tokyo 100-0004, Japan
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