1
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Ganapathy D, Sekaran S, Ramasamy P. Exploring the Potential Link Between COVID-19, MiRNA Dysregulation, and Oral Cancer Risk in Tobacco Chewers. Clin Oncol (R Coll Radiol) 2024; 36:e348-e349. [PMID: 38969527 DOI: 10.1016/j.clon.2024.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/07/2024]
Affiliation(s)
- D Ganapathy
- Department of Prosthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, Tamil Nadu, India
| | - S Sekaran
- Department of Prosthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, Tamil Nadu, India
| | - P Ramasamy
- Department of Prosthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, Tamil Nadu, India; Polymer Research Laboratory (PR Lab), Centre for Marine and Aquatic Research (CMAR), Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 602105, India.
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2
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Shibamoto A, Kitsu Y, Shibata K, Kaneko Y, Moriizumi H, Takahashi T. microRNA-guided immunity against respiratory virus infection in human and mouse lung cells. Biol Open 2024; 13:bio060172. [PMID: 38875000 PMCID: PMC11212637 DOI: 10.1242/bio.060172] [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: 09/27/2023] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Viral infectivity depends on multiple factors. Recent studies showed that the interaction between viral RNAs and endogenous microRNAs (miRNAs) regulates viral infectivity; viral RNAs function as a sponge of endogenous miRNAs and result in upregulation of its original target genes, while endogenous miRNAs target viral RNAs directly and result in repression of viral gene expression. In this study, we analyzed the possible interaction between parainfluenza virus RNA and endogenous miRNAs in human and mouse lungs. We showed that the parainfluenza virus can form base pairs with human miRNAs abundantly than mouse miRNAs. Furthermore, we analyzed that the sponge effect of endogenous miRNAs on viral RNAs may induce the upregulation of transcription regulatory factors. Then, we performed RNA-sequence analysis and observed the upregulation of transcription regulatory factors in the early stages of parainfluenza virus infection. Our studies showed how the differential expression of endogenous miRNAs in lungs could contribute to respiratory virus infection and species- or tissue-specific mechanisms and common mechanisms could be conserved in humans and mice and regulated by miRNAs during viral infection.
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Affiliation(s)
- Ayaka Shibamoto
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
| | - Yoshiaki Kitsu
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
| | - Keiko Shibata
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Yuka Kaneko
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Harune Moriizumi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Tomoko Takahashi
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
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3
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Bloomquist R, Mondal AK, Vashisht A, Sahajpal N, Jones K, Vashisht V, Singh H, Farmaha J, Kolhe R. Gene Regulatory Network Analysis of Post-Mortem Lungs Unveils Novel Insights into COVID-19 Pathogenesis. Viruses 2024; 16:853. [PMID: 38932146 PMCID: PMC11209433 DOI: 10.3390/v16060853] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
The novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the most significant global health crises in recent history. The clinical characteristics of COVID-19 patients have revealed the possibility of immune activity changes contributing to disease severity. Nevertheless, limited information is available regarding the immune response in human lung tissue, which is the primary site of infection. In this study, we conducted an extensive analysis of lung tissue to screen for differentially expressed miRNAs and mRNAs in five individuals who died due to COVID-19 and underwent a rapid autopsy, as well as seven control individuals who died of other causes unrelated to COVID-19. To analyze the host response gene expression, miRNA microarray and Nanostring's nCounter XT gene expression assay were performed. Our study identified 37 downregulated and 77 upregulated miRNAs in COVID-19 lung biopsy samples compared to the controls. A total of 653 mRNA transcripts were differentially expressed between the two sample types, with most transcripts (472) being downregulated in COVID-19-positive specimens. Hierarchical and PCA K-means clustering analysis showed distinct clustering between COVID-19 and control samples. Enrichment and network analyses revealed differentially expressed genes important for innate immunity and inflammatory response in COVID-19 lung biopsies. The interferon-signaling pathway was highly upregulated in COVID-19 specimens while genes involved in interleukin-17 signaling were downregulated. These findings shed light on the mechanisms of host cellular responses to COVID-19 infection in lung tissues and could help identify new targets for the prevention and treatment of COVID-19 infection.
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Affiliation(s)
- Ryan Bloomquist
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
- School of Medicine, University of South Carolina, Columbia, SC 29209, USA
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | | | - Kimya Jones
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Vishakha Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Jaspreet Farmaha
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
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4
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Chakraborty C, Bhattacharya M, Lee SS. Regulatory role of miRNAs in the human immune and inflammatory response during the infection of SARS-CoV-2 and other respiratory viruses: A comprehensive review. Rev Med Virol 2024; 34:e2526. [PMID: 38446531 DOI: 10.1002/rmv.2526] [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: 01/16/2024] [Revised: 02/11/2024] [Accepted: 02/22/2024] [Indexed: 03/07/2024]
Abstract
miRNAs are single-stranded ncRNAs that act as regulators of different human body processes. Several miRNAs have been noted to control the human immune and inflammatory response during severe acute respiratory infection syndrome (SARS-CoV-2) infection. Similarly, many miRNAs were upregulated and downregulated during different respiratory virus infections. Here, an attempt has been made to capture the regulatory role of miRNAs in the human immune and inflammatory response during the infection of SARS-CoV-2 and other respiratory viruses. Firstly, the role of miRNAs has been depicted in the human immune and inflammatory response during the infection of SARS-CoV-2. In this direction, several significant points have been discussed about SARS-CoV-2 infection, such as the role of miRNAs in human innate immune response; miRNAs and its regulation of granulocytes; the role of miRNAs in macrophage activation and polarisation; miRNAs and neutrophil extracellular trap formation; miRNA-related inflammatory response; and miRNAs association in adaptive immunity. Secondly, the miRNAs landscape has been depicted during human respiratory virus infections such as human coronavirus, respiratory syncytial virus, influenza virus, rhinovirus, and human metapneumovirus. The article will provide more understanding of the miRNA-controlled mechanism of the immune and inflammatory response during COVID-19, which will help more therapeutics discoveries to fight against the future pandemic.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
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5
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Omer A. MicroRNAs as powerful tool against COVID-19: Computational perspective. WIREs Mech Dis 2023; 15:e1621. [PMID: 37345625 DOI: 10.1002/wsbm.1621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/13/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 is the virus that is responsible for the current pandemic, COVID-19 (SARS-CoV-2). MiRNAs, a component of RNAi technology, belong to the family of short, noncoding ssRNAs, and may be crucial in the battle against this global threat since they are involved in regulating complex biochemical pathways and may prevent viral proliferation, translation, and host expression. The complicated metabolic pathways are modulated by the activity of many proteins, mRNAs, and miRNAs working together in miRNA-mediated genetic control. The amount of omics data has increased dramatically in recent years. This massive, linked, yet complex metabolic regulatory network data offers a wealth of opportunity for iterative analysis; hence, extensive, in-depth, but time-efficient screening is necessary to acquire fresh discoveries; this is readily performed with the use of bioinformatics. We have reviewed the literature on microRNAs, bioinformatics, and COVID-19 infection to summarize (1) the function of miRNAs in combating COVID-19, and (2) the use of computational methods in combating COVID-19 in certain noteworthy studies, and (3) computational tools used by these studies against COVID-19 in several purposes. This article is categorized under: Infectious Diseases > Computational Models.
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Affiliation(s)
- Ankur Omer
- Government College Silodi, MPHED, Katni, Madhya Pradesh, India
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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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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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8
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Lin Y, Sun Q, Zhang B, Zhao W, Shen C. The regulation of lncRNAs and miRNAs in SARS-CoV-2 infection. Front Cell Dev Biol 2023; 11:1229393. [PMID: 37576600 PMCID: PMC10416254 DOI: 10.3389/fcell.2023.1229393] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) was a global endemic that continues to cause a large number of severe illnesses and fatalities. There is increasing evidence that non-coding RNAs (ncRNAs) are crucial regulators of viral infection and antiviral immune response and the role of non-coding RNAs in SARS-CoV-2 infection has now become the focus of scholarly inquiry. After SARS-CoV-2 infection, some ncRNAs' expression levels are regulated to indirectly control the expression of antiviral genes and viral gene replication. However, some other ncRNAs are hijacked by SARS-CoV-2 in order to help the virus evade the immune system by suppressing the expression of type I interferon (IFN-1) and controlling cytokine levels. In this review, we summarize the recent findings of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) among non-coding RNAs in SARS-CoV-2 infection and antiviral response, discuss the potential mechanisms of actions, and prospects for the detection, treatment, prevention and future directions of SARS-CoV-2 infection research.
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Affiliation(s)
| | | | | | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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9
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Csobonyeiova M, Smolinska V, Harsanyi S, Ivantysyn M, Klein M. The Immunomodulatory Role of Cell-Free Approaches in SARS-CoV-2-Induced Cytokine Storm-A Powerful Therapeutic Tool for COVID-19 Patients. Biomedicines 2023; 11:1736. [PMID: 37371831 DOI: 10.3390/biomedicines11061736] [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: 05/23/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, there is still no effective and definitive cure for the coronavirus disease 2019 (COVID-19) caused by the infection of the novel highly contagious severe acute respiratory syndrome virus (SARS-CoV-2), whose sudden outbreak was recorded for the first time in China in late December 2019. Soon after, COVID-19 affected not only the vast majority of China's population but the whole world and caused a global health public crisis as a new pandemic. It is well known that viral infection can cause acute respiratory distress syndrome (ARDS) and, in severe cases, can even be lethal. Behind the inflammatory process lies the so-called cytokine storm (CS), which activates various inflammatory cytokines that damage numerous organ tissues. Since the first outbreak of SARS-CoV-2, various research groups have been intensively trying to investigate the best treatment options; however, only limited outcomes have been achieved. One of the most promising strategies represents using either stem cells, such as mesenchymal stem cells (MSCs)/induced pluripotent stem cells (iPSCs), or, more recently, using cell-free approaches involving conditioned media (CMs) and their content, such as extracellular vesicles (EVs) (e.g., exosomes or miRNAs) derived from stem cells. As key mediators of intracellular communication, exosomes carry a cocktail of different molecules with anti-inflammatory effects and immunomodulatory capacity. Our comprehensive review outlines the complex inflammatory process responsible for the CS, summarizes the present results of cell-free-based pre-clinical and clinical studies for COVID-19 treatment, and discusses their future perspectives for therapeutic applications.
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Affiliation(s)
- Maria Csobonyeiova
- Institute of Histology and Embryology, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
- Apel, Dunajská 52, 811 08 Bratislava, Slovakia
- Regenmed Ltd., Medená 29, 811 08 Bratislava, Slovakia
| | - Veronika Smolinska
- Regenmed Ltd., Medená 29, 811 08 Bratislava, Slovakia
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Stefan Harsanyi
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
| | | | - Martin Klein
- Institute of Histology and Embryology, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
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10
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Frye CJ, Cunningham CL, Mihailescu MR. Host microRNA interactions with the SARS-CoV-2 viral genome 3'-untranslated region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541401. [PMID: 37292986 PMCID: PMC10245713 DOI: 10.1101/2023.05.18.541401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. While the viral life cycle is well understood, most of the interactions at the virus-host interface remain elusive. Furthermore, the molecular mechanisms behind disease severity and immune evasion are still largely unknown. Conserved elements of the viral genome such as secondary structures within the 5'- and 3'-untranslated regions (UTRs) serve as attractive targets of interest and could prove crucial in furthering our understanding of virus-host interactions. It has been proposed that microRNA (miR) interactions with viral components could be used by both the virus and host for their own benefit. Analysis of the SARS-CoV-2 viral genome 3'-UTR has revealed the potential for host cellular miR binding sites, providing sites for specific interactions with the virus. In this study, we demonstrate that the SARS-CoV-2 genome 3'-UTR binds the host cellular miRNAs miR-760-3p, miR-34a-5p, and miR-34b-5p, which have been shown to influence translation of interleukin-6 (IL-6), the IL-6 receptor (IL-6R), as well as progranulin (PGRN), respectively, proteins that have roles in the host immune response and inflammatory pathways. Furthermore, recent work suggests the potential of miR-34a-5p and miR-34b-5p to target and inhibit translation of viral proteins. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3'-UTR. Additionally, we investigated 2'-fluoro-D-arabinonucleic acid (FANA) analogs of these miRNAs as competitive binding inhibitors for these miR binding interactions. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2 infection, and provide a potential molecular basis for cytokine release syndrome and immune evasion which could implicate the host-virus interface.
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Affiliation(s)
- Caleb J Frye
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
| | - Caylee L Cunningham
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
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11
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Hicks SD, Zhu D, Sullivan R, Kannikeswaran N, Meert K, Chen W, Suresh S, Sethuraman U. Saliva microRNA Profile in Children with and without Severe SARS-CoV-2 Infection. Int J Mol Sci 2023; 24:ijms24098175. [PMID: 37175883 PMCID: PMC10179619 DOI: 10.3390/ijms24098175] [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: 03/10/2023] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) may impair immune modulating host microRNAs, causing severe disease. Our objectives were to determine the salivary miRNA profile in children with SARS-CoV-2 infection at presentation and compare the expression in those with and without severe outcomes. Children <18 years with SARS-CoV-2 infection evaluated at two hospitals between March 2021 and February 2022 were prospectively enrolled. Severe outcomes included respiratory failure, shock or death. Saliva microRNAs were quantified with RNA sequencing. Data on 197 infected children (severe = 45) were analyzed. Of the known human miRNAs, 1606 (60%) were measured and compared across saliva samples. There were 43 miRNAs with ≥2-fold difference between severe and non-severe cases (adjusted p-value < 0.05). The majority (31/43) were downregulated in severe cases. The largest between-group differences involved miR-4495, miR-296-5p, miR-548ao-3p and miR-1273c. These microRNAs displayed enrichment for 32 gene ontology pathways including viral processing and transforming growth factor beta and Fc-gamma receptor signaling. In conclusion, salivary miRNA levels are perturbed in children with severe COVID-19, with the majority of miRNAs being down regulated. Further studies are required to validate and determine the utility of salivary miRNAs as biomarkers of severe COVID-19.
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Affiliation(s)
- Steven D Hicks
- Department of Pediatrics, Pennsylvania State University Medical Center, Hershey, PA 17033, USA
| | - Dongxiao Zhu
- Department of Computer Science, Wayne State University, Detroit, MI 48201, USA
| | - Rhea Sullivan
- Department of Pediatrics, Pennsylvania State University Medical Center, Hershey, PA 17033, USA
| | - Nirupama Kannikeswaran
- Division of Emergency Medicine, Department of Pediatrics, Children's Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | - Kathleen Meert
- Division of Critical Care, Department of Pediatrics, Children's Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
| | - Wei Chen
- Population Science, Department of Oncology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Srinivasan Suresh
- Department of Pediatrics, University of Pittsburgh, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Usha Sethuraman
- Division of Emergency Medicine, Department of Pediatrics, Children's Hospital of Michigan, Central Michigan University, Detroit, MI 48201, USA
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12
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Guiot J, Henket M, Remacle C, Cambier M, Struman I, Winandy M, Moermans C, Louis E, Malaise M, Ribbens C, Louis R, Njock MS. Systematic review of overlapping microRNA patterns in COVID-19 and idiopathic pulmonary fibrosis. Respir Res 2023; 24:112. [PMID: 37061683 PMCID: PMC10105547 DOI: 10.1186/s12931-023-02413-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Pulmonary fibrosis is an emerging complication of SARS-CoV-2 infection. In this study, we speculate that patients with COVID-19 and idiopathic pulmonary fibrosis (IPF) may share aberrant expressed microRNAs (miRNAs) associated to the progression of lung fibrosis. OBJECTIVE To identify miRNAs presenting similar alteration in COVID-19 and IPF, and describe their impact on fibrogenesis. METHODS A systematic review of the literature published between 2010 and January 2022 (PROSPERO, CRD42022341016) was conducted using the key words (COVID-19 OR SARS-CoV-2) AND (microRNA OR miRNA) or (idiopathic pulmonary fibrosis OR IPF) AND (microRNA OR miRNA) in Title/Abstract. RESULTS Of the 1988 references considered, 70 original articles were appropriate for data extraction: 27 studies focused on miRNAs in COVID-19, and 43 on miRNAs in IPF. 34 miRNAs were overlapping in COVID-19 and IPF, 7 miRNAs presenting an upregulation (miR-19a-3p, miR-200c-3p, miR-21-5p, miR-145-5p, miR-199a-5p, miR-23b and miR-424) and 9 miRNAs a downregulation (miR-17-5p, miR-20a-5p, miR-92a-3p, miR-141-3p, miR-16-5p, miR-142-5p, miR-486-5p, miR-708-3p and miR-150-5p). CONCLUSION Several studies reported elevated levels of profibrotic miRNAs in COVID-19 context. In addition, the balance of antifibrotic miRNAs responsible of the modulation of fibrotic processes is impaired in COVID-19. This evidence suggests that the deregulation of fibrotic-related miRNAs participates in the development of fibrotic lesions in the lung of post-COVID-19 patients.
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Affiliation(s)
- Julien Guiot
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Fibropole Research Group, University Hospital of Liège, Liège, Belgium
| | - Monique Henket
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Claire Remacle
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Laboratory of Molecular Angiogenesis, GIGA Research Center, University of Liège, Liège, Belgium
| | - Maureen Cambier
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Laboratory of Molecular Angiogenesis, GIGA Research Center, University of Liège, Liège, Belgium
| | - Ingrid Struman
- Laboratory of Molecular Angiogenesis, GIGA Research Center, University of Liège, Liège, Belgium
| | - Marie Winandy
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Catherine Moermans
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
| | - Edouard Louis
- Laboratory of Gastroenterology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Fibropole Research Group, University Hospital of Liège, Liège, Belgium
| | - Michel Malaise
- Laboratory of Rheumatology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Fibropole Research Group, University Hospital of Liège, Liège, Belgium
| | - Clio Ribbens
- Laboratory of Rheumatology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Fibropole Research Group, University Hospital of Liège, Liège, Belgium
| | - Renaud Louis
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Fibropole Research Group, University Hospital of Liège, Liège, Belgium
| | - Makon-Sébastien Njock
- Laboratory of Pneumology, GIGA Research Center, University of Liège, University Hospital of Liège, Liège, Belgium
- Fibropole Research Group, University Hospital of Liège, Liège, Belgium
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13
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Capistrano KJ, Richner J, Schwartz J, Mukherjee SK, Shukla D, Naqvi AR. Host microRNAs exhibit differential propensity to interact with SARS-CoV-2 and variants of concern. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166612. [PMID: 36481486 PMCID: PMC9721271 DOI: 10.1016/j.bbadis.2022.166612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 10/19/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
A significant number of SARS-CoV-2-infected individuals naturally overcome viral infection, suggesting the existence of a potent endogenous antiviral mechanism. As an innate defense mechanism, microRNA (miRNA) pathways in mammals have evolved to restrict viruses, besides regulating endogenous mRNAs. In this study, we systematically examined the complete repertoire of human miRNAs for potential binding sites on SARS-CoV-2 Wuhan-Hu-1, Beta, Delta, and Omicron. Human miRNA and viral genome interaction were analyzed using RNAhybrid 2.2 with stringent parameters to identify highly bonafide miRNA targets. Using publicly available data, we filtered for miRNAs expressed in lung epithelial cells/tissue and oral keratinocytes, concentrating on the miRNAs that target SARS-CoV-2 S protein mRNAs. Our results show a significant loss of human miRNA and SARS-CoV-2 interactions in Omicron (130 miRNAs) compared to Wuhan-Hu-1 (271 miRNAs), Beta (279 miRNAs), and Delta (275 miRNAs). In particular, hsa-miR-3150b-3p and hsa-miR-4784 show binding affinity for S protein of Wuhan strain but not Beta, Delta, and Omicron. Loss of miRNA binding sites on N protein was also observed for Omicron. Through Ingenuity Pathway Analysis (IPA), we examined the experimentally validated and highly predicted functional role of these miRNAs. We found that hsa-miR-3150b-3p and hsa-miR-4784 have several experimentally validated or highly predicted target genes in the Toll-like receptor, IL-17, Th1, Th2, interferon, and coronavirus pathogenesis pathways. Focusing on the coronavirus pathogenesis pathway, we found that hsa-miR-3150b-3p and hsa-miR-4784 are highly predicted to target MAPK13. Exploring miRNAs to manipulate viral genome/gene expression can provide a promising strategy with successful outcomes by targeting specific VOCs.
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Affiliation(s)
- Kristelle J Capistrano
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Justin Richner
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Joel Schwartz
- Molecular Pathology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Sunil K Mukherjee
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Deepak Shukla
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago 60612, IL, USA; Department of Ophthalmology and Visual Sciences, Ocular Virology Laboratory, University of Illinois Chicago, Chicago 60612, IL, USA
| | - Afsar R Naqvi
- Mucosal Immunology Lab, College of Dentistry, University of Illinois Chicago, Chicago 60612, IL, USA.
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14
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Gaytán-Pacheco N, Ibáñez-Salazar A, Herrera-Van Oostdam AS, Oropeza-Valdez JJ, Magaña-Aquino M, Adrián López J, Monárrez-Espino J, López-Hernández Y. miR-146a, miR-221, and miR-155 are Involved in Inflammatory Immune Response in Severe COVID-19 Patients. Diagnostics (Basel) 2022; 13:133. [PMID: 36611425 PMCID: PMC9818442 DOI: 10.3390/diagnostics13010133] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023] Open
Abstract
COVID-19 infection triggered a global public health crisis during the 2020-2022 period, and it is still evolving. This highly transmissible respiratory disease can cause mild symptoms up to severe pneumonia with potentially fatal respiratory failure. In this cross-sectional study, 41 PCR-positive patients for SARS-CoV-2 and 42 healthy controls were recruited during the first wave of the pandemic in Mexico. The plasmatic expression of five circulating miRNAs involved in inflammatory and pathological host immune responses was assessed using RT-qPCR (Reverse Transcription quantitative Polymerase Chain Reaction). Compared with controls, a significant upregulation of miR-146a, miR-155, and miR-221 was observed; miR-146a had a positive correlation with absolute neutrophil count and levels of brain natriuretic propeptide (proBNP), and miR-221 had a positive correlation with ferritin and a negative correlation with total cholesterol. We found here that CDKN1B gen is a shared target of miR-146a, miR-221-3p, and miR-155-5p, paving the way for therapeutic interventions in severe COVID-19 patients. The ROC curve built with adjusted variables (miR-146a, miR-221-3p, miR-155-5p, age, and male sex) to differentiate individuals with severe COVID-19 showed an AUC of 0.95. The dysregulation of circulating miRNAs provides new insights into the underlying immunological mechanisms, and their possible use as biomarkers to discriminate against patients with severe COVID-19. Functional analysis showed that most enriched pathways were significantly associated with processes related to cell proliferation and immune responses (innate and adaptive). Twelve of the predicted gene targets have been validated in plasma/serum, reflecting their potential use as predictive prognosis biomarkers.
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Affiliation(s)
- Noemí Gaytán-Pacheco
- Clinical Analysis Laboratory UAZ-Siglo-XXI, Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98000, Mexico
| | - Alejandro Ibáñez-Salazar
- Clinical Analysis Laboratory UAZ-Siglo-XXI, Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98000, Mexico
| | | | - Juan José Oropeza-Valdez
- Metabolomics and Proteomics Laboratory, Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98600, Mexico
| | | | - Jesús Adrián López
- MicroRNAs and Cancer Laboratory, Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98000, Mexico
| | - Joel Monárrez-Espino
- Department of Health Research, Christus Muguerza del Parque Hospital Chihuahua, University of Monterrey, San Pedro Garza García 66238, Mexico
| | - Yamilé López-Hernández
- CONACyT-Metabolomics and Proteomics Laboratory, Autonomous University of Zacatecas, Zacatecas 98000, Mexico
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15
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Neeb ZT, Ritter AJ, Chauhan LV, Katzman S, Lipkin WI, Mishra N, Sanford JR. A potential role for SARS-CoV-2 small viral RNAs in targeting host microRNAs and modulating gene expression. Sci Rep 2022; 12:21694. [PMID: 36522444 PMCID: PMC9753033 DOI: 10.1038/s41598-022-26135-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, with symptoms ranging from mild to severe, including fatality. The molecular mechanisms surrounding the effects of viral infection on the host RNA machinery remain poorly characterized. We used a comparative transcriptomics approach to investigate the effects of SARS-CoV-2 infection on the host mRNA and sRNA expression machinery in a human lung epithelial cell line (Calu-3) and an African green monkey kidney cell line (Vero-E6). Upon infection, we observed global changes in host gene expression and differential expression of dozens of host miRNAs, many with known links to viral infection and immune response. Additionally, we discovered an expanded landscape of more than a hundred SARS-CoV-2-derived small viral RNAs (svRNAs) predicted to interact with differentially expressed host mRNAs and miRNAs. svRNAs are derived from distinct regions of the viral genome and sequence signatures suggest they are produced by a non-canonical biogenesis pathway. 52 of the 67 svRNAs identified in Calu-3 cells are predicted to interact with differentially expressed miRNAs, with many svRNAs having multiple targets. Accordingly, we speculate that these svRNAs may play a role in SARS-CoV-2 propagation by modulating post-transcriptional gene regulation, and that methods for antagonizing them may have therapeutic value.
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Affiliation(s)
- Zachary T Neeb
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alexander J Ritter
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lokendra V Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sol Katzman
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Jeremy R Sanford
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
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16
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Hardin LT, Xiao N. miRNAs: The Key Regulator of COVID-19 Disease. Int J Cell Biol 2022; 2022:1645366. [PMID: 36345541 PMCID: PMC9637033 DOI: 10.1155/2022/1645366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/30/2022] [Indexed: 01/12/2024] Open
Abstract
As many parts of the world continue to fight the innumerable waves of COVID-19 infection, SARS-CoV-2 continues to sculpt its antigenic determinants to enhance its virulence and evolvability. Several vaccines were developed and used around the world, and oral antiviral medications are being developed against SARS-CoV-2. However, studies showed that the virus is mutating in line with the antibody's neutralization escape; thus, new therapeutic alternatives are solicited. We hereby review the key role that miRNAs can play as epigenetic mediators of the cross-talk between SARS-CoV-2 and the host cells. The limitations resulting from the "virus intelligence" to escape and antagonize the host miRNAs as well as the possible mechanisms that could be used in the viral evasion strategies are discussed. Lastly, we suggest new therapeutic approaches based on viral miRNAs.
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Affiliation(s)
- Leyla Tahrani Hardin
- Department of Biomedical Sciences at the Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, 94103 CA, USA
| | - Nan Xiao
- Department of Biomedical Sciences at the Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, 94103 CA, USA
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17
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Micro-Players of Great Significance-Host microRNA Signature in Viral Infections in Humans and Animals. Int J Mol Sci 2022; 23:ijms231810536. [PMID: 36142450 PMCID: PMC9504570 DOI: 10.3390/ijms231810536] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Over time, more and more is becoming known about micro-players of great significance. This is particularly the case for microRNAs (miRNAs; miR), which have been found to participate in the regulation of many physiological and pathological processes in both humans and animals. One such process is viral infection in humans and animals, in which the host miRNAs—alone or in conjunction with the virus—interact on two levels: viruses may regulate the host’s miRNAs to evade its immune system, while the host miRNAs can play anti- or pro-viral roles. The purpose of this comprehensive review is to present the key miRNAs involved in viral infections in humans and animals. We summarize the data in the available literature, indicating that the signature miRNAs in human viral infections mainly include 12 miRNAs (i.e., miR-155, miR-223, miR-146a, miR-122, miR-125b, miR-132, miR-34a, miR -21, miR-16, miR-181 family, let-7 family, and miR-10a), while 10 miRNAs are commonly found in animals (i.e., miR-155, miR-223, miR-146a, miR-145, miR-21, miR-15a/miR-16 cluster, miR-181 family, let-7 family, and miR-122) in this context. Knowledge of which miRNAs are involved in different viral infections and the biological functions that they play can help in understanding the pathogenesis of viral diseases, facilitating the future development of therapeutic agents for both humans and animals.
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18
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Yadav V. Computational evidence based perspective on the plausible repositioning of fluoroquinolones for COVID-19 treatment. Curr Comput Aided Drug Des 2022; 18:CAD-EPUB-126248. [PMID: 36093826 DOI: 10.2174/1573409918666220909094645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/13/2022] [Accepted: 07/22/2022] [Indexed: 11/22/2022]
Abstract
The coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a serious global healthcare crisis, so there is an emergence of identifying efficacious therapeutic options. In a setting where there is an unavailability of definitive medication along with the constant eruption of vaccine-related controversies, the drug-repositioning approach seems to be an ideal step for the management of COVID-19 patients. Fluoroquinolones (FQs) are commonly prescribed antibiotics for the treatment of genitourinary tract and upper respiratory tract infections, including severe community-acquired pneumonia. Research over the years has postulated multifaceted implications of FQs in various pathological conditions. Previously, it has been reported that few, but not all FQs, possess strong antiviral activity with an unknown mechanism of action. Herein, an interesting perspective is discussed on repositioning possibilities of FQs for the SARS-CoV-2 infections based on the recent in silico evidential support. Noteworthy, FQs possess immunomodulatory and bactericidal activity which could be valuable for patients dealing with COVID-19 related complications. Conclusively, the current perspective could pave the way to initiate pre-clinical testing of FQs against several strains of SARS-CoV-2.
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Affiliation(s)
- Vikas Yadav
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, Sart-Tilman, 4000, Liège, Belgium
- Department of Translational Medicine, Skane University Hospital, Clinical Research Centre, Lund University, Malmö, Sweden
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19
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Latini A, Vancheri C, Amati F, Morini E, Grelli S, Claudia M, Vita P, Colona VL, Murdocca M, Andreoni M, Malagnino V, Raponi M, Cocciadiferro D, Novelli A, Borgiani P, Novelli G. Expression analysis of miRNA hsa-let7b-5p in naso-oropharyngeal swabs of COVID-19 patients supports its role in regulating ACE2 and DPP4 receptors. J Cell Mol Med 2022; 26:4940-4948. [PMID: 36073344 PMCID: PMC9538662 DOI: 10.1111/jcmm.17492] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the novel coronavirus responsible for worldwide coronavirus disease (COVID-19). We previously observed that Angiotensin-converting enzyme 2 (ACE2) and Dipeptidyl peptidase-4 (DPP4) are significantly overexpressed in naso-oropharyngeal swabs (NPS) of COVID-19 patients, suggesting their putative functional role in the disease progression. ACE2 and DPP4 overexpression in COVID-19 patients may be associated to epigenetic mechanism, such as miRNA differential expression. We investigated if hsa-let7b-5p, reported to target both ACE2 and DPP4 transcripts, could be involved in the regulation of these genes. We verified that the inhibition and overexpression of hsa-let7b-5p matched to a modulation of both ACE2 and DPP4 levels. Then, we observed a statistically significant downregulation (FC = -1.5; p < 0.05) of hsa-let7b-5p in the same COVID-19 and control samples of our previous study. This is the first study that shows hsa-let7b-5p low expression in naso-oropharyngeal swabs of COVID-19 patients and demonstrates a functional role of this miR in regulating ACE2 and DPP4 levels. These data suggest the involvement of hsa-let7b-5p in the regulation of genes necessary for SARS-CoV-2 infections and its putative role as a therapeutic target for COVID-19.
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Affiliation(s)
- Andrea Latini
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Chiara Vancheri
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Francesca Amati
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Elena Morini
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Matteucci Claudia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Petrone Vita
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Michela Murdocca
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Vincenzo Malagnino
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | | | | | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy.,Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy.,Neuromed IRCCS Institute, Pozzilli, Italy.,School of Medicine, Reno University of Nevada, Reno, Nevada, USA
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20
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Moatar AI, Chis AR, Marian C, Sirbu IO. Gene Network Analysis of the Transcriptome Impact of SARS-CoV-2 Interacting MicroRNAs in COVID-19 Disease. Int J Mol Sci 2022; 23:ijms23169239. [PMID: 36012503 PMCID: PMC9409149 DOI: 10.3390/ijms23169239] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 02/07/2023] Open
Abstract
According to the World Health Organization (WHO), as of June 2022, over 536 million confirmed COVID-19 disease cases and over 6.3 million deaths had been globally reported. COVID-19 is a multiorgan disease involving multiple intricated pathological mechanisms translated into clinical, biochemical, and molecular changes, including microRNAs. MicroRNAs are essential post-transcriptional regulators of gene expression, being involved in the modulation of most biological processes. In this study, we characterized the biological impact of SARS-CoV-2 interacting microRNAs differentially expressed in COVID-19 disease by analyzing their impact on five distinct tissue transcriptomes. To this end, we identified the microRNAs’ predicted targets within the list of differentially expressed genes (DEGs) in tissues affected by high loads of SARS-CoV-2 virus. Next, we submitted the tissue-specific lists of the predicted microRNA-targeted DEGs to gene network functional enrichment analysis. Our data show that the upregulated microRNAs control processes such as mitochondrial respiration and cytokine and cell surface receptor signaling pathways in the heart, lymph node, and kidneys. In contrast, downregulated microRNAs are primarily involved in processes related to the mitotic cell cycle in the heart, lung, and kidneys. Our study provides the first exploratory, systematic look into the biological impact of the microRNAs associated with COVID-19, providing a new perspective for understanding its multiorgan physiopathology.
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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
- Center for Complex Network Science, 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
| | - 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
| | - 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
- Correspondence: ; Tel.: +40-756-136-272
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21
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Ganapathy D, Sekaran S, Pitchaiah S. Is prognostic monitoring of high-risk populations at risk for oral cancer necessary after infection with COVID-19? Oral Oncol 2022; 131:105968. [PMID: 35724527 PMCID: PMC9192939 DOI: 10.1016/j.oraloncology.2022.105968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/02/2022] [Accepted: 06/10/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Dhanraj Ganapathy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute for Medical and Technical Sciences, Chennai 600077, Tamil Nadu, India.
| | - Saravanan Sekaran
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute for Medical and Technical Sciences, Chennai 600077, Tamil Nadu, India
| | - Sivaperumal Pitchaiah
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute for Medical and Technical Sciences, Chennai 600077, Tamil Nadu, India
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22
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Ahmed JQ, Maulud SQ, Dhawan M, Priyanka, Choudhary OP, Jalal PJ, Ali RK, Tayib GA, Hasan DA. MicroRNAs in the development of potential therapeutic targets against COVID-19: A narrative review. J Infect Public Health 2022; 15:788-799. [PMID: 35751930 PMCID: PMC9221922 DOI: 10.1016/j.jiph.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 12/12/2022] Open
Abstract
Background As the therapeutic regimens against the COVID-19 remain scarce, the microRNAs (miRNAs) can be exploited to generate efficient therapeutic targets. The miRNAs have been found to play pivotal roles in the several regulatory functions influencing the prognosis of viral infection. The miRNAs have a prospective role in the up and down regulation of the ACE2 receptors. This review examines the clinical applications, as well as the possible threats associated with the use of miRNAs to combat the deleterious consequences of SARS-CoV-2 infection. Methodology This article was compiled to evaluate how the miRNAs are involved in the SARS-CoV-2 pathogenesis and infection, and their potential functions which could help in the development of therapeutic targets against the COVID-19. The sources of the collected information include the several journals, databases and scientific search engines such as the Google scholar, Pubmed, Science direct, official website of WHO, among the other sites. The investigations on the online platform were conducted using the keywords miRNA biogenesis, miRNA and ACE2 interaction, therapeutic role of miRNAs against SARS-CoV-2 and miRNA therapy side effects. Results This review has highlighted that the miRNAs can be exploited to generate potential therapeutic targets against the COVID-19. Changes in the miRNA levels following viral replication are an essential component of the host response to infection. The collection and modification of miRNA modulates may help to minimize the deleterious consequences of SARS-CoV-2 infection, such as by controlling or inhibiting the generation of cytokines and chemokines. The degradation of viral RNA by the cellular miRNAs, along with the reduced expression of ACE2 receptors, can substantially reduce the viral load. Specific miRNAs have been found to have an antiviral influence, allowing the immune system to combat the infection or forcing the virus into a latency stage. Conclusion This review summarizes several studies revealing the involvement of miRNAs in diverse and complex processes during the infection process of SARS-CoV-2. The miRNAs can substantially reduce the viral load by degradation of viral RNA and reduced expression of ACE2 receptors, besides mitigating the deleterious consequences of the exaggerated secretion of cytokines. Extensive investigations need to be done by the scientific community to utilize the miRNA based strategies for the development of effective therapeutic targets against the COVID-19.
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Affiliation(s)
- Jivan Qasim Ahmed
- Department of Pathology and Microbiology, University of Duhok, Kurdistan Region, Iraq
| | - Sazan Qadir Maulud
- Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004 Punjab, India; Trafford College, Altrincham, Manchester, WA14 5PQ, UK
| | - Priyanka
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda 151103, Punjab, India.
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, 796015, Mizoram, India.
| | - Paywast Jamal Jalal
- Department of Biology, College of Science, University of Sulaimani, Kurdistan Region, Iraq
| | - Rezhna Kheder Ali
- Department of Biology, College of Education, Salahaddin University-Erbil, Kurdistan Region, Iraq
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23
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Matusewicz L, Golec M, Czogalla A, Kuliczkowski K, Konka A, Zembala-John J, Sikorski AF. COVID-19 therapies: do we see substantial progress? Cell Mol Biol Lett 2022; 27:42. [PMID: 35641916 PMCID: PMC9152818 DOI: 10.1186/s11658-022-00341-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/29/2022] [Indexed: 12/15/2022] Open
Abstract
The appearance of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its spread all over the world is the cause of the coronavirus disease 2019 (COVID-19) pandemic, which has recently resulted in almost 400 million confirmed cases and 6 million deaths, not to mention unknown long-term or persistent side effects in convalescent individuals. In this short review, we discuss approaches to treat COVID-19 that are based on current knowledge of the mechanisms of viral cell receptor recognition, virus–host membrane fusion, and inhibition of viral RNA and viral assembly. Despite enormous progress in antiviral therapy and prevention, new effective therapies are still in great demand.
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Affiliation(s)
- Lucyna Matusewicz
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, ul. F. Joliot Curie 14a, 50-383, Wrocław, Poland
| | - Marlena Golec
- Silesian Park of Medical Technology Kardio-Med Silesia, ul. M. Curie-Skłodowskiej 10c, 41-800, Zabrze, Poland
| | - Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, ul. F. Joliot Curie 14a, 50-383, Wrocław, Poland
| | - Kazimierz Kuliczkowski
- Silesian Park of Medical Technology Kardio-Med Silesia, ul. M. Curie-Skłodowskiej 10c, 41-800, Zabrze, Poland
| | - Adam Konka
- Silesian Park of Medical Technology Kardio-Med Silesia, ul. M. Curie-Skłodowskiej 10c, 41-800, Zabrze, Poland
| | - Joanna Zembala-John
- Chair and Department of Medicine and Environmental Epidemiology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, H. Jordana 19, 41-800, Zabrze, Poland.,Acellmed Ltd., M. Curie-Skłodowskiej 10C, 41-800, Zabrze, Poland
| | - Aleksander F Sikorski
- Research and Development Centre, Regional Specialist Hospital, Kamieńskiego 73a, 51-154, Wroclaw, Poland. .,Acellmed Ltd., M. Curie-Skłodowskiej 10C, 41-800, Zabrze, Poland.
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24
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Li C, Wang R, Wu A, Yuan T, Song K, Bai Y, Liu X. SARS-COV-2 as potential microRNA sponge in COVID-19 patients. BMC Med Genomics 2022; 15:94. [PMID: 35461273 PMCID: PMC9034446 DOI: 10.1186/s12920-022-01243-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
Background MicroRNAs (miRNAs) are a class of small non-coding RNA that can downregulate their targets by selectively binding to the 3′ untranslated region (3′UTR) of most messenger RNAs (mRNAs) in the human genome. MiRNAs can interact with other molecules such as viruses and act as a mediator for viral infection. In this study, we examined whether, and to what extent, the SARS-CoV-2 virus can serve as a “sponge” for human miRNAs. Results We identified multiple potential miRNA/target pairs that may be disrupted during SARS-CoV-2 infection. Using miRNA expression profiles and RNA-seq from published studies, we further identified a highly confident list of 5 miRNA/target pairs that could be disrupted by the virus’s miRNA sponge effect, namely hsa-miR-374a-5p/APOL6, hsa-let-7f-1-3p/EIF4A2, hsa-miR-374a-3p/PARP11, hsa-miR-548d-3p/PSMA2 and hsa-miR-23b-3p/ZNFX1 pairs. Using single-cell RNA-sequencing based data, we identified two important miRNAs, hsa-miR-302c-5p and hsa-miR-16-5p, to be potential virus targeting miRNAs across multiple cell types from bronchoalveolar lavage fluid samples. We further validated some of our findings using miRNA and gene enrichment analyses and the results confirmed with findings from previous studies that some of these identified miRNA/target pairs are involved in ACE2 receptor network, regulating pro-inflammatory cytokines and in immune cell maturation and differentiation. Conclusion Using publicly available databases and patient-related expression data, we found that acting as a “miRNA sponge” could be one explanation for SARS-CoV-2-mediated pathophysiological changes. This study provides a novel way of utilizing SARS-CoV-2 related data, with bioinformatics approaches, to help us better understand the etiology of the disease and its differential manifestation across individuals. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01243-7.
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Affiliation(s)
- Chang Li
- USF Genomics and College of Public Health, University of South Florida, Tampa, FL, USA.
| | | | | | - Tina Yuan
- The Roeper School, Birmingham, MI, USA
| | | | - Yongsheng Bai
- Next-Gen Intelligent Science Training, Ann Arbor, MI, USA. .,Department of Biology, Eastern Michigan University, Ypsilanti, MI, 48197, USA.
| | - Xiaoming Liu
- USF Genomics and College of Public Health, University of South Florida, Tampa, FL, USA.
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25
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Figueiredo DLA, Ximenez JPB, Seiva FRF, Panis C, Bezerra RDS, Ferrasa A, Cecchini AL, de Medeiros AI, Almeida AMF, Ramão A, Boldt ABW, Moya CF, Chin CM, de Paula D, Rech D, Gradia DF, Malheiros D, Venturini D, Tavares ER, Carraro E, Ribeiro EMDSF, Pereira EM, Tuon FF, Follador FAC, Fernandes GSA, Volpato H, Cólus IMDS, de Oliveira JC, Rodrigues JHDS, dos Santos JL, Visentainer JEL, Brandi JC, Serpeloni JM, Bonini JS, de Oliveira KB, Fiorentin K, Lucio LC, Faccin-Galhardi LC, Ferreto LED, Lioni LMY, Consolaro MEL, Vicari MR, Arbex MA, Pileggi M, Watanabe MAE, Costa MAR, Giannini MJSM, Amarante MK, Khalil NM, de Lima QA, Herai RH, Guembarovski RL, Shinsato RN, Mainardes RM, Giuliatti S, Yamada-Ogatta SF, Gerber VKDQ, Pavanelli WR, da Silva WC, Petzl-Erler ML, Valente V, Soares CP, Cavalli LR, Silva WA. COVID-19: The question of genetic diversity and therapeutic intervention approaches. Genet Mol Biol 2022; 44:e20200452. [PMID: 35421211 PMCID: PMC9075701 DOI: 10.1590/1678-4685-gmb-2020-0452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/24/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), is the largest pandemic in modern history with very high infection rates and considerable mortality. The disease, which emerged in China's Wuhan province, had its first reported case on December 29, 2019, and spread rapidly worldwide. On March 11, 2020, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic and global health emergency. Since the outbreak, efforts to develop COVID-19 vaccines, engineer new drugs, and evaluate existing ones for drug repurposing have been intensively undertaken to find ways to control this pandemic. COVID-19 therapeutic strategies aim to impair molecular pathways involved in the virus entrance and replication or interfere in the patients' overreaction and immunopathology. Moreover, nanotechnology could be an approach to boost the activity of new drugs. Several COVID-19 vaccine candidates have received emergency-use or full authorization in one or more countries, and others are being developed and tested. This review assesses the different strategies currently proposed to control COVID-19 and the issues or limitations imposed on some approaches by the human and viral genetic variability.
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Affiliation(s)
- David Livingstone Alves Figueiredo
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina, Guarapuava, PR, Brazil
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - João Paulo Bianchi Ximenez
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicologia e Ciência de Alimentos, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Fábio Rodrigues Ferreira Seiva
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carolina Panis
- Universidade Estadual do Oeste do Paraná, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rafael dos Santos Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Adriano Ferrasa
- Universidade Estadual de Ponta Grossa, Ponta Grossa, Programa de Pós Graduação em Computação Aplicada, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alessandra Lourenço Cecchini
- Universidade Estadual de Londrina, Departamento de Patologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alexandra Ivo de Medeiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ana Marisa Fusco Almeida
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Anelisa Ramão
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Ciências Biológicas, Guarapuava, PR, Brazil
| | - Angelica Beate Winter Boldt
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carla Fredrichsen Moya
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina Veterinária, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Chung Man Chin
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- União das Faculdades dos Grandes Lagos (UNILAGO), Centro de Pesquisa Avançada em Medicina, São José do Rio Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel de Paula
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel Rech
- Universidade Estadual do Oeste do Paraná (UNIOESTE), Hospital do Câncer Francisco Beltrão, Laboratório de Biologia de Tumores, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniela Fiori Gradia
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Malheiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Venturini
- Universidade Estadual de Londrina, Centro de Ciências da Saúde, Departamento de patologia, clínica e toxicologia, Laboratório de bioquímica clínica, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Eliandro Reis Tavares
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Emerson Carraro
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Virologia Clínica, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Enilze Maria de Souza Fonseca Ribeiro
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Evani Marques Pereira
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Felipe Francisco Tuon
- Universidade Católica do Paraná, Laboratório de Doenças Infecciosas Emergentes, Pontifícia Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Franciele Aní Caovilla Follador
- Universidade Estadual do Oeste do Paraná, Departamento de Ciências da Vida, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Glaura Scantamburlo Alves Fernandes
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Hélito Volpato
- Universidade Estadual do Paraná (UNESPAR), Faculdade de Ciências Biológicas, Centro de Ciências Humanas e Educação, Paranavaí, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ilce Mara de Syllos Cólus
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jaqueline Carvalho de Oliveira
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Henrique da Silva Rodrigues
- Universidade do Estado de São Paulo (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Leandro dos Santos
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jeane Eliete Laguila Visentainer
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Cristina Brandi
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Mara Serpeloni
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Sartori Bonini
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karen Brajão de Oliveira
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Genética Molecular e Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karine Fiorentin
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Léia Carolina Lucio
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ligia Carla Faccin-Galhardi
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lirane Elize Defante Ferreto
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lucy Megumi Yamauchi Lioni
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
| | - Marcia Edilaine Lopes Consolaro
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Abdo Arbex
- Universidade de Araraquara, Faculdade de Medicina, Área temática de Pneumologia, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Pileggi
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Angelica Ehara Watanabe
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Antônia Ramos Costa
- Universidade do Estado do Paraná, Colegiada de Enfermagem, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria José S. Mendes Giannini
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marla Karine Amarante
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Najeh Maissar Khalil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Quirino Alves de Lima
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberto H. Herai
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberta Losi Guembarovski
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rogério N. Shinsato
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rubiana Mara Mainardes
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Silvana Giuliatti
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Viviane Knuppel de Quadros Gerber
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wander Rogério Pavanelli
- Universidade Estadual de Londrina, Laboratório de Imunoparasitologia de Doenças Negligenciadas e Câncer, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Weber Claudio da Silva
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Luiza Petzl-Erler
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Valeria Valente
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Christiane Pienna Soares
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Luciane Regina Cavalli
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wilson Araujo Silva
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Instituto Nacional de Ciência e Tecnologia em Células-Tronco e Terapia Celular (INCT/CNPq), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
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Maranini B, Ciancio G, Ferracin M, Cultrera R, Negrini M, Sabbioni S, Govoni M. microRNAs and Inflammatory Immune Response in SARS-CoV-2 Infection: A Narrative Review. Life (Basel) 2022; 12:life12020288. [PMID: 35207576 PMCID: PMC8879390 DOI: 10.3390/life12020288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
The current SARS-CoV-2 pandemic has emerged as an international challenge with strong medical and socioeconomic impact. The spectrum of clinical manifestations of SARS-CoV-2 is wide, covering asymptomatic or mild cases up to severe and life-threatening complications. Critical courses of SARS-CoV-2 infection are thought to be driven by the so-called “cytokine storm”, derived from an excessive immune response that induces the release of proinflammatory cytokines and chemokines. In recent years, non-coding RNAs (ncRNAs) emerged as potential diagnostic and therapeutic biomarkers in both inflammatory and infectious diseases. Therefore, the identification of SARS-CoV-2 miRNAs and host miRNAs is an important research topic, investigating the host–virus crosstalk in COVID-19 infection, trying to answer the pressing question of whether miRNA-based therapeutics can be employed to tackle SARS-CoV-2 complications. In this review, we aimed to directly address ncRNA role in SARS-CoV-2-immune system crosstalk upon COVID-19 infection, particularly focusing on inflammatory pathways and cytokine storm syndromes.
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Affiliation(s)
- Beatrice Maranini
- Rheumatology Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (G.C.); (M.G.)
- Correspondence:
| | - Giovanni Ciancio
- Rheumatology Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (G.C.); (M.G.)
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40138 Bologna, Italy;
| | - Rosario Cultrera
- Infectious Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy;
| | - Massimo Negrini
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy;
| | - Silvia Sabbioni
- Department of Life Sciences and Biotechnologies, University of Ferrara, 44121 Ferrara, Italy;
| | - Marcello Govoni
- Rheumatology Unit, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (G.C.); (M.G.)
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Kucher AN, Koroleva IA, Zarubin AA, Nazarenko MS. MicroRNAs as the Potential Regulators of SARS-CoV-2 Infection and Modifiers of the COVID-19 Clinical Features. Mol Biol 2022; 56:29-45. [PMID: 35464324 PMCID: PMC9016216 DOI: 10.1134/s0026893322010034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 12/27/2022]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) warrants the identification of factors that may determine both risk and severity of infection. The factors include microRNAs that have a wide regulatory potential and hence are particularly interesting. The review focuses on the potential roles of human microRNAs and the viral genome as well as microRNAs in SARS-CoV-2 infection and clinical features of COVID-19. The review summarizes the information about the human microRNAs that are thought to specifically bind to the SARS-CoV-2 genome and considers their expression levels in various organs (cells) in both healthy state and pathologies that are risk factors for severe COVID-19. Potential mechanisms whereby SARS-CoV-2 may affect the clinical features of COVID-19 are discussed in brief. The mechanisms include blocking of human microRNAs and RNA-binding proteins, changes in gene expression in infected cells, and possible epigenetic modifications of the human genome with the participation of coronavirus microRNAs.
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Affiliation(s)
- A. N. Kucher
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - Iu. A. Koroleva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - A. A. Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - M. S. Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
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28
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Molinero M, Benítez ID, González J, Gort-Paniello C, Moncusí-Moix A, Rodríguez-Jara F, García-Hidalgo MC, Torres G, Vengoechea JJ, Gómez S, Cabo R, Caballero J, Bermejo-Martin JF, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Torres A, Barbé F, de Gonzalo-Calvo D. Bronchial Aspirate-Based Profiling Identifies MicroRNA Signatures Associated With COVID-19 and Fatal Disease in Critically Ill Patients. Front Med (Lausanne) 2022; 8:756517. [PMID: 35186962 PMCID: PMC8850692 DOI: 10.3389/fmed.2021.756517] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
Background The pathophysiology of COVID-19-related critical illness is not completely understood. Here, we analyzed the microRNA (miRNA) profile of bronchial aspirate (BAS) samples from COVID-19 and non-COVID-19 patients admitted to the ICU to identify prognostic biomarkers of fatal outcomes and to define molecular pathways involved in the disease and adverse events. Methods Two patient populations were included (n = 89): (i) a study population composed of critically ill COVID-19 and non-COVID-19 patients; (ii) a prospective study cohort composed of COVID-19 survivors and non-survivors among patients assisted by invasive mechanical ventilation (IMV). BAS samples were obtained by bronchoaspiration during the ICU stay. The miRNA profile was analyzed using RT-qPCR. Detailed biomarker and bioinformatics analyses were performed. Results The deregulation in five miRNA ratios (miR-122-5p/miR-199a-5p, miR-125a-5p/miR-133a-3p, miR-155-5p/miR-486-5p, miR-214-3p/miR-222-3p, and miR-221-3p/miR-27a-3p) was observed when COVID-19 and non-COVID-19 patients were compared. In addition, five miRNA ratios segregated between ICU survivors and nonsurvivors (miR-1-3p/miR-124-3p, miR-125b-5p/miR-34a-5p, miR-126-3p/miR-16-5p, miR-199a-5p/miR-9-5p, and miR-221-3p/miR-491-5p). Through multivariable analysis, we constructed a miRNA ratio-based prediction model for ICU mortality that optimized the best combination of miRNA ratios (miR-125b-5p/miR-34a-5p, miR-199a-5p/miR-9-5p, and miR-221-3p/miR-491-5p). The model (AUC 0.85) and the miR-199a-5p/miR-9-5p ratio (AUC 0.80) showed an optimal discrimination value and outperformed the best clinical predictor for ICU mortality (days from first symptoms to IMV initiation, AUC 0.73). The survival analysis confirmed the usefulness of the miRNA ratio model and the individual ratio to identify patients at high risk of fatal outcomes following IMV initiation. Functional enrichment analyses identified pathological mechanisms implicated in fibrosis, coagulation, viral infections, immune responses and inflammation. Conclusions COVID-19 induces a specific miRNA signature in BAS from critically ill patients. In addition, specific miRNA ratios in BAS samples hold individual and collective potential to improve risk-based patient stratification following IMV initiation in COVID-19-related critical illness. The biological role of the host miRNA profiles may allow a better understanding of the different pathological axes of the disease.
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Affiliation(s)
- Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Iván D. Benítez
- 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
| | - Clara Gort-Paniello
- 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
| | - Anna Moncusí-Moix
- 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
| | - Fátima Rodríguez-Jara
- 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
| | - María C. García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Gerard Torres
- 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
| | - J. J. Vengoechea
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Silvia Gómez
- 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
| | - Ramón Cabo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Jesús F. Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, 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
- *Correspondence: David de Gonzalo-Calvo
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Zhang S, Amahong K, Zhang C, Li F, Gao J, Qiu Y, Zhu F. RNA-RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Brief Bioinform 2022; 23:bbab397. [PMID: 34585235 PMCID: PMC8500159 DOI: 10.1093/bib/bbab397] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/11/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
Some studies reported that genomic RNA of SARS-CoV-2 can absorb a few host miRNAs that regulate immune-related genes and then deprive their function. In this perspective, we conjecture that the absorption of the SARS-CoV-2 genome to host miRNAs is not a coincidence, which may be an indispensable approach leading to viral survival and development in host. In our study, we collected five datasets of miRNAs that were predicted to interact with the genome of SARS-CoV-2. The targets of these miRNAs in the five groups were consistently enriched immune-related pathways and virus-infectious diseases. Interestingly, the five datasets shared no one miRNA but their targets shared 168 genes. The signaling pathway enrichment of 168 shared targets implied an unbalanced immune response that the most of interleukin signaling pathways and none of the interferon signaling pathways were significantly different. Protein-protein interaction (PPI) network using the shared targets showed that PPI pairs, including IL6-IL6R, were related to the process of SARS-CoV-2 infection and pathogenesis. In addition, we found that SARS-CoV-2 absorption to host miRNA could benefit two popular mutant strains for more infectivity and pathogenicity. Conclusively, our results suggest that genomic RNA absorption to host miRNAs may be a vital approach by which SARS-CoV-2 disturbs the host immune system and infects host cells.
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Affiliation(s)
- Song Zhang
- College of Pharmaceutical Sciences in Zhejiang University, and the First Affiliated Hospital of Zhejiang University School of Medicine, China
| | | | - Chenyang Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Yunqing Qiu
- First Affiliated Hospital in Zhejiang University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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30
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Xue M, Feng L. The Role of Unfolded Protein Response in Coronavirus Infection and Its Implications for Drug Design. Front Microbiol 2022; 12:808593. [PMID: 35003039 PMCID: PMC8740020 DOI: 10.3389/fmicb.2021.808593] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus is an important pathogen with a wide spectrum of infection and potential threats to humans and animals. Its replication occurs in the cytoplasm and is closely related to the endoplasmic reticulum (ER). Studies reported that coronavirus infection causes ER stress, and cells simultaneously initiate unfolded protein response (UPR) to alleviate the disturbance of ER homeostasis. Activation of the three branches of UPR (PERK, IRE1, and ATF6) modulates various signaling pathways, such as innate immune response, microRNA, autophagy, and apoptosis. Therefore, a comprehensive understanding of the relationship between coronavirus and ER stress is helpful to understand the replication and pathogenesis of coronavirus. This paper summarizes the current knowledge of the complex interplay between coronavirus and UPR branches, focuses on the effect of ER stress on coronavirus replication and coronavirus resistance to host innate immunity, and summarizes possible drug targets to regulate the impact of coronavirus infection.
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Affiliation(s)
- Mei Xue
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
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31
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Yang CY, Chen YH, Liu PJ, Hu WC, Lu KC, Tsai KW. The emerging role of miRNAs in the pathogenesis of COVID-19: Protective effects of nutraceutical polyphenolic compounds against SARS-CoV-2 infection. Int J Med Sci 2022; 19:1340-1356. [PMID: 35928726 PMCID: PMC9346380 DOI: 10.7150/ijms.76168] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/08/2022] [Indexed: 11/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause immunosuppression and cytokine storm, leading to lung damage and death. The clinical efficacy of anti-SARS-CoV-2 drugs in preventing viral entry into host cells and suppressing viral replication remains inadequate. MicroRNAs (miRNAs) are crucial to the immune response to and pathogenesis of coronaviruses, such as SARS-CoV-2. However, the specific roles of miRNAs in the life cycle of SARS-CoV-2 remain unclear. miRNAs can participate in SARS-CoV-2 infection and pathogenesis through at least four possible mechanisms: 1. host cell miRNA expression interfering with SARS-CoV-2 cell entry, 2. SARS-CoV-2-derived RNA transcripts acting as competitive endogenous RNAs (ceRNAs) that may attenuate host cell miRNA expression, 3. host cell miRNA expression modulating SARS-CoV-2 replication, and 4. SARS-CoV-2-encoded miRNAs silencing the expression of host protein-coding genes. SARS-CoV-2-related miRNAs may be used as diagnostic or prognostic biomarkers for predicting outcomes among patients with SARS-CoV-2 infection. Furthermore, accumulating evidence suggests that dietary polyphenolic compounds may protect against SARS-CoV-2 infection by modulating host cell miRNA expression. These findings have major implications for the future diagnosis and treatment of COVID-19.
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Affiliation(s)
- Chih-Yun Yang
- Division of Chest Medicine, Kaohsiung Municipal Min-Sheng Hospital, Kaohsiung, Taiwan, ROC
| | - Yu-Hsuan Chen
- Division of Chest Medicine, Department of Internal Medicine, CHENG HSIN General Hospital, Taipei, Taiwan, ROC
| | - Pei-Jung Liu
- Division of Chest Medicine, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Wan-Chung Hu
- Department of Clinical Pathology and Medical Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC.,Division of Nephrology, Department of Medicine, Fu-Jen Catholic University Hospital, School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan, ROC
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
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32
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Bautista-Becerril B, Pérez-Dimas G, Sommerhalder-Nava PC, Hanono A, Martínez-Cisneros JA, Zarate-Maldonado B, Muñoz-Soria E, Aquino-Gálvez A, Castillejos-López M, Juárez-Cisneros A, Lopez-Gonzalez JS, Camarena A. miRNAs, from Evolutionary Junk to Possible Prognostic Markers and Therapeutic Targets in COVID-19. Viruses 2021; 14:41. [PMID: 35062245 PMCID: PMC8781105 DOI: 10.3390/v14010041] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic has been a public health issue around the world in the last few years. Currently, there is no specific antiviral treatment to fight the disease. Thus, it is essential to highlight possible prognostic predictors that could identify patients with a high risk of developing complications. Within this framework, miRNA biomolecules play a vital role in the genetic regulation of various genes, principally, those related to the pathophysiology of the disease. Here, we review the interaction of host and viral microRNAs with molecular and cellular elements that could potentiate the main pulmonary, cardiac, renal, circulatory, and neuronal complications in COVID-19 patients. miR-26a, miR-29b, miR-21, miR-372, and miR-2392, among others, have been associated with exacerbation of the inflammatory process, increasing the risk of a cytokine storm. In addition, increased expression of miR-15b, -199a, and -491 are related to the prognosis of the disease, and miR-192 and miR-323a were identified as clinical predictors of mortality in patients admitted to the intensive care unit. Finally, we address miR-29, miR-122, miR-155, and miR-200, among others, as possible therapeutic targets. However, more studies are required to confirm these findings.
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Affiliation(s)
- Brandon Bautista-Becerril
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (B.B.-B.); (A.J.-C.)
- Escuela Superior de Medicina, Departamento de Posgrado, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (G.P.-D.); (E.M.-S.)
| | - Guillermo Pérez-Dimas
- Escuela Superior de Medicina, Departamento de Posgrado, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (G.P.-D.); (E.M.-S.)
| | - Paola C. Sommerhalder-Nava
- Facultad de Ciencias de la Salud, Universidad Anáhuac México Norte, Mexico City 52786, Mexico; (P.C.S.-N.); (A.H.); (B.Z.-M.)
| | - Alejandro Hanono
- Facultad de Ciencias de la Salud, Universidad Anáhuac México Norte, Mexico City 52786, Mexico; (P.C.S.-N.); (A.H.); (B.Z.-M.)
| | | | - Bárbara Zarate-Maldonado
- Facultad de Ciencias de la Salud, Universidad Anáhuac México Norte, Mexico City 52786, Mexico; (P.C.S.-N.); (A.H.); (B.Z.-M.)
| | - Evangelina Muñoz-Soria
- Escuela Superior de Medicina, Departamento de Posgrado, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (G.P.-D.); (E.M.-S.)
| | - Arnoldo Aquino-Gálvez
- Laboratorio de Biología Molecular, Departamento de Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Manuel Castillejos-López
- Departamento de Epidemiología Hospitalaria e Infectología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Armida Juárez-Cisneros
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (B.B.-B.); (A.J.-C.)
| | - Jose S. Lopez-Gonzalez
- Laboratorio de Cáncer Pulmonar, Departamento de Enfermedades Crónico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Angel Camarena
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (B.B.-B.); (A.J.-C.)
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Hu J, Stojanović J, Yasamineh S, Yasamineh P, Karuppannan SK, Hussain Dowlath MJ, Serati-Nouri H. The potential use of microRNAs as a therapeutic strategy for SARS-CoV-2 infection. Arch Virol 2021; 166:2649-2672. [PMID: 34278528 PMCID: PMC8286877 DOI: 10.1007/s00705-021-05152-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/21/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To date, there is no effective therapeutic approach for treating SARS-CoV-2 infections. MicroRNAs (miRNAs) have been recognized to target the viral genome directly or indirectly, thereby inhibiting viral replication. Several studies have demonstrated that host miRNAs target different sites in SARS-CoV-2 RNA and constrain the production of essential viral proteins. Furthermore, miRNAs have lower toxicity, are more immunogenic, and are more diverse than protein-based and even plasmid-DNA-based therapeutic agents. In this review, we emphasize the role of miRNAs in viral infection and their potential use as therapeutic agents against COVID-19 disease. The potential of novel miRNA delivery strategies, especially EDV™ nanocells, for targeting lung tissue for treatment of SARS-CoV-2 infection is also discussed.
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Affiliation(s)
- Jiulue Hu
- Zhang Zhongjing College of Chinese Medicine, Nanyang Institute of Technology, Nanyang, 473004, Henan, China
| | - Jelena Stojanović
- Faculty of Mathematics and Computer Science in Belgrade, ALFA BK University, Belgrade, Serbia
| | - Saman Yasamineh
- Young Researcher and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | - Pooneh Yasamineh
- Young Researcher and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Sathish Kumar Karuppannan
- Center for Environmental Nuclear Research, Directorate of Research and Virtual Education, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, 603203, Kanchipuram, Chennai, Tamil Nadu, India
| | - Mohammed Junaid Hussain Dowlath
- Center for Environmental Nuclear Research, Directorate of Research and Virtual Education, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, 603203, Kanchipuram, Chennai, Tamil Nadu, India
| | - Hamed Serati-Nouri
- Stem cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Serpeloni JM, Lima Neto QA, Lucio LC, Ramão A, Carvalho de Oliveira J, Gradia DF, Malheiros D, Ferrasa A, Marchi R, Figueiredo DLA, Silva WA, Ribeiro EMSF, Cólus IMS, Cavalli LR. Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection. Immunobiology 2021; 226:152130. [PMID: 34425415 PMCID: PMC8378551 DOI: 10.1016/j.imbio.2021.152130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
In this review, we highlight the interaction of SARS-CoV-2 virus and host genomes, reporting the current studies on the sequence analysis of SARS-CoV-2 isolates and host genomes from diverse world populations. The main genetic variants that are present in both the virus and host genomes were particularly focused on the ACE2 and TMPRSS2 genes, and their impact on the patients' susceptibility to the virus infection and severity of the disease. Finally, the interaction of the virus and host non-coding RNAs is described in relation to their regulatory roles in target genes and/or signaling pathways critically associated with SARS-CoV-2 infection. Altogether, these studies provide a significant contribution to the knowledge of SARS-CoV-2 mechanisms of infection and COVID-19 pathogenesis. The described genetic variants and molecular factors involved in host/virus genome interactions have significantly contributed to defining patient risk groups, beyond those based on patients' age and comorbidities, and they are promising candidates to be potentially targeted in treatment strategies for COVID-19 and other viral infectious diseases.
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Affiliation(s)
- Juliana M Serpeloni
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Quirino Alves Lima Neto
- Departamento de Ciências Básicas da Saúde, CCS, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Léia Carolina Lucio
- Programa de Pós-graduação em Ciências Aplicadas à Saúde, CCS, Universidade Estadual do Oeste do Paraná, Francisco Beltrão, PR, Brazil
| | - Anelisa Ramão
- Departamento de Ciências Biológicas, Universidade Estadual do Centro-Oeste, Guarapuava, PR, Brazil
| | | | | | - Danielle Malheiros
- Departamento de Genética, SCB, Universidade Federal do Paraná, PR, Brazil
| | - Adriano Ferrasa
- Departamento de Informática, SECATE, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Rafael Marchi
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - David L A Figueiredo
- Departamento de Medicina, Universidade Estadual do Centro-Oeste, UNICENTRO e Instituto de Pesquisa para o Câncer, IPEC, Guarapuava, PR, Brazil
| | - Wilson A Silva
- Departamento de Genética, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, SP, e Instituto de Pesquisa para o Câncer, IPEC, Guarapuava, PR, Brazil
| | | | - Ilce M S Cólus
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Luciane R Cavalli
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
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Plowman T, Lagos D. Non-Coding RNAs in COVID-19: Emerging Insights and Current Questions. Noncoding RNA 2021; 7:54. [PMID: 34564316 PMCID: PMC8482139 DOI: 10.3390/ncrna7030054] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/15/2022] Open
Abstract
The highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as the causative agent of coronavirus disease 2019 (COVID-19) in late 2019, igniting an unprecedented pandemic. A mechanistic picture characterising the acute immunopathological disease in severe COVID-19 is developing. Non-coding RNAs (ncRNAs) constitute the transcribed but un-translated portion of the genome and, until recent decades, have been undiscovered or overlooked. A growing body of research continues to demonstrate their interconnected involvement in the immune response to SARS-CoV-2 and COVID-19 development by regulating several of its pathological hallmarks: cytokine storm syndrome, haemostatic alterations, immune cell recruitment, and vascular dysregulation. There is also keen interest in exploring the possibility of host-virus RNA-RNA and RNA-RBP interactions. Here, we discuss and evaluate evidence demonstrating the involvement of short and long ncRNAs in COVID-19 and use this information to propose hypotheses for future mechanistic and clinical studies.
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Affiliation(s)
- Tobias Plowman
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5DD, UK;
- Hull York Medical School, University of York, Wentworth Way, York YO10 5DD, UK
| | - Dimitris Lagos
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5DD, UK;
- Hull York Medical School, University of York, Wentworth Way, York YO10 5DD, UK
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Srivastava M, Hall D, Omoru OB, Gill HM, Smith S, Janga SC. Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components. Microorganisms 2021; 9:1794. [PMID: 34576690 PMCID: PMC8464733 DOI: 10.3390/microorganisms9091794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/14/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid evolution has led to a global health crisis. Increasing mutations across the SARS-CoV-2 genome have severely impacted the development of effective therapeutics and vaccines to combat the virus. However, the new SARS-CoV-2 variants and their evolutionary characteristics are not fully understood. Host cellular components such as the ACE2 receptor, RNA-binding proteins (RBPs), microRNAs, small nuclear RNA (snRNA), 18s rRNA, and the 7SL RNA component of the signal recognition particle (SRP) interact with various structural and non-structural proteins of the SARS-CoV-2. Several of these viral proteins are currently being examined for designing antiviral therapeutics. In this review, we discuss current advances in our understanding of various host cellular components targeted by the virus during SARS-CoV-2 infection. We also summarize the mutations across the SARS-CoV-2 genome that directs the evolution of new viral strains. Considering coronaviruses are rapidly evolving in humans, this enables them to escape therapeutic therapies and vaccine-induced immunity. In order to understand the virus's evolution, it is essential to study its mutational patterns and their impact on host cellular machinery. Finally, we present a comprehensive survey of currently available databases and tools to study viral-host interactions that stand as crucial resources for developing novel therapeutic strategies for combating SARS-CoV-2 infection.
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Affiliation(s)
- Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Informatics and Communications Technology Complex, 535 West Michigan Street, Indianapolis, IN 46202, USA; (M.S.); (D.H.); (O.B.O.); (H.M.G.); (S.S.)
| | - Dwight Hall
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Informatics and Communications Technology Complex, 535 West Michigan Street, Indianapolis, IN 46202, USA; (M.S.); (D.H.); (O.B.O.); (H.M.G.); (S.S.)
| | - Okiemute Beatrice Omoru
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Informatics and Communications Technology Complex, 535 West Michigan Street, Indianapolis, IN 46202, USA; (M.S.); (D.H.); (O.B.O.); (H.M.G.); (S.S.)
| | - Hunter Mathias Gill
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Informatics and Communications Technology Complex, 535 West Michigan Street, Indianapolis, IN 46202, USA; (M.S.); (D.H.); (O.B.O.); (H.M.G.); (S.S.)
| | - Sarah Smith
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Informatics and Communications Technology Complex, 535 West Michigan Street, Indianapolis, IN 46202, USA; (M.S.); (D.H.); (O.B.O.); (H.M.G.); (S.S.)
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis, Informatics and Communications Technology Complex, 535 West Michigan Street, Indianapolis, IN 46202, USA; (M.S.); (D.H.); (O.B.O.); (H.M.G.); (S.S.)
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, USA
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McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler J, Mason CE, Chatterjee A, Meller R, Beheshti A. The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33948587 DOI: 10.1101/2021.04.23.441024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.
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Narożna M, Rubiś B. Anti-SARS-CoV-2 Strategies and the Potential Role of miRNA in the Assessment of COVID-19 Morbidity, Recurrence, and Therapy. Int J Mol Sci 2021; 22:8663. [PMID: 34445368 PMCID: PMC8395427 DOI: 10.3390/ijms22168663] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/07/2021] [Accepted: 08/08/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, we have experienced a serious pandemic. Despite significant technological advances in molecular technologies, it is very challenging to slow down the infection spread. It appeared that due to globalization, SARS-CoV-2 spread easily and adapted to new environments or geographical or weather zones. Additionally, new variants are emerging that show different infection potential and clinical outcomes. On the other hand, we have some experience with other pandemics and some solutions in virus elimination that could be adapted. This is of high importance since, as the latest reports demonstrate, vaccine technology might not follow the new, mutated virus outbreaks. Thus, identification of novel strategies and markers or diagnostic methods is highly necessary. For this reason, we present some of the latest views on SARS-CoV-2/COVID-19 therapeutic strategies and raise a solution based on miRNA. We believe that in the face of the rapidly increasing global situation and based on analogical studies of other viruses, the possibility of using the biological potential of miRNA technology is very promising. It could be used as a promising diagnostic and prognostic factor, as well as a therapeutic target and tool.
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Affiliation(s)
- Maria Narożna
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4 Święcickiego St., 60-781 Poznan, Poland;
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, 49 Przybyszewskiego St., 60-355 Poznan, Poland
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40
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Halim FS, Parmin NA, Hashim U, Gopinath SCB, Dahalan FA, Zakaria II, Ang WC, Jaapar NF. MicroRNA of N-region from SARS-CoV-2: Potential sensing components for biosensor development. Biotechnol Appl Biochem 2021; 69:1696-1711. [PMID: 34378814 PMCID: PMC8427135 DOI: 10.1002/bab.2239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/29/2022]
Abstract
An oligonucleotide DNA probe has been developed for the application in the DNA electrochemical biosensor for the early diagnosis of coronavirus disease (COVID-19). Here, the virus microRNA from the N-gene of severe acute respiratory syndrome-2 (SARS-CoV-2) was used for the first time as a specific target for detecting the virus and became a framework for developing the complementary DNA probe. The sequence analysis of the virus microRNA was carried out using bioinformatics tools including basic local alignment search tools, multiple sequence alignment from CLUSTLW, microRNA database (miRbase), microRNA target database, and gene analysis. Cross-validation of distinct strains of coronavirus and human microRNA sequences was completed to validate the percentage of identical and consent regions. The percent identity parameter from the bioinformatics tools revealed the virus microRNAs' sequence has a 100% match with the genome of SARS-CoV-2 compared with other coronavirus strains, hence improving the selectivity of the complementary DNA probe. The 30 mer with 53.0% GC content of complementary DNA probe 5' GCC TGA GTT GAG TCA GCA CTG CTC ATG GAT 3' was designed and could be used as a bioreceptor for the biosensor development in the clinical and environmental diagnosis of COVID-19.
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Affiliation(s)
- Fatin Syakirah Halim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - N A Parmin
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Uda Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia.,Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia
| | - Farrah Aini Dahalan
- Faculty of Civil Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute (MGI), National Institute of Biotechnology (NIBM), Kajang, Selangor, Malaysia
| | - Wei Chern Ang
- Clinical Research Centre, Ministry of Health Malaysia, Hospital Tuanku Fauziah Perlis, Kangar, Perlis, 01000, Malaysia
| | - Nurfareezah Fareezah Jaapar
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
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41
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Milenkovic D, Ruskovska T, Rodriguez-Mateos A, Heiss C. Polyphenols Could Prevent SARS-CoV-2 Infection by Modulating the Expression of miRNAs in the Host Cells. Aging Dis 2021; 12:1169-1182. [PMID: 34341700 PMCID: PMC8279534 DOI: 10.14336/ad.2021.0223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/23/2021] [Indexed: 12/19/2022] Open
Abstract
Coronaviruses (CoVs) are single-stranded RNA viruses which following virus attachment and entry into the host cell, particularly type 2 pneumocytes but also endothelial cells, release RNA into cytosol where it serves as a matrix for the host translation machinery to produce viral proteins. The viral RNA in cytoplasm can interact with host cell microRNAs which can degrade viral RNA and/or prevent viral replication. As such host cellular miRNAs represent key cellular mediators of antiviral defense. Polyphenols, plant food bioactives, exert antiviral properties, which is partially due to their capacity to modulate the expression of miRNAs. The objective of this work was to assess if polyphenols can play a role in prevention of SARS-CoV-2 associated complications by modulating the expression of host miRNAs. To test this hypothesis, we performed literature search to identify miRNAs that could bind SARS-CoV-2 RNA as well as miRNAs which expression can be modulated by polyphenols in lung, type 2 pneumocytes or endothelial cells. We identified over 600 miRNAs that have capacity to bind viral RNA and 125 miRNAs which expression can be modulated by polyphenols in the cells of interest. We identified that there are 17 miRNAs with both the capacity to bind viral RNA and which expression can be modulated by polyphenols. Some of these miRNAs have been identified as having antiviral properties or can target genes involved in regulation of processes of viral replication, apoptosis or viral infection. Taken together this analysis suggests that polyphenols could modulate expression of miRNAs in alveolar and endothelial cells and exert antiviral capacity.
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Affiliation(s)
- Dragan Milenkovic
- Université Clermont Auvergne, INRAE, UNH, F-63000 Clermont-Ferrand, France.
- Department of Internal Medicine, Division of Cardiovascular Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA.
| | - Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, Stip, North Macedonia.
| | | | - Christian Heiss
- Department of Nutritional Sciences, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK.
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Winkle M, El-Daly SM, Fabbri M, Calin GA. Noncoding RNA therapeutics - challenges and potential solutions. Nat Rev Drug Discov 2021; 20:629-651. [PMID: 34145432 PMCID: PMC8212082 DOI: 10.1038/s41573-021-00219-z] [Citation(s) in RCA: 759] [Impact Index Per Article: 253.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 02/07/2023]
Abstract
Therapeutic targeting of noncoding RNAs (ncRNAs), such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), represents an attractive approach for the treatment of cancers, as well as many other diseases. Over the past decade, substantial effort has been made towards the clinical application of RNA-based therapeutics, employing mostly antisense oligonucleotides and small interfering RNAs, with several gaining FDA approval. However, trial results have so far been ambivalent, with some studies reporting potent effects whereas others demonstrated limited efficacy or toxicity. Alternative entities such as antimiRNAs are undergoing clinical testing, and lncRNA-based therapeutics are gaining interest. In this Perspective, we discuss key challenges facing ncRNA therapeutics - including issues associated with specificity, delivery and tolerability - and focus on promising emerging approaches that aim to boost their success.
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Affiliation(s)
- Melanie Winkle
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
| | - Sherien M El-Daly
- Medical Biochemistry Department, Medical Research Division - Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences - National Research Centre, Cairo, Egypt
| | - Muller Fabbri
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - George A Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
- The RNA Interference and Non-codingRNA Center, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
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Gusev E, Sarapultsev A, Hu D, Chereshnev V. Problems of Pathogenesis and Pathogenetic Therapy of COVID-19 from the Perspective of the General Theory of Pathological Systems (General Pathological Processes). Int J Mol Sci 2021; 22:7582. [PMID: 34299201 PMCID: PMC8304657 DOI: 10.3390/ijms22147582] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic examines not only the state of actual health care but also the state of fundamental medicine in various countries. Pro-inflammatory processes extend far beyond the classical concepts of inflammation. They manifest themselves in a variety of ways, beginning with extreme physiology, then allostasis at low-grade inflammation, and finally the shockogenic phenomenon of "inflammatory systemic microcirculation". The pathogenetic core of critical situations, including COVID-19, is this phenomenon. Microcirculatory abnormalities, on the other hand, lie at the heart of a specific type of general pathological process known as systemic inflammation (SI). Systemic inflammatory response, cytokine release, cytokine storm, and thrombo-inflammatory syndrome are all terms that refer to different aspects of SI. As a result, the metabolic syndrome model does not adequately reflect the pathophysiology of persistent low-grade systemic inflammation (ChSLGI). Diseases associated with ChSLGI, on the other hand, are risk factors for a severe COVID-19 course. The review examines the role of hypoxia, metabolic dysfunction, scavenger receptors, and pattern-recognition receptors, as well as the processes of the hemophagocytic syndrome, in the systemic alteration and development of SI in COVID-19.
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Affiliation(s)
- Evgenii Gusev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia; (E.G.); (V.C.)
| | - Alexey Sarapultsev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia; (E.G.); (V.C.)
- School of Medical Biology, South Ural State University, 454080 Chelyabinsk, Russia
| | - Desheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 200092, China;
| | - Valeriy Chereshnev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia; (E.G.); (V.C.)
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Keikha R, Hashemi-Shahri SM, Jebali A. The relative expression of miR-31, miR-29, miR-126, and miR-17 and their mRNA targets in the serum of COVID-19 patients with different grades during hospitalization. Eur J Med Res 2021; 26:75. [PMID: 34256840 PMCID: PMC8276226 DOI: 10.1186/s40001-021-00544-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The aim of this study was to evaluate the expression of four up/down-regulated inflammatory miRNAs and their mRNA targets in the serum samples of COVID-19 patients with different grades. Also, we investigated the relative expression of these miRNAs and mRNAs during hospitalization. METHODS In this cross-sectional study, 5 mL of blood sample were taken from COVID-19 patients with different grades and during hospitalization from several health centers of Yazd, Tehran, and Zahedan province of Iran from December 20, 2020 to March 2, 2021. The relative expression of miRNAs and mRNAs was evaluated by q-PCR. RESULTS We found that the relative expression of hsa-miR-31-3p, hsa-miR-29a-3p, and hsa-miR-126-3p was significantly decreased and the relative expression of their mRNA targets (ZMYM5, COL5A3, and CAMSAP1) was significantly increased with the increase of disease grade. Conversely, the relative expression of hsa-miR-17-3p was significantly increased and its mRNA target (DICER1) was significantly decreased with the increase of disease grade. This pattern was exactly seen during hospitalization of COVID-19 patients who did not respond to treatment. In COVID-19 patients who responded to treatment, the expression of selected miRNAs and their mRNA targets returned to the normal level. A negative significant correlation was seen between (1) the expression of hsa-miR-31-3p and ZMYM5, (2) hsa-miR-29a-3p and COL5A3, (3) hsa-miR-126-3p and CAMSAP1, and (4) hsa-miR-17-3p and DICER1 in COVID-19 patients with any grade (P < 0.05) and during hospitalization. CONCLUSIONS In this study, we gained a more accurate understanding of the expression of up/down-regulated inflammatory miRNAs in the blood of COVID-19 patients. The obtained data may help us in the diagnosis and prognosis of COVID-19. TRIAL REGISTRATION The ethics committee of Zahedan University of Medical Sciences, Zahedan, Iran. (Ethical Code: IR.ZAUMS.REC.1399.316) was registered for this project.
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Affiliation(s)
- Reza Keikha
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Pathology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed Mohammad Hashemi-Shahri
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ali Jebali
- Department of Medical Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
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Mariappan V, Manoharan PS, R P, Shanmugam L, Rao SR, Pillai AB. Potential biomarkers for the early prediction of SARS-COV-2 disease outcome. Microb Pathog 2021; 158:105057. [PMID: 34153419 PMCID: PMC8215377 DOI: 10.1016/j.micpath.2021.105057] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/18/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
Abstract
The current pandemic due to the fast spreading of SARS-CoV-2 infection has caused severe impairment in health, social, economic, scientific, and medical sectors across the globe. Owing to the not so well understood mechanism of disease pathogenesis in terms of variations in immune responses, there remains obscure why some of the patients who are infected by the novel SARS-CoV-2 develop an unpredictable clinical course that rapidly causes severe and deadly complications/manifestations. Currently, several assays are available for the confirmation of SARS-CoV-2 infection at the point of care. However, none of these assays can predict the severity of the COVID-19 disease. Thus, the identification of a prognostic biomarker that forecasts the condition of SARS-CoV-2 patients to develop a severe form of the disease could enable the clinicians for more efficient patient triage and treatment. In this regard, the present review describes the role of selected biomolecules that are crucially involved in the immune-pathogenesis of SARS-CoV-2 infection such as hyper-immune responsiveness, bradykinin storm and vascular leakage assuming these may serve as an effective prognostic biomarker in COVID-19 to understand the outcome of the disease. Based on the review, we also propose the development of a cost-effective SERS-based prognostic biosensor for the detection and quantification of biomolecules for use as a point-of-care system during a disease outbreak.
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Affiliation(s)
- Vignesh Mariappan
- Central Inter-Disciplinary Research Facility (CIDRF), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India.
| | - P S Manoharan
- Indira Gandhi Institute of Dental Science (IGIDS), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India.
| | - Pajanivel R
- Mahatma Gandhi Medical College and Research Institute (MGMCRI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India.
| | - Lokesh Shanmugam
- Mahatma Gandhi Medical College and Research Institute (MGMCRI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India.
| | - S R Rao
- Vice-President (Research, Innovation & Development), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India.
| | - Agieshkumar Balakrishna Pillai
- Central Inter-Disciplinary Research Facility (CIDRF), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India.
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Yong SJ. Diseased lungs may hinder COVID-19 development: A possible reason for the low prevalence of COPD in COVID-19 patients. Med Hypotheses 2021; 153:110628. [PMID: 34139599 PMCID: PMC8188770 DOI: 10.1016/j.mehy.2021.110628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022]
Abstract
Presently, it remains unclear why the prevalence of lung diseases, namely chronic obstructive pulmonary disease (COPD), is much lower than other medical comorbidities and the general population among patients with coronavirus disease 2019 (COVID-19). If COVID-19 is a respiratory disease, why is COPD not the leading risk factor for contracting COVID-19? The same odd phenomenon was also observed with other pathogenic human coronaviruses causing severe acute respiratory distress syndrome (SARS) and Middle East respiratory syndrome (MERS), but not other respiratory viral infections such as influenza and respiratory syncytial viruses. One commonly proposed reason for the low COPD rates among COVID-19 patients is the usage of inhaled corticosteroids or bronchodilators that may protect against COVID-19. However, another possible reason not discussed elsewhere is that lungs in a diseased state may not be conducive for the severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) to establish COVID-19. For one, COPD causes mucous plugging in large and small airways, which may hinder SARS-CoV-2 from reaching deeper parts of the lungs (i.e., alveoli). Thus, SARS-CoV-2 may only localize to the upper respiratory tract of persons with COPD, causing mild or asymptomatic infections requiring no hospital attention. Even if SARS-CoV-2 reaches the alveoli, cells therein are probably under a heavy burden of endoplasmic reticulum (ER) stress and extensively damaged where it may not support efficient viral replication. As a result, limited SARS-CoV-2 virions would be produced in diseased lungs, preventing the development of COVID-19.
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Affiliation(s)
- Shin Jie Yong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor, Malaysia.
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Tu SM. Stem Cell Theory of Cancer: Implications of a Viral Etiology in Certain Malignancies. Cancers (Basel) 2021; 13:cancers13112738. [PMID: 34205851 PMCID: PMC8199000 DOI: 10.3390/cancers13112738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 02/04/2023] Open
Abstract
Simple Summary We postulate that a virus is more likely to cause cancer when it infects a progenitor stem-like cell rather than a progeny differentiated cell. We propose that the virus may turn out to be a surreptitious agent and a serendipitous model in our quest to investigate the origin of cancer. When it pertains, oncology recapitulates ontogeny, although genetic makeup is king. Cellular context may be the key to elucidating a stem cell origin of cancer. Abstract In 1911, Peyton Rous (Nobel Prize winner in 1966) demonstrated that a virus (i.e., RSV) caused cancer in chickens. In 1976, Bishop and Varmus (Nobel Prize winners in 1989) showed that the cellular origin of retroviral oncogenes was actually normal cellular genes (i.e., proto-oncogenes). In this article, we revisit the role viruses play in the genetic origin of cancer. We review a link between viruses or cancer and autoimmunity in an alternative stem cell origin of cancer. We propose that a virus is more likely to cause cancer when it infects a progenitor stem-like cell rather than a progeny differentiated cell. We postulate that both known (e.g., HBV and HPV) and novel viruses (e.g., SARS-CoV-2) pose an imminent threat in the emergence of chronic viral diseases as well as virally induced malignancies. Knowing the origin of cancer has profound implications on our current conception and perception of cancer. It affects our conduct in cancer research and our delivery of cancer care. It would be ironic if viruses turn out to be a useful tool and an ideal means in our quest to verify a genetic versus stem cell origin of cancer. When it pertains, oncology recapitulates ontogeny; although genetic makeup is pivotal, cellular context may be paramount to elucidating a stem cell origin of cancer.
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Affiliation(s)
- Shi-Ming Tu
- Department of Genitourinary Medical Oncology, Unit 1374, The University of Texas, MD Anderson Cancer Center, 1155 Pressler Street, Houston, TX 77030-3721, USA
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Brimson JM, Prasanth MI, Malar DS, Brimson S, Thitilertdecha P, Tencomnao T. Drugs that offer the potential to reduce hospitalization and mortality from SARS-CoV-2 infection: The possible role of the sigma-1 receptor and autophagy. Expert Opin Ther Targets 2021; 25:435-449. [PMID: 34236922 PMCID: PMC8290373 DOI: 10.1080/14728222.2021.1952987] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Introduction: Despite the availability of new vaccines for SARS-CoV-2, there has been slow uptake and problems with supply in some parts of the world. Hence, there is still a necessity for drugs that can prevent hospitalization of patients and reduce the strain on health care systems. Drugs with sigma affinity potentially provide protection against the most severe symptoms of SARS-COV-2 and could prevent mortality via interactions with the sigma-1 receptor.Areas covered: This review examines the role of the sigma-1 receptor and autophagy in SARS-CoV-2 infections and how they may be linked. The authors reveal how sigma ligands may reduce the symptoms, complications, and deaths resulting from SARS-CoV-2 and offer insights on those patient cohorts that may benefit most from these drugs.Expert opinion: Drugs with sigma affinity potentially offer protection against the most severe symptoms of SARS-CoV-2 via interactions with the sigma-1 receptor. Agonists of the sigma-1 receptor may provide protection of the mitochondria, activate mitophagy to remove damaged and leaking mitochondria, prevent ER stress, manage calcium ion transport, and induce autophagy to prevent cell death in response to infection.
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Affiliation(s)
- James Michael Brimson
- Natural Products for Neuroprotection and Anti-ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Mani Iyer Prasanth
- Natural Products for Neuroprotection and Anti-ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Dicson Sheeja Malar
- Natural Products for Neuroprotection and Anti-ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Sirikalaya Brimson
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Premrutai Thitilertdecha
- Siriraj Research Group in Immunobiology and Therapeutic Sciences, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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Rizkita LD, Astuti I. The potential of miRNA-based therapeutics in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: A review. J Pharm Anal 2021; 11:265-271. [PMID: 33782640 PMCID: PMC7989072 DOI: 10.1016/j.jpha.2021.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Since the World Health Organization (WHO) declared COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a pandemic in March 2020, and more than 117 million people worldwide have been confirmed to have been infected. Scientists, medical professionals, and other stakeholders are racing against time to find and develop effective medicines for COVID-19. However, no drug with high efficacy to treat SARS-CoV-2 infection has been approved. With the increasing popularity of gene therapy, scientists have explored the utilization of small RNAs such as microRNAs (miRNAs) as therapeutics. miRNAs are non-coding RNAs with high affinity for the 3'-UTRs of targeted messenger RNAs (mRNAs). Interactions between host cells and viral genomes may induce the upregulation or downregulation of various miRNAs. Therefore, understanding the expression patterns of these miRNAs and their functions will provide insights into potential miRNA-based therapies. This review systematically summarizes the potential targets of miRNA-based therapies for SARS-CoV-2 infection and examines the viability of possible transfection methods.
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Affiliation(s)
- Leonny Dwi Rizkita
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Indwiani Astuti
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
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Ahmadi A, Moradi S. In silico analysis suggests the RNAi-enhancing antibiotic enoxacin as a potential inhibitor of SARS-CoV-2 infection. Sci Rep 2021; 11:10271. [PMID: 33986351 PMCID: PMC8119475 DOI: 10.1038/s41598-021-89605-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19 has currently become the biggest challenge in the world. There is still no specific medicine for COVID-19, which leaves a critical gap for the identification of new drug candidates for the disease. Recent studies have reported that the small-molecule enoxacin exerts an antiviral activity by enhancing the RNAi pathway. The aim of this study is to analyze if enoxacin can exert anti-SARS-CoV-2 effects. We exploit multiple computational tools and databases to examine (i) whether the RNAi mechanism, as the target pathway of enoxacin, could act on the SARS-CoV-2 genome, and (ii) microRNAs induced by enoxacin might directly silence viral components as well as the host cell proteins mediating the viral entry and replication. We find that the RNA genome of SARS-CoV-2 might be a suitable substrate for DICER activity. We also highlight several enoxacin-enhanced microRNAs which could target SARS-CoV-2 components, pro-inflammatory cytokines, host cell components facilitating viral replication, and transcription factors enriched in lung stem cells, thereby promoting their differentiation and lung regeneration. Finally, our analyses identify several enoxacin-targeted regulatory modules that were critically associated with exacerbation of the SARS-CoV-2 infection. Overall, our analysis suggests that enoxacin could be a promising candidate for COVID-19 treatment through enhancing the RNAi pathway.
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Affiliation(s)
- Amirhossein Ahmadi
- Department of Biological Science and Technology, Faculty of Nano and Bio Science and Technology, Persian Gulf University, Bushehr, 75169,, Iran
| | - Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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