1
|
Lee AR, Kim SH, Hong SY, Lee SH, Oh JS, Lee KY, Kim SJ, Ishikawa T, Shim SM, Lee HI, Seo SU. Characterization of genotype V Japanese encephalitis virus isolates from Republic of Korea. Emerg Microbes Infect 2024; 13:2362392. [PMID: 38808613 PMCID: PMC11168223 DOI: 10.1080/22221751.2024.2362392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/27/2024] [Indexed: 05/30/2024]
Abstract
Japanese encephalitis (JE), caused by the Japanese encephalitis virus (JEV) infection, continues to pose significant public health challenges worldwide despite efficient vaccines. The virus is classified into five genotypes, among which genotype V (GV) was not detected for a long period after its initial isolation in 1952, until reports emerged from China and the Republic of Korea (ROK) since 2009. The characteristics of the virus are crucial in estimating its potential epidemiological impact. However, characterization of GV JEVs has so far been limited to two strains: Muar, the original isolate, and XZ0934, isolated in China. Two additional ROK GV JEV isolates, NCCP 43279 and NCCP 43413, are currently available, but their characteristics have not been explored. Our phylogenetic analysis revealed that GV virus sequences from the ROK segregate into two clades. NCCP 43279 and NCCP 43413 belong to different clades and exhibit distinct in vitro phenotypes. NCCP 43279 forms larger plaques but demonstrates inefficient propagation in cell culture compared to NCCP 43413. In vivo, NCCP 43279 induces higher morbidity and mortality in mice than NCCP 43413. Notably, NCCP 43279 shows more severe blood-brain barrier damage, suggesting superior brain invasion capabilities. Consistent with its higher virulence, NCCP 43279 displays more pronounced histopathological and immunopathological outcomes. In conclusion, our study confirms that the two ROK isolates are not only classified into different clades but also exhibit distinct in vitro and in vivo characteristics.
Collapse
Affiliation(s)
- Ah-Ra Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang-Hyun Kim
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Su-Yeon Hong
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang-Ho Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Sang Oh
- Department of Neurosurgery, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung Yong Lee
- Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Seong-Jun Kim
- Center for Infectious Disease Vaccine and Diagnosis Innovation (CEVI), Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Tomohiro Ishikawa
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Sang-Mu Shim
- Division of Acute Virus Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Hee Il Lee
- Division of Vectors and Parasitic Diseases, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Sang-Uk Seo
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| |
Collapse
|
2
|
Islam S, Parves MR, Islam MJ, Ali MA, Efaz FM, Hossain MS, Ullah MO, Halim MA. Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study. J Biomol Struct Dyn 2024; 42:5770-5787. [PMID: 37403295 DOI: 10.1080/07391102.2023.2228919] [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: 01/10/2023] [Accepted: 06/17/2023] [Indexed: 07/06/2023]
Abstract
The L84S mutation has been observed frequently in the ORF8 protein of SARS-CoV-2, which is an accessory protein involved in various important functions such as virus propagation, pathogenesis, and evading the immune response. However, the specific effects of this mutation on the dimeric structure of ORF8 and its impacts on interactions with host components and immune responses are not well understood. In this study, we performed one microsecond molecular dynamics (MD) simulation and analyzed the dimeric behavior of the L84S and L84A mutants in comparison to the native protein. The MD simulations revealed that both mutations caused changes in the conformation of the ORF8 dimer, influenced protein folding mechanisms, and affected the overall structural stability. In particular, the 73YIDI76 motif has found to be significantly affected by the L84S mutation, leading to structural flexibility in the region connecting the C-terminal β4 and β5 strands. This flexibility might be responsible for virus immune modulation. The free energy landscape (FEL) and principle component analysis (PCA) have also supported our investigation. Overall, the L84S and L84A mutations affect the ORF8 dimeric interfaces by reducing the frequency of protein-protein interacting residues (Arg52, Lys53, Arg98, Ile104, Arg115, Val117, Asp119, Phe120, and Ile121) in the ORF8 dimer. Our findings provide detail insights for further research in designing structure-based therapeutics against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Shahadat Hossain
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| |
Collapse
|
3
|
Oktavianthi S, Lages AC, Kusuma R, Kurniasih TS, Trimarsanto H, Andriani F, Rustandi D, Meriyanti T, Yusuf I, Malik SG, Jo J, Suriapranata I. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia. Pathogens 2024; 13:279. [PMID: 38668234 PMCID: PMC11053823 DOI: 10.3390/pathogens13040279] [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: 11/06/2023] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/29/2024] Open
Abstract
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.
Collapse
Affiliation(s)
- Sukma Oktavianthi
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Aksar Chair Lages
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Rinaldy Kusuma
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Tri Shinta Kurniasih
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
- Menzies School of Health Research, Charles Darwin University, Darwin 0811, Australia
| | - Febi Andriani
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - David Rustandi
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Tandry Meriyanti
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Irawan Yusuf
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Safarina G. Malik
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Juandy Jo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Ivet Suriapranata
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| |
Collapse
|
4
|
Rad SMAH, Wannigama DL, Hirankarn N, McLellan AD. The impact of non-synonymous mutations on miRNA binding sites within the SARS-CoV-2 NSP3 and NSP4 genes. Sci Rep 2023; 13:16945. [PMID: 37805621 PMCID: PMC10560223 DOI: 10.1038/s41598-023-44219-y] [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: 02/27/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023] Open
Abstract
Non-synonymous mutations in the SARS-CoV-2 spike region affect cell entry, tropism, and immune evasion, while frequent synonymous mutations may modify viral fitness. Host microRNAs, a type of non-coding RNA, play a crucial role in the viral life cycle, influencing viral replication and the host immune response directly or indirectly. Recently, we identified ten miRNAs with a high complementary capacity to target various regions of the SARS-CoV-2 genome. We filtered our candidate miRNAs to those only expressed with documented expression in SARS-CoV-2 target cells, with an additional focus on miRNAs that have been reported in other viral infections. We determined if mutations in the first SARS-CoV-2 variants of concern affected these miRNA binding sites. Out of ten miRNA binding sites, five were negatively impacted by mutations, with three recurrent synonymous mutations present in multiple SARS-CoV-2 lineages with high-frequency NSP3: C3037U and NSP4: G9802U/C9803U. These mutations were predicted to negatively affect the binding ability of miR-197-5p and miR-18b-5p, respectively. In these preliminary findings, using a dual-reporter assay system, we confirmed the ability of these miRNAs in binding to the predicted NSP3 and NSP4 regions and the loss/reduced miRNA bindings due to the recurrent mutations.
Collapse
Affiliation(s)
- S M Ali Hosseini Rad
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand.
| | - Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Pathogen Hunter's Research Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata, 990-2212, Japan
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand.
| | - Alexander D McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
5
|
Makowski JA, Kensinger AH, Cunningham CL, Frye CJ, Shine M, Lackey PE, Mihailescu MR, Evanseck JD. Delta SARS-CoV-2 s2m Structure, Dynamics, and Entropy: Consequences of the G15U Mutation. ACS PHYSICAL CHEMISTRY AU 2023; 3:434-443. [PMID: 37780540 PMCID: PMC10540284 DOI: 10.1021/acsphyschemau.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 10/03/2023]
Abstract
Bioinformatic analysis of the Delta SARS-CoV-2 genome reveals a single nucleotide mutation (G15U) in the stem-loop II motif (s2m) relative to ancestral SARS-CoV-2. Despite sequence similarity, unexpected differences between SARS-CoV-2 and Delta SARS-CoV-2 s2m homodimerization experiments require the discovery of unknown structural and thermodynamic changes necessary to rationalize the data. Using our reported SARS-CoV-2 s2m model, we induced the G15U substitution and performed 3.5 microseconds of unbiased molecular dynamics simulation at 283 and 310 K. The resultant Delta s2m adopted a secondary structure consistent with our reported NMR data, resulting in significant deviations in the tertiary structure and dynamics from our SARS-CoV-2 s2m model. First, we find differences in the overall three-dimensional structure, where the characteristic 90° L-shaped kink of the SARS-CoV-2 s2m did not form in the Delta s2m resulting in a "linear" hairpin with limited bending dynamics. Delta s2m helical parameters are calculated to align closely with A-form RNA, effectively eliminating a hinge point to form the L-shape kink by correcting an upper stem defect in SARS-CoV-2 induced by a noncanonical and dynamic G:A base pair. Ultimately, the shape difference rationalizes the migration differences in reported electrophoresis experiments. Second, increased fluctuation of the Delta s2m palindromic sequence, within the terminal loop, compared to SARS-CoV-2 s2m results in an estimated increase of entropy of 6.8 kcal/mol at 310 K relative to the SARS-CoV-2 s2m. The entropic difference offers a unique perspective on why the Delta s2m homodimerizes less spontaneously, forming fewer kissing dimers and extended duplexes compared to SARS-CoV-2. In this work, both the L-shape reduction and palindromic entropic penalty provides an explanation of our reported in vitro electrophoresis homodimerization results. Ultimately, the structural, dynamical, and entropic differences between the SARS-CoV-2 s2m and Delta s2m serve to establish a foundation for future studies of the s2m function in the viral lifecycle.
Collapse
Affiliation(s)
- Joseph A. Makowski
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Adam H. Kensinger
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caylee L. Cunningham
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caleb J. Frye
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Morgan Shine
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Patrick E. Lackey
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Mihaela Rita Mihailescu
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffrey D. Evanseck
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Ergün S, Sankaranarayanan R, Petrović N. Clinically informative microRNAs for SARS-CoV-2 infection. Epigenomics 2023; 15:705-716. [PMID: 37661862 PMCID: PMC10476648 DOI: 10.2217/epi-2023-0179] [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: 05/23/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
COVID-19 is a viral respiratory infection induced by the newly discovered coronavirus SARS-CoV-2. miRNA is an example of a strong and direct regulator of a gene's transcriptional activity. The interaction between miRNAs and their target molecules is responsible for homeostasis. Virus-derived and host-derived miRNAs are involved in the activity of hiding from immune system cells, inducing the inflammatory reaction through interplay with associated genes, during SARS-COV-2 infection. Interest in miRNAs has raised the comprehension of the machinery and pathophysiology of SARS-COV-2 infection. In this review, the effects and biological roles of miRNAs on SARS-CoV-2 pathogenicity and life cycle are described. The therapeutic potential of miRNAs against SARS-CoV-2 infection are also mentioned.
Collapse
Affiliation(s)
- Sercan Ergün
- Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
- Department of Multidisciplinary Molecular Medicine, Institute of Graduate Studies, Ondokuz Mayis University, Samsun, Turkey
| | | | - Nina Petrović
- Laboratory for Radiobiology & Molecular Genetics, Department of Health & Environment, ‘VINČA’ Institute of Nuclear Sciences – National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovića Alasa 12–14, Belgrade, 11001, Serbia
- Department of Experimental Oncology, Institute for Oncology & Radiology of Serbia, Pasterova 14, Belgrade, 11000, Serbia
| |
Collapse
|
8
|
Peng O, Wu Y, Hu F, Xia Y, Geng R, Huang Y, Zeng S, Hu G, Xue C, Zhang H, Cao Y. Transcriptome Profiling of Vero E6 Cells during Original Parental or Cell-Attenuated Porcine Epidemic Diarrhea Virus Infection. Viruses 2023; 15:1426. [PMID: 37515115 PMCID: PMC10386749 DOI: 10.3390/v15071426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) has led to significant economic losses in the global porcine industry since the emergence of variant strains in 2010. The high mutability of coronaviruses endows PEDV with the ability to evade the host immune response, which impairs the effectiveness of vaccines. In our previous study, we generated a highly cell-passaged PEDV strain, CT-P120, which showed promise as a live attenuated vaccine candidate by providing satisfactory protection against variant PEDV infection in piglets. However, the mechanism by which the attenuated CT-P120 adapts to cells during passage, resulting in increased replication efficiency, remains unclear. To address this question, we conducted a comparative transcriptomic analysis of Vero E6 cells infected with either the original parental strain (CT-P10) or the cell-attenuated strain (CT-P120) of PEDV at 6, 12, and 24 h post-infection. Compared to CT-P10, CT-P120 infection resulted in a significant decrease in the number of differentially expressed genes (DEGs) at each time point. Functional enrichment analysis of genes revealed the activation of various innate immune-related pathways by CT-P10, notably attenuated during CT-P120 infection. To validate these results, we selected eight genes (TRAF3, IRF3, IFNL1, ISG15, NFKB1, MAP2K3, IL1A, and CCL2) involved in antiviral processes and confirmed their mRNA expression patterns using RT-qPCR, in line with the transcriptomic data. Subsequent protein-level analysis of selected genes via Western blotting and enzyme-linked immunosorbent assay corroborated these results, reinforcing the robustness of our findings. Collectively, our research elucidates the strategies underpinning PEDV attenuation and immune evasion, providing invaluable insights for the development of effective PEDV vaccines.
Collapse
Affiliation(s)
- Ouyang Peng
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yu Wu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Fangyu Hu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yu Xia
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Rui Geng
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yihui Huang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Siying Zeng
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Guangli Hu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chunyi Xue
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Hao Zhang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-Sen University, Guangzhou 510275, China
| |
Collapse
|
9
|
Saha I, Ghosh N, Plewczynski D. Identification of Human miRNA Biomarkers Targeting the SARS-CoV-2 Genome. ACS OMEGA 2022; 7:46411-46420. [PMID: 36570256 PMCID: PMC9773347 DOI: 10.1021/acsomega.2c05091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/06/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2 poses a great challenge toward mankind, majorly due to its evolution and frequently occurring variants. On the other hand, in human hosts, microRNA (miRNA) plays a vital role in replication and propagation during a viral infection and can control the biological processes. This may be essential for the progression of viral infection. Moreover, human miRNAs can play a therapeutic role in treatment of different viral diseases by binding to the target sites of the virus genome, thereby hindering the essential functioning of the virus. Motivated by this fact, we have hypothesized a new approach in order to identify human miRNAs that can target the mRNA (genome) of SARS-CoV-2 to degrade their protein synthesis. In this regard, the multiple sequence alignment technique Clustal Omega is used to align a complement of 2656 human miRNAs with the SARS-CoV-2 reference genome (mRNA). Thereafter, ranking of these aligned human miRNAs is performed with the help of a new scoring function that takes into account the (a) total number of nucleotide matches between the human miRNA and the SARS-CoV-2 genome, (b) number of consecutive nucleotide matches between the human miRNA and the SARS-CoV-2 genome, (c) number of nucleotide mismatches between the human miRNA and the SARS-CoV-2 genome, and (d) the difference in length before and after alignment of the human miRNA. As a result, from the 2656 ranked miRNAs, the top 20 human miRNAs are reported, which are targeting different coding and non-coding regions of the SARS-CoV-2 genome. Moreover, molecular docking of such human miRNAs with virus mRNA is performed to verify the efficacy of the interactions. Furthermore, 4 miRNAs out of the top 20 miRNAs are identified to have the seed region. In order to inhibit the virus, the key human targets of the seed regions may be targeted. Repurposable drugs like carfilzomib, bortezomib, hydralazine, and paclitaxel are identified for such purpose.
Collapse
Affiliation(s)
- Indrajit Saha
- Department
of Computer Science and Engineering, National
Institute of Technical Teachers’ Training and Research, FC Block, Sector III, Kolkata700106, West Bengal, India
| | - Nimisha Ghosh
- Department
of Computer Science and Information Technology, Institute of Technical
Education and Research, Siksha “O”
Anusandhan (Deemed to be) University, Jagamara Road, Bhubaneswar751030, Odisha, India
| | - Dariusz Plewczynski
- Laboratory
of Bioinformatics and Computational Genomics, Faculty of Mathematics
and Information Science, Warsaw University
of Technology, Plac Politechniki
1, Warsaw00-661, Poland
- Laboratory
of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Stefana Banacha 2, Warsaw02-097, Poland
| |
Collapse
|
10
|
Periwal N, Bhardwaj U, Sarma S, Arora P, Sood V. In silico analysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs. Front Cell Infect Microbiol 2022; 12:966870. [PMID: 36519126 PMCID: PMC9742375 DOI: 10.3389/fcimb.2022.966870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 has resulted in enormous deaths around the world. Clues from genomic sequences of parent and their mutants can be obtained to understand the evolving pathogenesis of this virus. Apart from the viral proteins, virus-encoded microRNAs (miRNAs) have been shown to play a vital role in regulating viral pathogenesis. Thus we sought to investigate the miRNAs encoded by SARS-CoV-2, its mutants, and the host. Here, we present the results obtained using a dual approach i.e (i) identifying host-encoded miRNAs that might regulate viral pathogenesis and (ii) identifying viral-encoded miRNAs that might regulate host cell signaling pathways and aid in viral pathogenesis. Analysis utilizing the first approach resulted in the identification of ten host-encoded miRNAs that could target the SARS, SARS-CoV-2, and its mutants. Interestingly our analysis revealed that there is a significantly higher number of host miRNAs that could target the SARS-CoV-2 genome as compared to the SARS reference genome. Results from the second approach resulted in the identification of a set of virus-encoded miRNAs which might regulate host signaling pathways. Our analysis further identified a similar "GA" rich motif in the SARS-CoV-2 and its mutant genomes that was shown to play a vital role in lung pathogenesis during severe SARS infections. In summary, we have identified human and virus-encoded miRNAs that might regulate the pathogenesis of SARS coronaviruses and describe similar non-coding RNA sequences in SARS-CoV-2 that were shown to regulate SARS-induced lung pathology in mice.
Collapse
Affiliation(s)
- Neha Periwal
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | | | - Sankritya Sarma
- Department of Zoology, Hansraj College, University of Delhi, Delhi, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, Delhi, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi, India,*Correspondence: Vikas Sood,
| |
Collapse
|
11
|
Sasi VM, Ullrich S, Ton J, Fry SE, Johansen-Leete J, Payne RJ, Nitsche C, Jackson CJ. Predicting Antiviral Resistance Mutations in SARS-CoV-2 Main Protease with Computational and Experimental Screening. Biochemistry 2022; 61:2495-2505. [DOI: 10.1021/acs.biochem.2c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vishnu M. Sasi
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Jennifer Ton
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Sarah E. Fry
- School of Chemistry, The University of Sydney, Sydney NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney NSW 2006, Australia
| | - Jason Johansen-Leete
- School of Chemistry, The University of Sydney, Sydney NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney NSW 2006, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney NSW 2006, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra ACT 2601, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Australian National University, Canberra ACT 2601, Australia
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Periwal N, Rathod SB, Sarma S, Johar GS, Jain A, Barnwal RP, Srivastava KR, Kaur B, Arora P, Sood V. Time Series Analysis of SARS-CoV-2 Genomes and Correlations among Highly Prevalent Mutations. Microbiol Spectr 2022; 10:e0121922. [PMID: 36069583 PMCID: PMC9603882 DOI: 10.1128/spectrum.01219-22] [Citation(s) in RCA: 6] [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: 04/04/2022] [Accepted: 08/03/2022] [Indexed: 12/30/2022] Open
Abstract
The efforts of the scientific community to tame the recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seem to have been diluted by the emergence of new viral strains. Therefore, it is imperative to understand the effect of mutations on viral evolution. We performed a time series analysis on 59,541 SARS-CoV-2 genomic sequences from around the world to gain insights into the kinetics of the mutations arising in the viral genomes. These 59,541 genomes were grouped according to month (January 2020 to March 2021) based on the collection date. Meta-analysis of these data led us to identify significant mutations in viral genomes. Pearson correlation of these mutations led us to the identification of 16 comutations. Among these comutations, some of the individual mutations have been shown to contribute to viral replication and fitness, suggesting a possible role of other unexplored mutations in viral evolution. We observed that the mutations 241C>T in the 5' untranslated region (UTR), 3037C>T in nsp3, 14408C>T in the RNA-dependent RNA polymerase (RdRp), and 23403A>G in spike are correlated with each other and were grouped in a single cluster by hierarchical clustering. These mutations have replaced the wild-type nucleotides in SARS-CoV-2 sequences. Additionally, we employed a suite of computational tools to investigate the effects of T85I (1059C>T), P323L (14408C>T), and Q57H (25563G>T) mutations in nsp2, RdRp, and the ORF3a protein of SARS-CoV-2, respectively. We observed that the mutations T85I and Q57H tend to be deleterious and destabilize the respective wild-type protein, whereas P323L in RdRp tends to be neutral and has a stabilizing effect. IMPORTANCE We performed a meta-analysis on SARS-CoV-2 genomes categorized by collection month and identified several significant mutations. Pearson correlation analysis of these significant mutations identified 16 comutations having absolute correlation coefficients of >0.4 and a frequency of >30% in the genomes used in this study. The correlation results were further validated by another statistical tool called hierarchical clustering, where mutations were grouped in clusters on the basis of their similarity. We identified several positive and negative correlations among comutations in SARS-CoV-2 isolates from around the world which might contribute to viral pathogenesis. The negative correlations among some of the mutations in SARS-CoV-2 identified in this study warrant further investigations. Further analysis of mutations such as T85I in nsp2 and Q57H in ORF3a protein revealed that these mutations tend to destabilize the protein relative to the wild type, whereas P323L in RdRp is neutral and has a stabilizing effect. Thus, we have identified several comutations which can be further characterized to gain insights into SARS-CoV-2 evolution.
Collapse
Affiliation(s)
- Neha Periwal
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
| | - Shravan B. Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat, India
| | - Sankritya Sarma
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | | | - Avantika Jain
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
- Delhi Institute of Pharmaceutical Sciences and Research, New Delhi, Delhi, India
| | - Ravi P. Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | | | - Baljeet Kaur
- Department of Computer Science, Hansraj College, University of Delhi, New Delhi, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | - Vikas Sood
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
| |
Collapse
|
14
|
Arisan ED, Dart DA, Grant GH, Dalby A, Kancagi DD, Turan RD, Yurtsever B, Karakus GS, Ovali E, Lange S, Uysal-Onganer P. microRNA 1307 Is a Potential Target for SARS-CoV-2 Infection: An in Vitro Model. ACS OMEGA 2022; 7:38003-38014. [PMID: 36275122 PMCID: PMC9578367 DOI: 10.1021/acsomega.2c05245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
microRNAs (miRs) are proposed as critical molecular targets in SARS-CoV-2 infection. Our recent in silico studies identified seven SARS-CoV-2 specific miR-like sequences, which are highly conserved with humans, including miR-1307-3p, with critical roles in COVID-19. In this current study, Vero cells were infected with SARS-CoV-2, and miR expression profiles were thereafter confirmed by qRT-PCR. miR-1307-3p was the most highly expressed miR in the infected cells; we, therefore, transiently inhibited its expression in both infected and uninfected cells. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) cell proliferation assay assessed cell viability following SARS-CoV-2 infection, identifying that miR-1307 expression is inversely correlated with cell viability. Lastly, changes in miR-1307-dependent pathways were analyzed through a detailed miRNOME and associated in silico analysis. In addition to our previously identified miRs, including miR-1307-3p, the upregulation of miR-193a-5p, miR-5100, and miR-23a-5p and downregulation of miR-130b-5p, miR34a-5p, miR-505-3p, miR181a-2-3p, miR-1271-5p, miR-598-3p, miR-34c-3p, and miR-129-5p were also established in Vero cells related to general lung disease-related genes following SARS-CoV-2 infection. Targeted anti-miR-1307-3p treatment rescued cell viability in infection when compared to SARS CoV-2 mediated cell cytotoxicity only. We furthermore identified by in silico analysis that miR-1307-3p is conserved in all SARS-CoV-2 sequences/strains, except in the BA.2 variant, possibly contributing to the lower disease severity of this variant, which warrants further investigation. Small RNA seq analysis was next used to evaluate alterations in the miRNOME, following miR-1307-3p manipulation, identifying critical pathobiological pathways linked to SARS-CoV-2 infection-mediated upregulation of this miR. On the basis of our findings, miRNAs like miR-1307-3p play a critical role in SARS-CoV-2 infection, including via effects on disease progression and severity.
Collapse
Affiliation(s)
- Elif Damla Arisan
- Gebze
Technical University, Institute of Biotechnology, Gebze, Kocaeli 41400, Turkiye
| | - D. Alwyn Dart
- Institute
of Medical and Biomedical Education, St
George’s University of London, Cranmer Terrace, Tooting, London SW17
0RE, United Kingdom
| | - Guy H. Grant
- School
of Life Sciences, University of Bedfordshire, Park Square, Luton LU1
3JU, United Kingdom
| | - Andrew Dalby
- School
of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
| | | | - Raife Dilek Turan
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
- Yeditepe
University, Institute of Biotechnology, İstanbul 34755, Turkiye
| | - Bulut Yurtsever
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
| | - Gozde Sir Karakus
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
| | - Ercument Ovali
- Acibadem
Labcell Cellular Therapy Laboratory, İstanbul 34457, Turkiye
| | - Sigrun Lange
- Tissue
Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
| | - Pinar Uysal-Onganer
- Cancer
Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, United Kingdom
| |
Collapse
|
15
|
Singh AK, Laskar R, Banerjee A, Mondal RK, Gupta B, Deb S, Dutta S, Patra S, Ghosh T, Sarkar S, Ghosh S, Bhattacharya S, Roy D, Chakraborty A, Chowdhury M, Mahaptra S, Paul A, Mazumder A, Chowdhury A, Chatterjee SS, Sarkar A, Ray R, Pal K, Jana A, Barik G, Ganguly S, Chatterjee M, Majhi D, Bandopadhyay B, Das S, Maitra A, Biswas NK. Contrasting Distribution of SARS-CoV-2 Lineages across Multiple Rounds of Pandemic Waves in West Bengal, the Gateway of East and North-East States of India. Microbiol Spectr 2022; 10:e0091422. [PMID: 35852336 PMCID: PMC9430150 DOI: 10.1128/spectrum.00914-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
The evolution of viral variants and their impact on viral transmission have been an area of considerable importance in this pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We analyzed the viral variants in different phases of the pandemic in West Bengal, a state in India that is important geographically, and compared the variants with other states like Delhi, Maharashtra, and Karnataka, located in other regions of the country. We have identified 57 pango-lineages in 3,198 SARS-CoV-2 genomes, alteration in their distribution, as well as contrasting profiles of amino acid mutational dynamics across different waves in different states. The evolving characteristics of Delta (B.1.617.2) sublineages and alterations in hydrophobicity profiles of the viral proteins caused by these mutations were also studied. Additionally, implications of predictive host miRNA binding/unbinding to emerging spike or nucleocapsid mutations were highlighted. Our results throw considerable light on interesting aspects of the viral genomic variation and provide valuable information for improved understanding of wave-defining mutations in unfolding the pandemic. IMPORTANCE Multiple waves of infection were observed in many states in India during the coronavirus disease 2019 (COVID19) pandemic. Fine-scale evolution of major SARS-CoV-2 lineages and sublineages during four wave-window categories: Pre-Wave 1, Wave 1, Pre-Wave 2, and Wave 2 in four major states of India: Delhi (North), Maharashtra (West), Karnataka (South), and West Bengal (East) was studied using large-scale virus genome sequencing data. Our comprehensive analysis reveals contrasting molecular profiles of the wave-defining mutations and their implications in host miRNA binding/unbinding of the lineages in the major states of India.
Collapse
Affiliation(s)
- Animesh K. Singh
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Anindita Banerjee
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Bishal Gupta
- School of Tropical Medicine, Kolkata, West Bengal, India
| | - Sonia Deb
- School of Tropical Medicine, Kolkata, West Bengal, India
| | - Shreelekha Dutta
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Subrata Patra
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Trinath Ghosh
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Sumanta Sarkar
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Shekhar Ghosh
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Debojyoti Roy
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Meghna Chowdhury
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Surajit Mahaptra
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Antara Paul
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Anup Mazumder
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | | | | | - Raja Ray
- Institute of Post-Graduate Medical Education and Research, Kolkata, West Bengal, India
| | - Kuhu Pal
- College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Angshuman Jana
- Bankura Sammilani Medical College, Bankura, West Bengal, India
| | - Goutam Barik
- Medical College and Hospital, Kolkata, West Bengal, India
| | - Swagata Ganguly
- Nil Ratan Sircar Medical College and Hospital, Kolkata, West Bengal, India
| | | | - Dipankar Majhi
- Department of Health and Family Welfare, Government of West Bengal, Kolkata, West Bengal, India
| | | | - Saumitra Das
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Nidhan K. Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| |
Collapse
|
16
|
Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
Collapse
Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| |
Collapse
|
17
|
Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
Collapse
|
18
|
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.
Collapse
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
| | | | | |
Collapse
|
19
|
Hill JM, Lukiw WJ. microRNA, the Innate-Immune System and SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:887800. [PMID: 35782132 PMCID: PMC9245018 DOI: 10.3389/fcimb.2022.887800] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/02/2022] [Indexed: 12/31/2022] Open
Abstract
The single-stranded viral RNA (ssvRNA) known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19 can be effectively inactivated by a number of natural ribonucleic acid-based host cell defenses. One of the most important of these defenses includes the actions of a class of small non-coding RNAs (sncRNAs) known as microRNAs (miRNAs). Via base-pair complementarity miRNAs are capable of specifically targeting ssvRNA sequences such as SARS-CoV-2 promoting its inactivation and neutralization. RNA-sequencing and bioinformatics analysis indicate that multiple naturally-occurring human miRNAs have extensive complementarity to the SARS-CoV-2 ssvRNA genome. Since miRNA abundance, speciation, and complexity vary significantly amongst human individuals, this may in part explain the variability in the innate-immune and pathophysiological response of different individuals to SARS-CoV-2 and overall susceptibility to ssvRNA-mediated viral infection.
Collapse
Affiliation(s)
- James M. Hill
- Louisiana State University (LSU) Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA, United States
- Department of Ophthalmology, LSU Health Science Center, New Orleans, LA, United States
- Department of Pharmacology, Louisiana State University (LSU) Health Science Center, New Orleans, LA, United States
- Department of Microbiology, Louisiana State University (LSU) Health Science Center, New Orleans, LA, United States
| | - Walter J. Lukiw
- Louisiana State University (LSU) Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA, United States
- Department of Ophthalmology, LSU Health Science Center, New Orleans, LA, United States
- Department Neurology, Louisiana State University Health Science Center, New Orleans, LA, United States
- *Correspondence: Walter J. Lukiw,
| |
Collapse
|
20
|
Kooshkaki O, Asghari A, Mahdavi R, Azarkar G, Parsamanesh N. Potential of MicroRNAs As Biomarkers and Therapeutic Targets in Respiratory Viruses: A Literature Review. DNA Cell Biol 2022; 41:544-563. [PMID: 35699380 DOI: 10.1089/dna.2021.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression through recognition of cognate sequences and interference of transcriptional, translational, or epigenetic processes. Hundreds of miRNA genes have been found in diverse viruses, and many of these are phylogenetically conserved. Respiratory viruses are the most frequent causative agents of disease in humans, with a significant impact on morbidity and mortality worldwide. Recently, the role of miRNAs in respiratory viral gene regulation, as well as host gene regulation during disease progression, has become a field of interest. This review highlighted the importance of various miRNAs and their potential role in fighting with respiratory viruses as therapeutic molecules with a focus on COVID-19.
Collapse
Affiliation(s)
- Omid Kooshkaki
- Department of Hematology, Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Arghavan Asghari
- Department of Hematology, Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran.,Department of Hematology, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Reza Mahdavi
- Department of Hematology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ghodsiyeh Azarkar
- Department of Hematology, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Negin Parsamanesh
- Department of Hematology, Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Science, Zanjan, Iran
| |
Collapse
|
21
|
Zeng Q, Qi X, Ma J, Hu F, Wang X, Qin H, Li M, Huang S, Yang Y, Li Y, Bai H, Jiang M, Ren D, Kang Y, Zhao Y, Chen X, Ding X, Ye D, Wang Y, Jiang J, Li D, Chen X, Hu K, Zhang B, Shi B, Zhang C. Distinct miRNAs associated with various clinical presentations of SARS-CoV-2 infection. iScience 2022; 25:104309. [PMID: 35502319 PMCID: PMC9044631 DOI: 10.1016/j.isci.2022.104309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/04/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) have been shown to play important roles in viral infections, but their associations with SARS-CoV-2 infection remain poorly understood. Here, we detected 85 differentially expressed miRNAs (DE-miRNAs) from 2,336 known and 361 novel miRNAs that were identified in 233 plasma samples from 61 healthy controls and 116 patients with COVID-19 using the high-throughput sequencing and computational analysis. These DE-miRNAs were associated with SASR-CoV-2 infection, disease severity, and viral persistence in the patients with COVID-19, respectively. Gene ontology and KEGG pathway analyses of the DE-miRNAs revealed their connections to viral infections, immune responses, and lung diseases. Finally, we established a machine learning model using the DE-miRNAs between various groups for classification of COVID-19 cases with different clinical presentations. Our findings may help understand the contribution of miRNAs to the pathogenesis of COVID-19 and identify potential biomarkers and molecular targets for diagnosis and treatment of SARS-CoV-2 infection. 2,336 known and 361 novel miRNAs identified in this study 85 miRNAs associated with COVID-19 A panel of miRNAs targeting the viral or cellular genes Machine learning using miRNAs for classification of COVID-19
Collapse
Affiliation(s)
- Qiqi Zeng
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Junpeng Ma
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Fang Hu
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Xiaorui Wang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Hongyu Qin
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Mengyang Li
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Shaoxin Huang
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China
| | - Yong Yang
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China
| | - Yixin Li
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Han Bai
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Meng Jiang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Doudou Ren
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Ye Kang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China
| | - Yang Zhao
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuhan 430060, China
| | - Xiaobei Chen
- Department of Infectious Diseases, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Xi Ding
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Di Ye
- Department of Rehabilitation, The Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan 430060, China
| | - Yankui Wang
- Dialysis Center, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Jianguo Jiang
- LC-Bio Technologies (Hangzhou) Co., Ltd., Hanghzhou 310000, China
| | - Dong Li
- Department of Clinical Laboratory, The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Xi Chen
- SpecAlly Life Technology Co, Ltd, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430075, China.,Wuhan Institute of Biotechnology, Wuhan East Lake High-tech Development Zone, 666 Gaoxin Road, Wuhan 430040, China
| | - Ke Hu
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, 99 Zhangzhidong Road, Wuhan 430060, China
| | - Binghong Zhang
- The Renmin Hospital of Wuhan University, East Campus, East Lake New Technology Development Zone, Gaoxin 6th Road, Wuhan 430040, China
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China
| | - Chengsheng Zhang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Western China Science and Technology Innovation Harbor, Building 21, Xi'an 710000, China.,Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, China.,The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| |
Collapse
|
22
|
Azhar A, Khan WH, Al-Hosaini K, Kamal MA. miRNAs in SARS-CoV-2 Infection: An Update. Curr Drug Metab 2022; 23:283-298. [PMID: 35319361 DOI: 10.2174/1389200223666220321102824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 02/08/2023]
Abstract
Coronavirus disease-2019 (COVID-19) is a highly infectious disease caused by newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the inception of SARS-CoV-2 from Wuhan, China, the virus has traveled to more than 200 countries globally. The role of SARS-CoV-2 in COVID-19 has been thoroughly investigated and reviewed in the last 22 months or so; however, a comprehensive outline of miRNAs in SARS-CoV-2 infection is still missing. The genetic material of SARS-CoV-2 is a single-stranded RNA molecule nearly 29 kb in size. RNA is composed of numerous sub-constituents, including microRNAs (miRNAs). miRNAs play an essential role in biological processes like apoptosis, cellular metabolism, cell death, cell movement, oncogenesis, intracellular signaling, immunity, and infection. Lately, miRNAs have been involved in SARS-CoV-2 infection, though the clear demonstration of miRNAs in the SARS-CoV-2 infection is not fully elucidated. The present review article summarizes recent findings of miRNAs associated with SARS-CoV-2 infection. We presented various facets of miRNAs such as miRNAs as the protagonist in viral infection, the occurrence of miRNA in cellular receptors, expression of miRNAs in multiple diseases, miRNA as a biomarker, and miRNA as a therapeutic tool discussed in detail. We also presented the vaccine status available in various countries.
Collapse
Affiliation(s)
- Asim Azhar
- Aligarh College of Education, Aligarh, UP, India
| | - Wajihul Hasan Khan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Khaled Al-Hosaini
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Post Box 2457, Riyadh 11451, Kingdom of Saudi Arabia
| | - Mohammad Amjad Kamal
- West China School of Nursing / Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- King Fahd Medical Research Center, King Abdulaziz University, P. O. Box 80216, Jeddah 21589, Saudi Arabia
- Enzymoics, NSW; Novel Global Community Educational Foundation, Australia
| |
Collapse
|
23
|
Abusalah MAH, Khalifa M, Al-Hatamleh MAI, Jarrar M, Mohamud R, Chan YY. Nucleic Acid-Based COVID-19 Therapy Targeting Cytokine Storms: Strategies to Quell the Storm. J Pers Med 2022; 12:386. [PMID: 35330388 PMCID: PMC8948998 DOI: 10.3390/jpm12030386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has shaken the world and triggered drastic changes in our lifestyle to control it. Despite the non-typical efforts, COVID-19 still thrives and plagues humanity worldwide. The unparalleled degree of infection has been met with an exceptional degree of research to counteract it. Many drugs and therapeutic technologies have been repurposed and discovered, but no groundbreaking antiviral agent has been introduced yet to eradicate COVID-19 and restore normalcy. As lethality is directly correlated with the severity of disease, hospitalized severe cases are of the greatest importance to reduce, especially the cytokine storm phenomenon. This severe inflammatory phenomenon characterized by elevated levels of inflammatory mediators can be targeted to relieve symptoms and save the infected patients. One of the promising therapeutic strategies to combat COVID-19 is nucleic acid-based therapeutic approaches, including microRNAs (miRNAs). This work is an up-to-date review aimed to comprehensively discuss the current nucleic acid-based therapeutics against COVID-19 and their mechanisms of action, taking into consideration the emerging SARS-CoV-2 variants of concern, as well as providing potential future directions. miRNAs can be used to run interference with the expression of viral proteins, while endogenous miRNAs can be targeted as well, offering a versatile platform to control SARS-CoV-2 infection. By targeting these miRNAs, the COVID-19-induced cytokine storm can be suppressed. Therefore, nucleic acid-based therapeutics (miRNAs included) have a latent ability to break the COVID-19 infection in general and quell the cytokine storm in particular.
Collapse
Affiliation(s)
- Mai Abdel Haleem Abusalah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia;
| | - Moad Khalifa
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Kelantan, Malaysia;
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia; (M.A.I.A.-H.); (R.M.)
| | - Mu’taman Jarrar
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
- Medical Education Department, King Fahd Hospital of the University, Al-Khobar 34445, Saudi Arabia
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia; (M.A.I.A.-H.); (R.M.)
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia;
| |
Collapse
|
24
|
Conserved MicroRNAs in Human Nasopharynx Tissue Samples from Swabs Are Differentially Expressed in Response to SARS-CoV-2. Genes (Basel) 2022; 13:genes13020348. [PMID: 35205390 PMCID: PMC8871708 DOI: 10.3390/genes13020348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The use of high-throughput small RNA sequencing is well established as a technique to unveil the miRNAs in various tissues. The miRNA profiles are different between infected and non-infected tissues. We compare the SARS-CoV-2 positive and SARS-CoV-2 negative RNA samples extracted from human nasopharynx tissue samples to show different miRNA profiles. We explored differentially expressed miRNAs in response to SARS-CoV-2 in the RNA extracted from nasopharynx tissues of 10 SARS-CoV-2-positive and 10 SARS-CoV-2-negative patients. miRNAs were identified by small RNA sequencing, and the expression levels of selected miRNAs were validated by real-time RT-PCR. We identified 943 conserved miRNAs, likely generated through posttranscriptional modifications. The identified miRNAs were expressed in both RNA groups, NegS and PosS: miR-148a, miR-21, miR-34c, miR-34b, and miR-342. The most differentially expressed miRNA was miR-21, which is likely closely linked to the presence of SARS-CoV-2 in nasopharynx tissues. Our results contribute to further understanding the role of miRNAs in SARS-CoV-2 pathogenesis, which may be crucial for understanding disease symptom development in humans.
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Zanganeh S, Goodarzi N, Doroudian M, Movahed E. Potential COVID-19 therapeutic approaches targeting angiotensin-converting enzyme 2; An updated review. Rev Med Virol 2021; 32:e2321. [PMID: 34958163 DOI: 10.1002/rmv.2321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022]
Abstract
COVID-19 has spread swiftly throughout the world posing a global health emergency. The significant numbers of deaths attributed to this pandemic have researchers battling to understand this new, dangerous virus. Researchers are looking to find possible treatment regimens and develop effective therapies. This study aims to provide an overview of published scientific information on potential treatments, emphasizing angiotensin-converting enzyme II (ACE2) inhibitors as one of the most important drug targets. SARS-CoV-2 receptor-binding domain (RBD); as a viral attachment or entry inhibitor against SARS-CoV-2, human recombinant soluble ACE2; as a genetically modified soluble form of ACE2 to compete with membrane-bound ACE2, and microRNAs (miRNAs); as a negative regulator of the expression of ACE2/TMPRSS2 to inhibit SARS-CoV2 entry into cells, are the potential therapeutic approaches discussed thoroughly in this article. This review provides the groundwork for the ongoing development of therapeutic agents and effective treatments against SARS-COV-2.
Collapse
Affiliation(s)
- Saba Zanganeh
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Nima Goodarzi
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Doroudian
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, New Year, USA
| |
Collapse
|
28
|
Arghiani N, Nissan T, Matin MM. Role of microRNAs in COVID-19 with implications for therapeutics. Biomed Pharmacother 2021; 144:112247. [PMID: 34601190 PMCID: PMC8463393 DOI: 10.1016/j.biopha.2021.112247] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 02/09/2023] Open
Abstract
COVID-19 is a pneumonia-like disease with highly transmittable and pathogenic properties caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infects both animals and humans. Although many efforts are currently underway to test possible therapies, there is no specific FDA approved drug against SARS-CoV-2 yet. miRNA-directed gene regulation controls the majority of biological processes. In addition, the development and progression of several human diseases are associated with dysregulation of miRNAs. In this regard, it has been shown that changes in miRNAs are linked to severity of COVID-19 especially in patients with respiratory diseases, diabetes, heart failure or kidney problems. Therefore, targeting these small noncoding-RNAs could potentially alleviate complications from COVID-19. Here, we will review the roles and importance of host and RNA virus encoded miRNAs in COVID-19 pathogenicity and immune response. Then, we focus on potential miRNA therapeutics in the patients who are at increased risk for severe disease.
Collapse
Affiliation(s)
- Nahid Arghiani
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; School of Life Science, Department of Biochemistry and Biomedicine, University of Sussex, Brighton, United Kingdom
| | - Tracy Nissan
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; School of Life Science, Department of Biochemistry and Biomedicine, University of Sussex, Brighton, United Kingdom.
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran; Stem Cell and Regenerative Medicine Research Group, Iranian Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran.
| |
Collapse
|
29
|
AbdelHamid SG, Refaat AA, Benjamin AM, Elmawardy LA, Elgendy LA, Manolly MM, Elmaksoud NA, Sherif N, Hamdy NM. Deciphering epigenetic(s) role in modulating susceptibility to and severity of COVID-19 infection and/or outcome: a systematic rapid review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:54209-54221. [PMID: 34383213 PMCID: PMC8359636 DOI: 10.1007/s11356-021-15588-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/19/2021] [Indexed: 05/14/2023]
Abstract
COVID-19 pandemic waves hitting worldwide result in drastic postinfection complications with interindividual variations, which raised the question for the cause of these observed variations. This urged to think "the impact of environment-affected genes"? In an attempt to unravel the impact of environment-affected genes, a systematic rapid review was conducted to study "the impact of host or viral epigenetic modulation on COVID-19 infection susceptibility and/or outcome." Electronic databases including Web of Science, SCOPUS, Cochrane Central Register of Controlled Trials, PubMed, and Google Scholar, and other databases were searched. The search strings included "COVID-19" OR "SARS-CoV-2" AND (Epigenetics'). Articles with randomized clinical trials (RCTs) and observational study designs, conducted on humans and available in the English language, were selected, with respect to "The interplay between the SARS-CoV-2 virus and Epigenetics" published from 2020 to February 2021 (but not limited to 2020, being expanded to 2015). Database search yielded 1330 articles; after screening, exclusion, and further filtrations, 51 articles were included. Susceptibility to COVID-19 infection is related to the viral-microRNAs (miRNAs) which alter virulence of the transmitted SARS-CoV-2 strains and impact host-miRNA-related innate immunity. Host-DNA methylation and/or chromatin remodeling may be implicated in severe cytokine storm that can ultimately results in fatal outcome.
Collapse
Affiliation(s)
- Sherihan G AbdelHamid
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Aya A Refaat
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Anthony M Benjamin
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Laila A Elmawardy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Lougine A Elgendy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Mark M Manolly
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Nada Abd Elmaksoud
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Nourhan Sherif
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, 11566, Abassia, Cairo, Egypt.
| |
Collapse
|
30
|
de Gonzalo-Calvo D, Benítez ID, Pinilla L, Carratalá A, Moncusí-Moix A, Gort-Paniello C, Molinero M, González J, Torres G, Bernal M, Pico S, Almansa R, Jorge N, Ortega A, Bustamante-Munguira E, Gómez JM, González-Rivera M, Micheloud D, Ryan P, Martinez A, Tamayo L, Aldecoa C, Ferrer R, Ceccato A, Fernández-Barat L, Motos A, Riera J, Menéndez R, Garcia-Gasulla D, Peñuelas O, Torres A, Bermejo-Martin JF, Barbé F. Circulating microRNA profiles predict the severity of COVID-19 in hospitalized patients. Transl Res 2021; 236:147-159. [PMID: 34048985 PMCID: PMC8149473 DOI: 10.1016/j.trsl.2021.05.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
We aimed to examine the circulating microRNA (miRNA) profile of hospitalized COVID-19 patients and evaluate its potential as a source of biomarkers for the management of the disease. This was an observational and multicenter study that included 84 patients with a positive nasopharyngeal swab Polymerase chain reaction (PCR) test for SARS-CoV-2 recruited during the first pandemic wave in Spain (March-June 2020). Patients were stratified according to disease severity: hospitalized patients admitted to the clinical wards without requiring critical care and patients admitted to the intensive care unit (ICU). An additional study was completed including ICU nonsurvivors and survivors. Plasma miRNA profiling was performed using reverse transcription polymerase quantitative chain reaction (RT-qPCR). Predictive models were constructed using least absolute shrinkage and selection operator (LASSO) regression. Ten circulating miRNAs were dysregulated in ICU patients compared to ward patients. LASSO analysis identified a signature of three miRNAs (miR-148a-3p, miR-451a and miR-486-5p) that distinguishes between ICU and ward patients [AUC (95% CI) = 0.89 (0.81-0.97)]. Among critically ill patients, six miRNAs were downregulated between nonsurvivors and survivors. A signature based on two miRNAs (miR-192-5p and miR-323a-3p) differentiated ICU nonsurvivors from survivors [AUC (95% CI) = 0.80 (0.64-0.96)]. The discriminatory potential of the signature was higher than that observed for laboratory parameters such as leukocyte counts, C-reactive protein (CRP) or D-dimer [maximum AUC (95% CI) for these variables = 0.73 (0.55-0.92)]. miRNA levels were correlated with the duration of ICU stay. Specific circulating miRNA profiles are associated with the severity of COVID-19. Plasma miRNA signatures emerge as a novel tool to assist in the early prediction of vital status deterioration among ICU patients.
Collapse
Key Words
- auc, area under the roc curve
- crp, c-reactive protein
- cq, quantification cycle
- icu, intensive care unit
- lasso, least absolute shrinkage and selection operator
- ldh, lactate dehydrogenase
- mirna, microrna
- mse, mean square error
- ncrna, noncoding rna
- pca, principal component analysis
- roc, receiver operating characteristic
- rt, reverse transcription
Collapse
Affiliation(s)
- David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Lucía Pinilla
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Amara Carratalá
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, 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, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, 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, Lleida, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María Bernal
- Laboratory Medicine Department, University Hospital Arnau de Vilanova, Lleida, Spain
| | - Silvia Pico
- Laboratory Medicine Department, University Hospital Arnau de Vilanova, Lleida, Spain
| | - Raquel Almansa
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Noelia Jorge
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Alicia Ortega
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | | | | | | | | | - Pablo Ryan
- Hospital Universitario Infanta Leonor, Madrid, Spain
| | | | - Luis Tamayo
- Hospital Universitario Río Hortega, Valladolid, Spain
| | - César Aldecoa
- Hospital Universitario Río Hortega, Valladolid, 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), 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
| | - 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
| | - 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), 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
| | | | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario de Getafe, Madrid, 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
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
| | | |
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Fiorino S, Tateo F, Biase DD, Gallo CG, Orlandi PE, Corazza I, Budriesi R, Micucci M, Visani M, Loggi E, Hong W, Pica R, Lari F, Zippi M. SARS-CoV-2: lessons from both the history of medicine and from the biological behavior of other well-known viruses. Future Microbiol 2021; 16:1105-1133. [PMID: 34468163 PMCID: PMC8412036 DOI: 10.2217/fmb-2021-0064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is the etiological agent of the current pandemic worldwide and its associated disease COVID-19. In this review, we have analyzed SARS-CoV-2 characteristics and those ones of other well-known RNA viruses viz. HIV, HCV and Influenza viruses, collecting their historical data, clinical manifestations and pathogenetic mechanisms. The aim of the work is obtaining useful insights and lessons for a better understanding of SARS-CoV-2. These pathogens present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne, whereas HIV and HCV are bloodborne. However, these viruses exhibit some potential similar clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2.
Collapse
Affiliation(s)
- Sirio Fiorino
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Fabio Tateo
- Institute of Geosciences & Earth Resources, CNR, c/o Department of Geosciences, Padova University, 35127, Italy
| | - Dario De Biase
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Claudio G Gallo
- Fisiolaserterapico Emiliano, Castel San Pietro Terme, Bologna, 40024, Italy
| | | | - Ivan Corazza
- Department of Experimental, Diagnostic & Specialty Medicine, University of Bologna, Bologna, 40126, Italy
| | - Roberta Budriesi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Matteo Micucci
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Michela Visani
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Loggi
- Hepatology Unit, Department of Medical & Surgical Sciences, University of Bologna, Bologna, 40126, Italy
| | - Wandong Hong
- Department of Gastroenterology & Hepatology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang, 325035, PR China
| | - Roberta Pica
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
| | - Federico Lari
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Maddalena Zippi
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Srivastava SP, Srivastava R, Chand S, Goodwin JE. Coronavirus Disease (COVID)-19 and Diabetic Kidney Disease. Pharmaceuticals (Basel) 2021; 14:751. [PMID: 34451848 PMCID: PMC8398861 DOI: 10.3390/ph14080751] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 01/08/2023] Open
Abstract
The present review describes COVID-19 severity in diabetes and diabetic kidney disease. We discuss the crucial effect of COVID-19-associated cytokine storm and linked injuries and associated severe mesenchymal activation in tubular epithelial cells, endothelial cells, and macrophages that influence neighboring cell homeostasis, resulting in severe proteinuria and organ fibrosis in diabetes. Altered microRNA expression disrupts cellular homeostasis and the renin-angiotensin-system, targets reno-protective signaling proteins, such as angiotensin-converting enzyme 2 (ACE2) and MAS1 receptor (MAS), and facilitates viral entry and replication in kidney cells. COVID-19-associated endotheliopathy that interacts with other cell types, such as neutrophils, platelets, and macrophages, is one factor that accelerates prethrombotic reactions and thrombus formation, resulting in organ failures in diabetes. Apart from targeting vital signaling through ACE2 and MAS, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are also associated with higher profibrotic dipeptidyl transferase-4 (DPP-4)-mediated mechanisms and suppression of AMP-activated protein kinase (AMPK) activation in kidney cells. Lowered DPP-4 levels and restoration of AMPK levels are organ-protective, suggesting a pathogenic role of DPP-4 and a protective role of AMPK in diabetic COVID-19 patients. In addition to standard care provided to COVID-19 patients, we urgently need novel drug therapies that support the stability and function of both organs and cell types in diabetes.
Collapse
Affiliation(s)
- Swayam Prakash Srivastava
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Rohit Srivastava
- Laboratory of Medical Transcriptomics, Department of Endocrinology, Nephrology Services, Hadassah Hebrew-University Medical Center, Jerusalem 91905, Israel;
| | - Subhash Chand
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Julie E. Goodwin
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06511, USA
| |
Collapse
|
35
|
Juscamayta-López E, Carhuaricra D, Tarazona D, Valdivia F, Rojas N, Maturrano L, Gavilán R. Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru. J Med Virol 2021; 93:5961-5968. [PMID: 34185310 PMCID: PMC8426889 DOI: 10.1002/jmv.27167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID‐19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To investigate early transmission events and the genomic diversity of SARS‐CoV‐2 isolates circulating in Peru in the early COVID‐19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community‐driven transmission of SARS‐CoV‐2 as suggested by clusters of related viruses found in patients living in different regions of Peru. This is the first snapshot of the sources of epidemic transmission and genomic diversity of SARS‐CoV‐2 lineages circulating in Peru during the early COVID‐19 pandemic. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia, and high diversity of genetic lineages circulating in Peru with predominance of the G614G variant (S gene,n= 136/149). We found evidence that early spread of the virus in Lima City was sustained by community transmission.
Collapse
Affiliation(s)
- Eduardo Juscamayta-López
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru.,Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Dennis Carhuaricra
- Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - David Tarazona
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru.,Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Faviola Valdivia
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Nancy Rojas
- Laboratorio de Virus Respiratorios, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Lenin Maturrano
- Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ronnie Gavilán
- Laboratorio de Enteropatógenos, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru.,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| |
Collapse
|
36
|
Sato A, Ogino Y, Tanuma SI, Uchiumi F. Human microRNA hsa-miR-15b-5p targets the RNA template component of the RNA-dependent RNA polymerase structure in severe acute respiratory syndrome coronavirus 2. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:790-797. [PMID: 34263708 DOI: 10.1080/15257770.2021.1950759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic of the coronavirus disease in 2019. RNA-dependent RNA polymerase (RdRp) plays an essential role in RNA replication and transcription in SARS-CoV-2. In this study, we focused on the RNA template component of viral RdRp structure and analyzed human microRNAs (miRNAs) targeting specific sequences in this RNA. By examining miRNA databases and using an in vitro RNA-RNA interaction assay, we observed hsa-miR-15b-5p interacting with the RNA component of viral RdRp. Our findings provide evidence that hsa-miR15b-5p may suppresses viral infection and proliferation by targeting the RNA template component of SARS-CoV-2 RdRp.
Collapse
Affiliation(s)
- Akira Sato
- Department of Biochemistry and Molecular Biology, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Yoko Ogino
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Sei-Ichi Tanuma
- Department of Genomic Medicinal Science, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan
| | - Fumiaki Uchiumi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| |
Collapse
|
37
|
Ying H, Ebrahimi M, Keivan M, Khoshnam SE, Salahi S, Farzaneh M. miRNAs; a novel strategy for the treatment of COVID-19. Cell Biol Int 2021; 45:2045-2053. [PMID: 34180562 PMCID: PMC8426984 DOI: 10.1002/cbin.11653] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/08/2021] [Accepted: 06/17/2021] [Indexed: 11/09/2022]
Abstract
Coronavirus disease 2019 (COVID‐19) is the seventh member of the bat severe acute respiratory syndrome family. COVID‐19 can fuse their envelopes with the host cell membranes and deliver their genetic material. COVID‐19 attacks the respiratory system and stimulates the host inflammatory responses, enhances the recruitment of immune cells, and promotes angiotensin‐converting enzyme 2 activities. Patients with confirmed COVID‐19 may have experienced fever, dry cough, headache, dyspnea, acute kidney injury, acute respiratory distress syndrome, and acute heart injury. Several strategies such as oxygen therapy, ventilation, antibiotic or antiviral therapy, and renal replacement therapy are commonly used to decrease COVID‐19‐associated mortality. However, these approaches may not be good treatment options. Therefore, the search for an alternative‐novel therapy is urgently important to prevent the disease progression. Recently, microRNAs (miRNAs) have emerged as a promising strategy for COVID‐19. The design of oligonucleotide against the genetic material of COVID‐19 might suppress virus RNA translation. Several previous studies have shown that host miRNAs play an antiviral role and improve the treatment of patients with COVID‐19. miRNAs by binding to the 3′‐untranslated region (UTR) or 5′‐UTR of viral RNA play an important role in COVID‐19‐host interplay and viral replication. miRNAs interact with multiple pathways and reduce inflammatory biomarkers, thrombi formation, and tissue damage to accelerate the patient outcome. The information in this review provides a summary of the current clinical application of miRNAs for the treatments of patients with COVID‐19.
Collapse
Affiliation(s)
- Hao Ying
- Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, China
| | - Mohsen Ebrahimi
- Neonatal and Children's Health Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mona Keivan
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sarvenaz Salahi
- Minimally Invasive Surgery Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| |
Collapse
|
38
|
Siniscalchi C, Di Palo A, Russo A, Potenza N. Human MicroRNAs Interacting With SARS-CoV-2 RNA Sequences: Computational Analysis and Experimental Target Validation. Front Genet 2021; 12:678994. [PMID: 34163530 PMCID: PMC8215607 DOI: 10.3389/fgene.2021.678994] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 12/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel RNA virus affecting humans, causing a form of acute pulmonary respiratory disorder named COVID-19, declared a pandemic by the World Health Organization. MicroRNAs (miRNA) play an emerging and important role in the interplay between viruses and host cells. Although the impact of host miRNAs on SARS-CoV-2 infection has been predicted, experimental data are still missing. This study started by a bioinformatics prediction of cellular miRNAs potentially targeting viral RNAs; then, a number of criteria also based on experimental evidence and virus biology were applied, giving rise to eight promising binding miRNAs. Their interaction with viral sequences was experimentally validated by transfecting luciferase-based reporter plasmids carrying viral target sequences or their inverted sequences into the lung A549 cell line. Transfection of the reporter plasmids resulted in a reduction of luciferase activity for five out of the eight potential binding sites, suggesting responsiveness to endogenously expressed miRNAs. Co-transfection of the reporter plasmids along with miRNA mimics led to a further and strong reduction of luciferase activity, validating the interaction between miR-219a-2-3p, miR-30c-5p, miR-378d, miR-29a-3p, miR-15b-5p, and viral sequences. miR-15b was also able to repress plasmid-driven Spike expression. Intriguingly, the viral target sequences are fully conserved in more recent variants such as United Kingdom variant B.1.1.7 and South Africa 501Y.V2. Overall, this study provides a first experimental evidence of the interaction between specific cellular miRNAs and SARS-CoV-2 sequences, thus contributing to understanding the molecular mechanisms underlying virus infection and pathogenesis to envisage innovative therapeutic interventions and diagnostic tools.
Collapse
Affiliation(s)
- Chiara Siniscalchi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Armando Di Palo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Aniello Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Nicoletta Potenza
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| |
Collapse
|
39
|
Barreda-Manso MA, Nieto-Díaz M, Soto A, Muñoz-Galdeano T, Reigada D, Maza RM. In Silico and In Vitro Analyses Validate Human MicroRNAs Targeting the SARS-CoV-2 3'-UTR. Int J Mol Sci 2021; 22:6094. [PMID: 34198800 PMCID: PMC8201247 DOI: 10.3390/ijms22116094] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic is caused by betacoronavirus SARS-CoV-2. The genome of this virus is composed of a single strand of RNA with 5' and 3'-UTR flanking a region of protein-coding ORFs closely resembling cells' mRNAs. MicroRNAs are endogenous post-transcriptional regulators that target mRNA to modulate protein expression and mediate cellular functions, including antiviral defense. In the present study, we carried out a bioinformatics screening to search for endogenous human microRNAs targeting the 3'-UTR of SARS-CoV-2. Results from the computational techniques allowed us to identify 10 potential candidates. The capacity of 3 of them, together with hsa-miR-138-5p, to target the SARS-CoV-2 3'-UTR was validated in vitro by gene reporter assays. Available information indicates that two of these microRNAs, namely, hsa-miR-3941 and hsa-miR-138-5p, combine effective targeting of SARS-CoV-2 genome with complementary antiviral or protective effects in the host cells that make them potential candidates for therapeutic treatment of most, if not all, COVID-19 variants known to date. All information obtained while conducting the present analysis is available at Open Science Framework repository.
Collapse
Affiliation(s)
| | - Manuel Nieto-Díaz
- Molecular Neuroprotection Group, Research Unit, National Hospital for Paraplegics (SESCAM), 45071 Toledo, Spain; (M.A.B.-M.); (A.S.); (T.M.-G.); (D.R.)
| | | | | | | | - Rodrigo M. Maza
- Molecular Neuroprotection Group, Research Unit, National Hospital for Paraplegics (SESCAM), 45071 Toledo, Spain; (M.A.B.-M.); (A.S.); (T.M.-G.); (D.R.)
| |
Collapse
|
40
|
De Sanctis JB, García AH, Moreno D, Hajduch M. Coronavirus infection: An immunologists' perspective. Scand J Immunol 2021; 93:e13043. [PMID: 33783027 PMCID: PMC8250184 DOI: 10.1111/sji.13043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus infections are frequent viral infections in several species. As soon as the severe acute respiratory syndrome (SARS) appeared in the early 2000s, most of the research focused on pulmonary disease. However, disorders in immune response and organ dysfunctions have been documented. Elderly individuals with comorbidities exhibit worse outcomes in all the coronavirus that cause SARS. Disease severity in SARS-CoV-2 infection is related to severe inflammation and tissue injury, and effective immune response against the virus is still under analysis. ACE2 receptor expression and polymorphism, age, gender and immune genetics are factors that also play an essential role in patients' clinical features and immune responses and have been partially discussed. The present report aims to review the physiopathology of SARS-CoV-2 infection and propose new research topics to understand the complex mechanisms of viral infection and viral clearance.
Collapse
Affiliation(s)
- Juan Bautista De Sanctis
- Institute of Molecular and Translational MedicineFaculty of Medicine and DentistryPalacky UniversityOlomoucCzech Republic
- Institute of ImmunologyFaculty of MedicineUniversidad Central de VenezuelaCaracasVenezuela
| | - Alexis Hipólito García
- Institute of ImmunologyFaculty of MedicineUniversidad Central de VenezuelaCaracasVenezuela
| | - Dolores Moreno
- Chair of General Pathology and PathophysiologyFaculty of MedicineCentral University of VenezuelaCaracasVenezuela
| | - Marián Hajduch
- Institute of Molecular and Translational MedicineFaculty of Medicine and DentistryPalacky UniversityOlomoucCzech Republic
| |
Collapse
|
41
|
Hassan SS, Aljabali AAA, Panda PK, Ghosh S, Attrish D, Choudhury PP, Seyran M, Pizzol D, Adadi P, Abd El-Aziz TM, Soares A, Kandimalla R, Lundstrom K, Lal A, Azad GK, Uversky VN, Sherchan SP, Baetas-da-Cruz W, Uhal BD, Rezaei N, Chauhan G, Barh D, Redwan EM, Dayhoff GW, Bazan NG, Serrano-Aroca Á, El-Demerdash A, Mishra YK, Palu G, Takayama K, Brufsky AM, Tambuwala MM. A unique view of SARS-CoV-2 through the lens of ORF8 protein. Comput Biol Med 2021; 133:104380. [PMID: 33872970 PMCID: PMC8049180 DOI: 10.1016/j.compbiomed.2021.104380] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/07/2023]
Abstract
Immune evasion is one of the unique characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attributed to its ORF8 protein. This protein modulates the adaptive host immunity through down-regulation of MHC-1 (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the host's interferon-mediated antiviral response. To understand the host's immune perspective in reference to the ORF8 protein, a comprehensive study of the ORF8 protein and mutations possessed by it have been performed. Chemical and structural properties of ORF8 proteins from different hosts, such as human, bat, and pangolin, suggest that the ORF8 of SARS-CoV-2 is much closer to ORF8 of Bat RaTG13-CoV than to that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 in SARS-CoV-2 can be grouped into four classes based on their predicted effects (Hussain et al., 2021) [1]. Based on the geo-locations and timescale of sample collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were found upon sequence similarity analyses and consideration of the amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of the rapidly evolving SARS-CoV-2 through the ORF8.
Collapse
Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 721140, India
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid, 566, Jordan
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi, 110007, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, West Bengal, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad, 500007, Telangana State, India
| | | | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran and Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Sur, 64849, Monterrey, NL, Mexico Tecnológico De Monterrey, Campus Monterrey, Monterrey, Nuevo León, Mexico
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), PatnaPatna, India
| | - Elrashdy M Redwan
- King Abdulazizi University, Faculty of Science, Department of Biological Science, Saudi Arabia
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, 70112, USA
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Translational Research Centre San Alberto Magno, Catholic University of Valencia San Vicente Mártir, C/Guillem de Castro 94, 46001, Valencia, Spain
| | - Amr El-Demerdash
- Natural Products and Medicinal Chemistry Department, Institute de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Yogendra K Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Italy
| | - Kazuo Takayama
- Center for IPS Cell Research and Application, Kyoto University, Kyoto, 606-8397, Japan
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| |
Collapse
|
42
|
Marchi R, Sugita B, Centa A, Fonseca AS, Bortoletto S, Fiorentin K, Ferreira S, Cavalli LR. The role of microRNAs in modulating SARS-CoV-2 infection in human cells: a systematic review. INFECTION GENETICS AND EVOLUTION 2021; 91:104832. [PMID: 33812037 PMCID: PMC8012164 DOI: 10.1016/j.meegid.2021.104832] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/11/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
MicroRNAs are gene expression regulators, associated with several human pathologies, including the ones caused by virus infections. Although their role in infection diseases is not completely known, they can exert double functions in the infected cell, by mediating the virus infection and/or regulating the immunity-related gene targets through complex networks of virus-host cell interactions. In this systematic review, the Pubmed, EMBASE, Scopus, Lilacs, Scielo, and EBSCO databases were searched for research articles published until October 22nd, 2020 that focused on describing the role, function, and/or association of miRNAs in SARS-CoV-2 human infection and COVID-19. Following the PRISMA 2009 protocol, 29 original research articles were selected. Most of the studies reported miRNA data based on the genome sequencing of SARS-CoV-2 isolates and computational prediction analysis. The latter predicted, by at least one independent study, 1266 host miRNAs to target the viral genome. Thirteen miRNAs were identified by four independent studies to target SARS-CoV-2 specific genes, suggested to act by interfering with their cleavage and/or translation process. The studies selected also reported on viral and host miRNAs that targeted host genes, on the expression levels of miRNAs in biological specimens of COVID-19 patients, and on the impact of viral genome mutations on miRNA function. Also, miRNAs that regulate the expression levels of the ACE2 and TMPRSS2 proteins, which are critical for the virus entrance in the host cells, were reported. In conclusion, despite the limited number of studies identified, based on the search terms and eligibility criteria applied, this systematic review provides evidence on the impact of miRNAs on SARS-CoV-2 infection and COVID-19. Although most of the reported viral/host miRNAs interactions were based on in silico prediction analysis, they demonstrate the relevance of the viral/host miRNA interaction for viral activity and host responses. In addition, the identified studies highlight the potential use of miRNAs as therapeutic targets against COVID-19, and other viral human diseases (This review was registered at the International Prospective Register of Systematic Reviews (PROSPERO) database (#CRD42020199290).
Collapse
Affiliation(s)
- Rafael Marchi
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Bruna Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Ariana Centa
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Aline S Fonseca
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Stefanne Bortoletto
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Karine Fiorentin
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Solange Ferreira
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Luciane R Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
| |
Collapse
|
43
|
Abstract
Nowadays, the SARS Coronavirus 2 (SARS-CoV-2) infection is recognized as the primary cause of mortality in humans. SARS-CoV-2 is transmitted through human-to-human contact and is asymptomatic in most patients. In addition to approved vaccines against SARS-CoV-2 infection, miRNAs may also be promising options against this new virus. miRNAs are small and noncoding RNAs 18–25 nucleotides in length that target the mRNAs to degrade them or obstruct their translation miRNAs act as an observer in cells. This study reviewed the literature on the potential role of cellular miRNAs in the SARS-CoV-2-host interplay as a therapeutic option in COVID-19 patients.
Collapse
Affiliation(s)
- Mona Fani
- Department of Pathobiology & Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeedeh Ebrahimi
- Department of Medical Microbiology, Faculty of Medicine Science, Kerman University of Medical Sciences, Kerman, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | | |
Collapse
|
44
|
Khan MT, Ali S, Khan AS, Muhammad N, Khalil F, Ishfaq M, Irfan M, Al-Sehemi AG, Muhammad S, Malik A, Khan TA, Wei DQ. SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. ACS OMEGA 2021; 6:6588-6599. [PMID: 33748571 PMCID: PMC7944396 DOI: 10.1021/acsomega.0c05163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Among viral outbreaks, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest ones, and it has triggered the global COVID-19 pandemic. In Pakistan, until 5th September 2020, a total of 6342 deaths have been reported, of which 1255 were from the Khyber Pakhtunkhwa (KPK) province. To understand the disease progression and control and also to produce vaccines and therapeutic efforts, whole genome sequence analysis is important. In the current investigation, we sequenced a single sample of SARS-CoV-2 genomes (accession no. MT879619) from a male suspect from Peshawar, the KPK capital city, during the first wave of infection. The local SARS-CoV-2 strain shows some unique characteristics compared to neighboring Iranian and Chinese isolates in phylogenetic tree and mutations. The circulating strains of SARS-CoV-2 represent an intermediate evolution from China and Iran. Furthermore, eight complete whole genome sequences, including the current Pakistani isolates which have been submitted to Global Initiative on Sharing All Influenza Data (GSAID), were also investigated for specific mutations and characters. Some novel mutations [NSP2 (D268del), NSP5 (N228K), and NS3 (F105S)] and specific characters have been detected in the coding regions, which may affect viral transmission, epidemiology, and disease severity. The computational modeling revealed that a majority of these mutations may have a stabilizing effect on the viral protein structure. In conclusion, the genome sequencing of local strains is important for better understanding the pathogenicity, immunogenicity, and epidemiology of causative agents.
Collapse
Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad 45320, Pakistan
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Noor Muhammad
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Faiza Khalil
- Department of Biochemistry, Khyber Medical
College, Peshawar 25160, Pakistan
- University
of Peshawar, Road No.
2, Rahat Abad, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ishfaq
- Centre for Omic Sciences, Islamia
College Peshawar. Grand Trunk Road, Rahat Abad, Peshawar 25120, Pakistan
| | - Muhammad Irfan
- Department
of Oral Biology, College of Dentistry, University
of Florida, Gainesville, Florida 32611, United States
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Shabbir Muhammad
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Arif Malik
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Phase V, Hayatabad, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| |
Collapse
|
45
|
Kadam SB, Sukhramani GS, Bishnoi P, Pable AA, Barvkar VT. SARS-CoV-2, the pandemic coronavirus: Molecular and structural insights. J Basic Microbiol 2021; 61:180-202. [PMID: 33460172 PMCID: PMC8013332 DOI: 10.1002/jobm.202000537] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022]
Abstract
The outbreak of a novel coronavirus associated with acute respiratory disease, called COVID-19, marked the introduction of the third spillover of an animal coronavirus (CoV) to humans in the last two decades. The genome analysis with various bioinformatics tools revealed that the causative pathogen (SARS-CoV-2) belongs to the subgenus Sarbecovirus of the genus Betacoronavirus, with highly similar genome as bat coronavirus and receptor-binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS-CoV-2 is likely to have originated from bat-derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further, spike protein S1/S2 cleavage site of SARS-CoV-2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS-CoV-2, roles of virus proteins in pathogenesis, commonalities, and differences between different corona viruses. Moreover, the crystal structures of SARS-CoV-2 proteins with unique characteristics differentiating it from other CoVs are discussed. Our review also provides comprehensive information on the molecular aspects of SARS-CoV-2 including secondary structures in the genome and protein-protein interactions which can be useful to understand the aggressive spread of the SARS-CoV-2. The mutations and the haplotypes reported in the SARS-CoV-2 genome are summarized to understand the virus evolution.
Collapse
Affiliation(s)
| | | | | | - Anupama A. Pable
- Department of MicrobiologySavitribai Phule Pune UniversityPuneIndia
| | | |
Collapse
|
46
|
Aldhumani AH, Hossain MI, Fairchild EA, Boesger H, Marino EC, Myers M, Hines JV. RNA sequence and ligand binding alter conformational profile of SARS-CoV-2 stem loop II motif. Biochem Biophys Res Commun 2021; 545:75-80. [PMID: 33545635 PMCID: PMC7834705 DOI: 10.1016/j.bbrc.2021.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
Abstract
Antiviral drug discovery continues to be an essential complement to vaccine development for overcoming the global pandemic caused by SARS-CoV-2. The genomic RNA of SARS-CoV-2 contains structural elements important for viral replication and/or pathogenesis making them potential therapeutic targets. Here we report on the stem-loop II motif, a highly conserved noncoding RNA element. Based on our homology model we determined that the G to U transversion in the SARS-CoV-2 stem-loop II motif (S2MG35U) forms a C–U base-pair isosteric to the C-G base-pair in the early 2000’s SARS-CoV (S2M). In addition, chemo-enzymatic probing and molecular dynamics simulations indicate the S2MG35U conformational profile is altered compared to S2M in the apical loop region. We explored S2MG35U as a potential drug target by docking a library of FDA approved drugs. Enzymatic probing of the best docking ligands (aminoglycosides and polymyxins) indicated that polymyxin binding alters the conformational profile and/or secondary structure of the RNA. The SARS-CoV-2 stem-loop II motif conformational differences due to nucleotide transversion and ligand binding are highly significant and provide insight for future drug discovery efforts since the conformation of noncoding RNA elements affects their function.
Collapse
Affiliation(s)
- Ali H Aldhumani
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States
| | - Md Ismail Hossain
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States
| | - Emily A Fairchild
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States
| | - Hannah Boesger
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, United States; Honors Tutorial College, Ohio University, Athens, OH, 45701, United States
| | - Emily C Marino
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, United States; Honors Tutorial College, Ohio University, Athens, OH, 45701, United States
| | - Mason Myers
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States; Honors Tutorial College, Ohio University, Athens, OH, 45701, United States
| | - Jennifer V Hines
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States.
| |
Collapse
|
47
|
Abedi F, Rezaee R, Hayes AW, Nasiripour S, Karimi G. MicroRNAs and SARS-CoV-2 life cycle, pathogenesis, and mutations: biomarkers or therapeutic agents? Cell Cycle 2021; 20:143-153. [PMID: 33382348 PMCID: PMC7889196 DOI: 10.1080/15384101.2020.1867792] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
To date, proposed therapies and antiviral drugs have been failed to cure coronavirus disease 2019 (COVID-19) patients. However, at least two drug companies have applied for emergency use authorization with the United States Food and Drug Administration for their coronavirus vaccine candidates and several other vaccines are in various stages of development to determine safety and efficacy. Recently, some studies have shown the role of different human and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) microRNAs (miRNAs) in the pathophysiology of COVID-19. miRNAs are non-coding single-stranded RNAs, which are involved in several physiological and pathological conditions, such as cell proliferation, differentiation, and metabolism. They act as negative regulators of protein synthesis through binding to the 3' untranslated region (3' UTR) of the complementary target mRNA, leading to mRNA degradation or inhibition. The databases of Google Scholar, Scopus, PubMed, and Web of Science were searched for literature regarding the importance of miRNAs in the SARS-CoV-2 life cycle, pathogenesis, and genomic mutations. Furthermore, promising miRNAs as a biomarker or antiviral agent in COVID-19 therapy are reviewed.
Collapse
Affiliation(s)
- Farshad Abedi
- Pharmaceutical Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ramin Rezaee
- Clinical Research Unit, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A. Wallace Hayes
- University of South Florida, Tampa, FL, USA
- Michigan State University, East Lansing, MI, USA
| | - Somayyeh Nasiripour
- Department of Clinical Pharmacy, School of Pharmacy, Iran University of Medical Sciences, Iran
| | - Gholamreza Karimi
- Pharmaceutical Research Center, Institute of Pharmaceutical Technology, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
48
|
Potential therapeutic approaches of microRNAs for COVID-19: Challenges and opportunities. J Oral Biol Craniofac Res 2020; 11:132-137. [PMID: 33398242 PMCID: PMC7772998 DOI: 10.1016/j.jobcr.2020.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/23/2020] [Indexed: 02/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) emerges as current outbreak cause by Novel Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2). This infection affects respiratory system and provides uncontrolled systemic inflammatory response as cytokine storm. The main concern about SARS-CoV-2 pandemic is high viral pathogenicity with no specific drugs. MicroRNAs (miRs) as small non-coding RNAs (21–25 nt) regulate gene expression. The SARS-CoV-2 encoded-miRs affect human genes that involved in transcription, translation, apoptosis, immune response and inflammation. Also, they alter self-gene regulation and hijacked host miRs that provide protective environment to maintain its latency. On the other hand, Host miRs play critical role in viral gene expression to restrict infection. Over expression/inhibition of miRs might result in cell cycle irregularity, impaired immune response or cancer. In this manner, exact role of each miR should be specified. Mimic encoded-miRs like antagomirs showed successful result in phases of clinical trial prevent from negative effects of viral encoded-miRs. Products of mimic miRs are inexpensive corresponds to synthesis of primer; they are short and nanoscale in size. Although SARS-CoV-2 genome is undergoing evaluation, detection of exact molecular pathogenesis open up opportunities to for vaccine development. Salivaomics can evaluate SARS-CoV-2 genome, transcriptome, proteome and biomarkers like miRs in oral related and cancer disease. In this review, we studied the challenge and opportunities of miRs in therapeutic approach for SARS-CoV-2 infection, then overviewed the role of miRs in saliva droplet during SARS-CoV-2 infection and related cancer.
Collapse
|
49
|
Zeng HL, Dichio V, Rodríguez Horta E, Thorell K, Aurell E. Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes. Proc Natl Acad Sci U S A 2020; 117:31519-31526. [PMID: 33203681 PMCID: PMC7733830 DOI: 10.1073/pnas.2012331117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to deeper understanding of microbial pathogenesis. We have considered all complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes deposited in the Global Initiative on Sharing All Influenza Data (GISAID) repository until four different cutoff dates, and used direct coupling analysis together with an assumption of quasi-linkage equilibrium to infer epistatic contributions to fitness from polymorphic loci. We find eight interactions, of which three are between pairs where one locus lies in gene ORF3a, both loci holding nonsynonymous mutations. We also find interactions between two loci in gene nsp13, both holding nonsynonymous mutations, and four interactions involving one locus holding a synonymous mutation. Altogether, we infer interactions between loci in viral genes ORF3a and nsp2, nsp12, and nsp6, between ORF8 and nsp4, and between loci in genes nsp2, nsp13, and nsp14. The paper opens the prospect to use prominent epistatically linked pairs as a starting point to search for combinatorial weaknesses of recombinant viral pathogens.
Collapse
Affiliation(s)
- Hong-Li Zeng
- New Energy Technology Engineering Laboratory of Jiangsu Province, School of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
- Nordic Institute for Theoretical Physics, Royal Institute of Technology and Stockholm University, 10691 Stockholm, Sweden
| | - Vito Dichio
- Nordic Institute for Theoretical Physics, Royal Institute of Technology and Stockholm University, 10691 Stockholm, Sweden
- Department of Physics, University of Trieste, 34151 Trieste, Italy
- Department of Computational Science and Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Edwin Rodríguez Horta
- Group of Complex Systems and Statistical Physics, Department of Theoretical Physics, Physics Faculty, University of Havana, 10400 Havana, Cuba
| | - Kaisa Thorell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Center for Translational Microbiome Research, Department of Microbiology, Cell and Tumor Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Erik Aurell
- Department of Computational Science and Technology, AlbaNova University Center, 10691 Stockholm, Sweden;
| |
Collapse
|
50
|
Jafarinejad-Farsangi S, Jazi MM, Rostamzadeh F, Hadizadeh M. High affinity of host human microRNAs to SARS-CoV-2 genome: An in silico analysis. Noncoding RNA Res 2020; 5:222-231. [PMID: 33251388 PMCID: PMC7680021 DOI: 10.1016/j.ncrna.2020.11.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/02/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) caused by a novel betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted top health concerns worldwide within a few months after its appearance. Since viruses are highly dependent on the host small RNAs (microRNAs) for their replication and propagation, in this study, top miRNAs targeting SARS-CoV-2 genome and top miRNAs targeting differentially expressed genes (DEGs) in lungs of patients infected with SARS-CoV-2, were predicted. METHODS All human mature miRNA sequences were acquired from miRBase database. MiRanda tool was used to predict the potential human miRNA binding sites on the SARS-CoV-2 genome. EdgeR identified differentially expressed genes (DEGs) in response to SARS-CoV-2 infection from GEO147507 data. Gene Set Enrichment Analysis (GSEA) and DEGs annotation analysis were performed using ToppGene and Metascape tools. RESULTS 160 miRNAs with a perfect matching in the seed region were identified. Among them, there was 15 miRNAs with more than three binding sites and 12 miRNAs with a free energy binding of -29 kCal/Mol. MiR-29 family had the most binding sites (11 sites) on the SARS-CoV-2 genome. MiR-21 occupied four binding sites and was among the top miRNAs that targeted up-regulated DEGs. In addition to miR-21, miR-16, let-7b, let-7e, and miR-146a were the top miRNAs targeting DEGs. CONCLUSION Collectively, more experimental studies especially miRNA-based studies are needed to explore detailed molecular mechanisms of SARS-CoV-2 infection. Moreover, the role of DEGs including STAT1, CCND1, CXCL-10, and MAPKAPK2 in SARS-CoV-2 should be investigated to identify the similarities and differences between SARS-CoV-2 and other respiratory viruses.
Collapse
Affiliation(s)
- Saeideh Jafarinejad-Farsangi
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Maryam Moazzam Jazi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzaneh Rostamzadeh
- Cardiovascular Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Morteza Hadizadeh
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| |
Collapse
|