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Ashraf S, Sufyan M, Aslam B, Khalid H, Albekairi NA, Alshammari A, Alharbi M, Nisar MA, Khurshid M, Ashfaq UA. Uncovering chikungunya virus-encoded miRNAs and host-specific targeted genes associated with antiviral immune responses: an integrated bioinformatics approach. Sci Rep 2024; 14:18614. [PMID: 39127786 PMCID: PMC11316756 DOI: 10.1038/s41598-024-67436-5] [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: 04/06/2023] [Accepted: 07/11/2024] [Indexed: 08/12/2024] Open
Abstract
Chikungunya virus (CHIKV) is a single-stranded RNA virus belonging to the genus Alphavirus and is responsible for causing Chikungunya fever, a type of arboviral fever. Despite extensive research, the pathogenic mechanism of CHIKV within host cells remains unclear. In this study, an in-silico approach was used to predict that CHIKV produces micro-RNAs that target host-specific genes associated with host cellular regulatory pathways. Putative micro-RNAs of CHIKV were predicted using the miRNAFold and Vmir RNA structure web servers, and secondary structure prediction was performed using RNAfold. Host-specific target genes were then predicted, and hub genes were identified using CytoHubba and module selection through MCODE. Functional annotations of hub genes revealed their association with various pathways, including osteoclast differentiation, neuroactive ligand-receptor interaction, and mRNA surveillance. We used the freely available dataset GSE49985 to determine the level of expression of host-specific target genes and found that two genes, F-box and leucine-rich repeat protein 16 (FBXL16) and retinoic acid receptor alpha (RARA), were down-regulated, while four genes, RNA binding protein with serine-rich domain 1 (RNPS1), RNA helicase and ATPase (UPF1), neuropeptide S receptor 1 (NPSR1), and vasoactive intestinal peptide receptor 1 (VIPR1), were up-regulated. These findings provide insight into novel miRNAs and hub genes associated with CHIKV infection and suggest potential targets for therapeutic intervention. Further experimental validation of these targets could lead to the development of effective treatments for CHIKV-mediated diseases.
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Affiliation(s)
- Sajida Ashraf
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Bilal Aslam
- Institite of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, 11451, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, 11451, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, 11451, Riyadh, Saudi Arabia
| | - Muhammad Atif Nisar
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Mohsin Khurshid
- Institite of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan.
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
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Shaikh MS, Faiyazuddin M, Khan MS, Pathan SK, Syed IJ, Gholap AD, Akhtar MS, Sah R, Mehta R, Sah S, Bonilla-Aldana DK, Luna C, Rodriguez-Morales AJ. Chikungunya virus vaccine: a decade of progress solving epidemiological dilemma, emerging concepts, and immunological interventions. Front Microbiol 2024; 15:1413250. [PMID: 39104592 PMCID: PMC11298817 DOI: 10.3389/fmicb.2024.1413250] [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: 04/06/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Chikungunya virus (CHIKV), a single-stranded RNA virus transmitted by Aedes mosquitoes, poses a significant global health threat, with severe complications observed in vulnerable populations. The only licensed vaccine, IXCHIQ, approved by the US FDA, is insufficient to address the growing disease burden, particularly in endemic regions lacking herd immunity. Monoclonal antibodies (mAbs), explicitly targeting structural proteins E1/E2, demonstrate promise in passive transfer studies, with mouse and human-derived mAbs showing protective efficacy. This article explores various vaccine candidates, including live attenuated, killed, nucleic acid-based (DNA/RNA), virus-like particle, chimeric, subunit, and adenovirus vectored vaccines. RNA vaccines have emerged as promising candidates due to their rapid response capabilities and enhanced safety profile. This review underscores the importance of the E1 and E2 proteins as immunogens, emphasizing their antigenic potential. Several vaccine candidates, such as CHIKV/IRES, measles vector (MV-CHIK), synthetic DNA-encoded antibodies, and mRNA-lipid nanoparticle vaccines, demonstrate encouraging preclinical and clinical results. In addition to identifying potential molecular targets for antiviral therapy, the study looks into the roles played by Toll-like receptors, RIG-I, and NOD-like receptors in the immune response to CHIKV. It also offers insights into novel tactics and promising vaccine candidates. This article discusses potential antiviral targets, the significance of E1 and E2 proteins, monoclonal antibodies, and RNA vaccines as prospective Chikungunya virus vaccine candidates.
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Affiliation(s)
| | - Md. Faiyazuddin
- School of Pharmacy, Al – Karim University, Katihar, India
- Centre for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | | | - Shahbaz K. Pathan
- Medmecs Medical Coding & Billing Services, Universal Business Park, Mumbai, Maharashtra, India
| | - Imran J. Syed
- Y. B. Chavan College of Pharmacy, Aurangabad, Maharashtra, India
- SBSPM’s B. Pharmacy College, Beed, Maharashtra, India
| | - Amol D. Gholap
- Department of Pharmaceutics, St. John Institute of Pharmacy and Research, Palghar, Maharashtra, India
| | - Mohammad Shabib Akhtar
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Ranjit Sah
- Green City Hospital, Kathmandu, Nepal
- Research Unit, Department of Microbiology, Dr. DY Patil Medical College, Hospital and Research Centre, DY Patil Vidyapeeth, Pune, Maharashtra, India
- Department of Public Health Dentistry, Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Rachana Mehta
- Dr Lal PathLabs Nepal, Kathmandu, Nepal
- Medical Laboratories Techniques Department, AL-Mustaqbal University, Hillah, Babil, Iraq
- Clinical Microbiology, School of Dental Science, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | | | | | - Camila Luna
- Faculty of Health Sciences, Universidad Científica del Sur, Lima, Peru
| | - Alfonso J. Rodriguez-Morales
- Faculty of Health Sciences, Universidad Científica del Sur, Lima, Peru
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas-Institución Universitaria Visión de las Américas, Pereira, Colombia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
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3
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Saini S, Khurana S, Saini D, Rajput S, Thakur CJ, Singh J, Jaswal A, Kapoor Y, Kumar V, Saini A. In silico analysis of genomic landscape of SARS-CoV-2 and its variant of concerns (Delta and Omicron) reveals changes in the coding potential of miRNAs and their target genes. Gene 2023; 853:147097. [PMID: 36470485 PMCID: PMC9721428 DOI: 10.1016/j.gene.2022.147097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 related morbidities and mortalities are still continued due to the emergence of new variants of SARS-CoV-2. In the last few years, viral miRNAs have been the centre of study to understand the disease pathophysiology. In this work, we aimed to predict the change in coding potential of the viral miRNAs in SARS-CoV-2's VOCs, Delta and Omicron compared to the Reference (Wuhan origin) strain using bioinformatics tools. After ab-intio based screening by the Vmir tool and validation, we retrieved 22, 6, and 6 pre-miRNAs for Reference, Delta, and Omicron. Most of the predicted unique pre-miRNAs of Delta and Omicron were found to be encoded from the terminal and origin of the genomic sequence, respectively. Mature miRNAs identified by MatureBayes from the unique pre-miRNAs were used for target identification using miRDB. A total of 1786, 216, and 143 high-confidence target genes were captured for GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The GO and KEGG pathways terms analysis revealed the involvement of Delta miRNAs targeted genes in the pathways such as Human cytomegalovirus infection, Breast cancer, Apoptosis, Neurotrophin signaling, and Axon guidance whereas the Sphingolipid signaling pathway was found for the Omicron. Furthermore, we focussed our analysis on target genes that were validated through GEO's (Gene Expression Omnibus) DEGs (Differentially Expressed Genes) dataset, in which FGL2, TNSF12, OGN, GDF11, and BMP11 target genes were found to be down-regulated by Reference miRNAs and YAE1 and RSU1 by Delta. Few genes were also observed to be validated among in up-regulated gene set of the GEO dataset, in which MMP14, TNFRSF21, SGMS1, and TMEM192 were related to Reference whereas ZEB2 was detected in all three strains. This study thus provides an in-silico based analysis that deciphered the unique pre-miRNAs in Delta and Omicron compared to Reference. However, the findings need future wet lab studies for validation.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India; Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India.
| | - Savi Khurana
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Dikshant Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Saru Rajput
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Jeevisha Singh
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Akanksha Jaswal
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Yogesh Kapoor
- Department of Engineering and Technology, Shoolini University, Solan, Himachal Pradesh, India
| | - Varinder Kumar
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India.
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4
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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.
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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
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Noor F, Saleem MH, Javed MR, Chen JT, Ashfaq UA, Okla MK, Abdel-Maksoud MA, Alwasel YA, Al-Qahtani WH, Alshaya H, Yasin G, Aslam S. Comprehensive computational analysis reveals H5N1 influenza virus-encoded miRNAs and host-specific targets associated with antiviral immune responses and protein binding. PLoS One 2022; 17:e0263901. [PMID: 35533150 PMCID: PMC9084522 DOI: 10.1371/journal.pone.0263901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/30/2022] [Indexed: 02/06/2023] Open
Abstract
H5N1 virus (H5N1V) is highly contagious among birds and it was first detected in humans in 1997 during a poultry outbreak in Hong Kong. As the mechanism of its pathogenesis inside the host is still lacking, in this in-silico study we hypothesized that H5N1V might create miRNAs, which could target the genes associated with host cellular regulatory pathways, thus provide persistent refuge to the virus. Using bioinformatics approaches, several H5N1V produced putative miRNAs as well as the host genes targeted by these miRNAs were found. Functional enrichment analysis of targeted genes revealed their involvement in many biological pathways that facilitate their host pathogenesis. Eventually, the microarray dataset (GSE28166) was analyzed to validate the altered expression level of target genes and found the genes involved in protein binding and adaptive immune responses. This study presents novel miRNAs and their targeted genes, which upon experimental validation could facilitate in developing new therapeutics against H5N1V infection.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | | | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Mohammad K. Okla
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mostafa A. Abdel-Maksoud
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Yasmeen A. Alwasel
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wahidah H. Al-Qahtani
- Department of food sciences & nutrition, College of food & Agriculture sciences, King Saud University, Riyadh, Saudi Arabia
| | - Huda Alshaya
- Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
| | - Ghulam Yasin
- Department of Botany, Bahauddin Zakariya University, Multan, Pakistan
| | - Sidra Aslam
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
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