Uncovering chikungunya virus-encoded miRNAs and host-specific targeted genes associated with antiviral immune responses: an integrated bioinformatics approach

• Published in: Scientific reports 2024-08, Vol.14 (1), p.18614-10, Article 18614
• Main Authors: Ashraf, Sajida, Sufyan, Muhammad, Aslam, Bilal, Khalid, Hina, Albekairi, Norah A., Alshammari, Abdulrahman, Alharbi, Metab, Nisar, Muhammad Atif, Khurshid, Mohsin, Ashfaq, Usman Ali
• Format: Article
• Language: English
• Subjects: 631/326/107; 631/326/421; 631/326/596; Bioinformatics; Chikungunya Fever - genetics; Chikungunya Fever - immunology; Chikungunya Fever - virology; Chikungunya virus; Chikungunya virus - genetics; Chikungunya virus - immunology; CHIKV; Computational Biology - methods; CytoHubba; DNA helicase; Fever; Gene expression; Gene Regulatory Networks; Host specificity; Host-Pathogen Interactions - genetics; Host-Pathogen Interactions - immunology; Hub genes; Humanities and Social Sciences; Humans; Immune response; KEGG; MicroRNAs - genetics; miRNA; mRNA; multidisciplinary; Osteoclastogenesis; Protein structure; RNA helicase; RNA viruses; RNA, Viral - genetics; RNA-binding protein; Science; Science (multidisciplinary); Secondary structure; Target genes; Vasoactive agents; Vasoactive intestinal peptide; Vector-borne diseases
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-67436-5

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.