Abstract
Aim: The study aims to identify high-impact single nucleotide polymorphisms (SNPs) in miRNA target sites of genes associated with lung cancer. Materials & methods: Lung cancer genes were obtained from Uniprot KB. miRNA target site SNPs were mined from MirSNP, miRdSNP and TargetScan. SNPs were shortlisted based on binding impact, minor allele frequency and conservation. Gene expression was analyzed in genes with high-impact SNPs in healthy versus lung cancer tissue. Additionally, enrichment, pathway and network analyzes were performed. Results: 19 high-impact SNPs were identified in miRNA target sites of lung cancer-associated genes. These SNPs affect miRNA binding and gene expression. The genes are involved in key cancer related pathways. Conclusion: The identified high-impact miRNA target site SNPs and associated genes provide a starting point for case–control studies in lung cancer patients in different populations.
The study aims to identify high-impact single nucleotide polymorphisms (SNPs) in microRNA (miRNA) target sites of genes associated with lung cancer.
Data collection
Genes involved in lung cancer were retrieved from the UniProt Knowledge Base.
SNP identification
miRNA target site SNPs were mined from databases such as MirSNP, miRdSNP and TargetScan.
Selection criteria
SNPs were shortlisted based on their impact on miRNA binding, minor allele frequency (MAF) and conservation.
Gene expression analysis
The expression of genes with high-impact SNPs was analyzed in healthy versus lung cancer tissues.
Bioinformatics analysis
Enrichment, pathway and network analyses were performed to understand the biological implications of these SNPs.
Results
High-Impact SNPs: 19 high-impact SNPs were identified in miRNA target sites of lung cancer-associated genes.
Gene expression
These SNPs affect miRNA binding and gene expression, with the genes involved in key cancer-related pathways.
Functional analysis
The study provided insights into the molecular functions and biological processes affected by these SNPs, including phosphotransferase and kinase activities, cell death and cell cycle regulation.
Network analysis
Gene network analysis showed relevant interactions among the genes with high-impact SNPs, indicating their role in lung cancer pathways.
Conclusion
The identified high-impact miRNA target site SNPs and associated genes offer a starting point for case-control studies in lung cancer patients across different populations. These findings could enhance the understanding of disease development and susceptibility in lung cancer.
Significance
The study highlights the importance of miRNA target site SNPs in lung cancer and suggests that these SNPs could serve as potential biomarkers for disease progression and susceptibility, aiding in the development of personalized treatment strategies.
Future directions
The study encourages further experimental validation and clinical application of the identified SNPs as biomarkers for lung cancer. It also suggests the need for randomized trials to explore the therapeutic potential of miRNA-mediated interventions in cancer treatment.
Supplemental material
Supplemental data for this article can be accessed at https://doi.org/10.1080/14622416.2024.2355864
Author contributions
I certify that each co-author listed on page 1 participated sufficiently in the work to take responsibility for the content and that all those who qualify are listed. Authorship credit should be based on (a) substantial contributions to the conception or design of the work or the acquisition, analysis, or interpretation of data for the work; (b) drafting the work or revising it critically for important intellectual content; (c) final approval of the version to be published; and (d) agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. Conditions (a), (b), (c) and (d) must all be met.
Financial disclosure
The authors have no financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
Competing interests disclosure
The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
Writing disclosure
No writing assistance was utilized in the production of this manuscript.