Publication: Elucidating IFI6 and RSAD2 protein expression in oral squamous cell carcinoma using immunohistochemistry and aptahistochemistry with novel in silico DNA-aptamers
| dc.contributor.author | Butt, Danial Qasim | |
| dc.date.accessioned | 2025-10-15T02:40:13Z | |
| dc.date.available | 2025-10-15T02:40:13Z | |
| dc.date.issued | 2025-07 | |
| dc.description.abstract | Emerging research highlights interferon-stimulated genes (ISGs) such as IFI6 and RSAD2 as potential protumorigenic biomarkers, contributing to cancer proliferation and survival. While their role in apoptotic dysregulation has been documented in various malignancies, their involvement in evading immune evasion, particularly in oral squamous cell carcinoma (OSCC), remains largely unexplored. Understanding their influence within the tumour microenvironment is, therefore, imperative. Advances in biomarker detection technologies offer substantial advantages in improving specificity, sensitivity, and reproducibility while mitigating cost and batch variation challenges in antibody-based OSCC diagnostics. This study aims to examine IFI6 and RSAD2 protein expression in cancer and immune cells (neutrophils, plasma cells, and lymphocytes) within the OSCC tumour microenvironment using immunohistochemistry (IHC) and aptahistochemistry (AHC), employing in silico-derived DNA aptamers. Additionally, it seeks to design, characterise, and validate these DNA aptamers for potential application in AHC. IFI6 and RSAD2 protein expression was analysed in OSCC (n=23) and healthy (n=7) tissue samples via IHC and AHC. The correlation between protein expression, cancer, immune cell presence, and histological tumor grades was statistically assessed. DNA aptamers for IFI6 and RSAD2 were designed in silico, and their binding interactions were characterised using molecular docking (binding energy), PyMOL, and Protein Ligand Interaction Profiler (PLIP) for hydrogen bonding analysis. Molecular dynamics simulations in GROMACS assessed complex stability (RMSD) and aptamer flexibility (RMSF). Stem-hairpin loop DNA aptamers (35–50 meters) were successfully developed for IFI6 and RSAD2. Among them, 35- and 50-mer IFI6 and 35- and 45-mer RSAD2 aptamers exhibited high binding affinity (-15.7 to -18.7 kcal/mol), strong hydrogen bonding (<4 Å), stable RMSD (<0.4 nm), and flexible loop regions (RMSF >0.4 nm). IHC and AHC analyses revealed significant IFI6 and RSAD2 expression in OSCC tissues while absent in healthy samples (p<0.05). Expression levels were markedly elevated in poorly differentiated tumour grades and tumour-associated immune cells (p<0.05). This study confirms IFI6 and RSAD2 expression in OSCC cancer and immune cells, correlating with higher tumour grades. These findings support their potential as prognostic biomarkers in the tumour microenvironment. The in silico-derived DNA aptamers demonstrate strong binding characteristics and hold promise for AHC-based OSCC detection, offering a cost-effective and reliable diagnostic alternative. | |
| dc.identifier.uri | https://erepo.usm.my/handle/123456789/22795 | |
| dc.language.iso | en | |
| dc.title | Elucidating IFI6 and RSAD2 protein expression in oral squamous cell carcinoma using immunohistochemistry and aptahistochemistry with novel in silico DNA-aptamers | |
| dc.type | Resource Types::text::thesis::doctoral thesis | |
| dspace.entity.type | Publication | |
| oairecerif.author.affiliation | Universiti Sains Malaysia |