Comparative Transcriptomics Analysis of Oral Squamous Cell Carcinoma in Patients from Gujarat and Telangana States, India

Oral squamous cell carcinoma (OSCC) is one of the most common malignant neoplasms in Indian states, predominantly caused by high smokeless tobacco consumption. Given the geographical diversity and varying tobacco consumption across India, region-specific transcriptomic analyses are essential to identify distinct or conserved molecular signatures in OSCC. The present study investigates regional transcriptomic variations in OSCC by evaluating whether differentially expressed genes in Gujarat patients demonstrate similar patterns in Telangana patients. Using OSCC and healthy control transcriptome datasets from Gujarat patients (NCBI, BioProject ID: PRJNA853478), we conducted RNA-seq analysis with the GATK and Tuxedo pipelines to identify differentially expressed genes associated with OSCC. We identified six differentially expressed genes—NOTCH1, NCBP2, TP53, PTEN, AURKB, and RB1—that showed significant associations with OSCC in the Gujarat cohort. To identify region-specific or conserved expression patterns, we analysed the expression of these six genes using qRT-PCR in age- and gender-matched Telangana OSCC patients on their paraffin-embedded tissue samples. Consistent with findings in Gujarat OSCC patients, only PTEN and NOTCH1 showed significant associations in Telangana patients, with PTEN downregulated and NOTCH1upregulated, while the remaining four genes exhibited no significant expression changes. Furthermore, across OSCC tumour stages (I–IV) in Telangana patients, none of the genes showed stage-dependent variation, suggesting their role in tumour initiation rather than progression. The consistent association of PTENand NOTCH1 with OSCC in both Gujarat and Telangana states suggests their potential as conserved prognostic biomarkers for OSCC detection in India, independent of geographic and lifestyle factors, including tobacco consumption.