Background: Oral squamous cell carcinoma of the gingivo-buccal region (OSCC-GB) has the highest incidence among males and the second highest overall among all cancers in India, emphasizing the need for precise molecular classifications to guide personalized therapy. Methods: We performed bulk RNA sequencing on tumor and adjacent normal tissue samples from 72 OSCC-GB patients, as well as leukoplakia tissue from 25 patients with concurrent leukoplakia. Findings: Our analysis revealed activated epithelial-mesenchymal transition, angiogenesis, and cell-cycle function in OSCC-GB. We found significant enhancement of glycolysis and reduction in oxidative phosphorylation, which are hallmarks of the Warburg effect. Immune profiling indicated enriched immune-related genes and cells in tumor tissues. We identified two distinct patient subtypes, one of which exhibited higher immune cell infiltration and showed potential for greater responsiveness to immune checkpoint inhibitors. CD226, CD38, and KBTBD8 were identified as potential biomarkers for classifying OSCC-GB patients and were validated in an independent cohort. Significantly more M1 macrophages and CD4+ T-cells in leukoplakia tissue than the normal indicate activated host defense mechanisms in pre-malignant lesions, highlighting the potential for early intervention to prevent malignancy. TCGA-HNSC data exhibited similar gene set enrichments, including glycolysis and immune-related pathways. However, unique profiles in a subset of TCGA-HNSC patients highlight the molecular heterogeneity of head and neck cancers. Conclusion: Our findings underscore the critical role of understanding these pathways in cancer biology and immunology, essential for developing effective treatment strategies for oral cancer and immunotherapy.

The authors have declared no competing interest.

The Department of Biotechnology, Government of India, through the International Cancer Genome Consortium India project and the Systems Medicine Cluster project.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Written informed consent was obtained from every participant recruited in this study. The following institutional Review Boards have approved the study: The Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Mumbai, INDIA; Dr. R. Ahmed Dental College & Hospital (RADCH), Kolkata, INDIA; Chittaranjan National Cancer Institute (CNCI), Kolkata, INDIA; National Institute of Biomedical Genomics (NIBMG), Kalyani, INDIA; and Indian Statistical Institute (ISI), Kolkata, INDIA.

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The aligned BAM files for RNA-Seq data from the 72 tumor-normal paired samples can be accessed from the European Genome-phenome Archive (EGA) under study ID EGAS00001003893. The BAM files for RNA-Seq data from the 25 oral leukoplakia samples are also available from the European Nucleotide Archive (ENA) under study accession PRJEB42982.