Integrated Genomic and Immune Profiling Reveals PIK3CA-Mutant HPV16-Positive Cervical Cancer as a Clinically Aggressive and Immunologically Distinct Subtype in Patients from Eastern India

Background: HPV16-driven cervical cancer (CaCx) is a leading cause of cancer-related mortality among Indian women. Identifying population-specific genomic and immune determinants may improve therapeutic strategies. Methods: We performed whole-exome sequencing on 49 HPV16-positive cervical tumors and matched blood samples. Available RNA-seq data from 29 out of 49 tumors were integrated, to identify recurrent mutations, altered pathways, and immune microenvironment features. Results: We identified 6,462 somatic mutations enriched in cancer-related pathways, particularly PI3K-Akt signaling. PIK3CA was the most recurrently mutated gene (42%), significantly higher frequency (p < 0.04) than in HPV16-positive TCGA-CESC tumors (26.21%). Unlike TCGA-CESC, where PIK3CA mutations were associated with early-stage disease, Indian PIK3CA-mutant tumors were enriched in advanced-stage disease. These tumors exhibited lower viral loads, higher tumor mutation burden, and more aggressive molecular phenotypes than PIK3CA-wild tumors. CIBERSORT-based immune profiling showed comparable immune-cell infiltration, including CD8+ T cells, between PIK3CA-mutant tumors and normal tissues, whereas PIK3CA-wild tumors showed significantly enhanced infiltration, compared to normal tissues. Both tumor subtypes portrayed mature tertiary lymphoid structures at higher levels than normal tissues. Compared to normal tissues, CD274 (PD-L1) expression was elevated significantly in both subtypes, while PDCD1 (PD-1) upregulation and PD-1/PD-L1 transcriptional coupling at significant levels, occurred exclusively in PIK3CA-mutant tumors. The CCL3-CCR1 axis was selectively activated in PIK3CA-mutant tumors and correlated with cytotoxic, interferon-response, myeloid, and immune checkpoint markers, indicating an immunosuppressive microenvironment. Conclusion: PIK3CA mutations define a molecularly aggressive, immunologically distinct subtype of HPV16-positive CaCx in Indian patients, underscoring their potential for targeted therapeutic interventions.