Background
Exfoliated cervical cells based next generation sequencing (NGS) on pap smears, cervical scrapes is emerging as a powerful minimally invasive tool for prognostication for cervical cancer and its pre-cursors. NGS from exfoliated cells can help cancer associated mutations without the need of a biopsy. This study demonstrates the use of NGS to prognosticate cervical cancers and suggests serial sampling of exfoliated cells can help in longitudinal disease monitoring.
Objectives
To evaluate the feasibility and clinical relevance of targeted NGS from exfoliated cervical cells for prognostication of cervical cancer, and to assess the distribution of HPV genotypes in relation to actionable somatic genomic alterations.
Methods
Exfoliated cervical cell samples from 70 patients with uterine cervix cancer were first tested for high-risk HPV DNA using the Roche Cobas® 4800 platform, which individually detects HPV16 and HPV18 and reports 12-pooled other high-risk (OHR) HPV types (HPV 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68). Genomic DNA extracted from the same exfoliated cell specimens was subjected to targeted NGS using a 126-gene multi-cancer panel covering driver mutations, gene fusions, copy number variations (CNVs), and microsatellite instability markers. Library preparation and sequencing were performed on the Illumina platform. Variant calling and clinical annotation were carried out using AI-driven iCARE software. Variant classification and therapeutic interpretation followed ACMG, AMP, ASCO, and CAP guidelines.
Results
HPV DNA testing showed the following distribution: HPV16 only in 48.6% (34/70), HPV18 only in 11.4% (8/70), other high-risk HPV (OHR) only in 22.9% (16/70), multiple HPV infections in 10.0% (7/70), and HPV-negative status in 7.1% (5/70). Molecular profiling revealed a high prevalence of PI3K–AKT–mTOR pathway alterations in 61.4% (43/70) of cases, driven primarily by PIK3CA mutations in 45.7% (32/70) of patients. Additional recurrent alterations included TP53 and PTEN in 11.4% (8/70) of cases each, and FGFR3 in 10.0% (7/70) of cases. Clinically significant Tier I/II variants were identified in 52.8% (37/70) of patients. Importantly, 41.4% (29/70) of patients harboured actionable genomic alterations with approved targeted therapeutic options, most commonly involving PI3K and mTOR inhibitors. Patients with PIK3CA mutations, either alone or in combination with PTEN or STK11 co-mutations, were treated with alpelisib, everolimus, temsirolimus, and sirolimus. Cases with PIK3CA and TP53 co-mutations demonstrated aggressive molecular features but remained eligible for PI3K-pathway–targeted therapies. FGFR3-mutated tumours represented a distinct subgroup with potential benefit from FGFR inhibitors such as erdafitinib.
Conclusion
Comprehensive molecular profiling of uterine cervix cancers revealed substantial genomic heterogeneity and a high burden of clinically actionable alterations, particularly involving the PI3K–AKT–mTOR pathway. These findings support the integration of NGS-guided precision oncology approaches to expand targeted treatment opportunities for patients with advanced and recurrent cervical cancer, highlighting the growing clinical relevance of biomarker-driven therapeutic strategies.