A four-subtype model of cervical cancer based on <i>PIK3CA</i> mutation, <i>STK11</i> mutation or deletion, and <i>YAP1</i> amplification: Multiple PI3K pathway inhibitors as suppressors of growth and cooperators with HPV-directed immunotherapy.

Abstract

e17522 Background: Cervical cancer is driven by human papillomavirus (HPV) infection yet lacks molecularly defined subtypes and approved targeted therapies. We defined molecular subtypes of cervical cancer and identify actionable therapeutic vulnerabilities. Methods: Whole-exome sequencing on cervical tumors from Guatemala and Venezuela, with validation in TCGA, AACR Genie, and Caris cohorts. Functional studies were conducted in cervical cancer cell lines using targeted inhibitors, immune co-culture assays, and proliferation analyses. Results: We identified four somatic mutation subtypes of cervical cancer: (I) No mutation ( PIK3CA / STK11 wild-type (wt) without YAP1 amplification); (II) PIK3CA -mutant, wt for STK11 , YAP1 ; (III) YAP1 -amplified, wt for PIK3CA , STK11 ; and (IV) STK11 -mutated or deleted, wt for PIK3CA , YAP1 . STK11 alterations were significantly enriched in adenocarcinomas compared with squamous cell carcinomas (23%, X 2 =4.4; p = 0.0037) and were confirmed in the AACR Project GENIE (p = 0.035) and Caris cohorts (p = 2.5e-06). YAP1 amplification and STK11 alterations were associated with younger age at diagnosis and poorer overall survival compared to subtype I. STK11 alterations also correlated with inferior outcomes following immunotherapy compared to subtype I. PI3Kα-specific inhibitors (alpelisib and inavolisib) selectively suppressed proliferation in PIK3CA -mutant cervical cancer cell lines but not in PIK3CA wt cell lines. However, the pan-AKT inhibitor capivasertib showed variable activity, inhibiting some but not all PIK3CA -mutated cell lines and the SiHa (PIK3CA wt) cell line. Alpelisib reduced the expression of HPV16 E7, CD274/PD-L1 , YAP1 , and EGFR exclusively in PIK3CA -mutant cell lines. We tested for synergy between PI3Kα inhibition and immune-directed therapy. In HPV16-positive, HLA-A2, PIK3CA -mutant cells, alpelisib enhanced antigen-specific T cell–mediated cytotoxicity, with maximal effect observed following drug pretreatment and washout prior to T cell exposure. Conclusions: Our findings define clinically relevant molecular subtypes of cervical cancer and identify PIK3CA -mutant tumors as sensitive to PI3Kα inhibition. In published clinical studies, 7 patients with PIK3CA -mutant cervical cancer treated with alpelisib achieved partial response or stable disease. Combining PI3K inhibitors with immunotherapy represents a promising strategy for advanced cervical cancer. Distribution of cervical cancer subtypes by histology. Type I WT Type II PIK3CA Type III YAP1 Type IV STK11 SCC AD SCC AD SCC AD SCC AD Sum 1425 641 724 241 174 23 105 83 % Adeno in type 31% 25% 12% 44% Total (%) 2068 (60%) 965 (28%) 197 (5.7%) 188 (5.5%) Pooled data from Guatemala, TCGA, AACR Genie, and Caris datasets. SCC, squamous cell carcinoma; AD, adenocarcinoma.