Accelerating precision immunotherapy for HPV-driven cancers

Background: HPV-related cancers affect nearly 48,000 Americans annually, with HPV16-driven cervical and oropharyngeal malignancies progressing rapidly and often outpacing current therapeutic timelines. Despite the success of prophylactic HPV vaccines in preventing infection in uninfected individuals, these agents provide no therapeutic benefit for patients with established invasive disease and fail to address the full spectrum of oncogenic HPV variants. To address this gap, we developed SNAP (Selective Neoantigen Peptide), a personalized therapeutic vaccine platform tailored to each patient's tumor-specific neoantigen expression profile. SNAP has demonstrated potent immunogenicity and tumor control in preclinical models, validating its promise for precision immunotherapy. However, the extended manufacturing timeline-typically exceeding 12 weeks-for generating personalized SNAP vaccine severely limits applicability in rapidly progressing HPV16-positive tumors. To overcome this limitation, we have developed a dual-vaccination strategy that integrates an off-the-shelf (OTS) therapeutic vaccine for immediate immune priming with subsequent administration of the personalized SNAP vaccine. This study covers the development of the OTS HPV vaccine. Methods: The OTS vaccine is a poly-epitope construct targeting conserved HPV16 oncoproteins E6, E7, and E2, plus recurrent PIK3CA hotspot mutations (detected in >40% of HPV+ cancers), Candidate OTS peptides underwent comprehensive in silico predictive modeling. We used a multi-tiered computational pipeline to identify and prioritize immunogenic peptides for vaccine development, anchored by ProtIQ, a modular antigen selection tool. Top 100 peptides were ranked by immunogenicity, coverage and stability. A subset was synthesized and validated via biolayer interferometry (BLI) for binding kinetics. Human IFN-gamma ELISPOT on HLA-matched donor PBMCs assessed T-cell activation to select final candidates. Results: In silico prediction of OTS peptides yielded high-confidence epitopes with high median immunogenicity scores, across prevalent HLA class I and II alleles. BLI confirmed stable peptide-MHC complexes (KD range 102-103 nanomoles) in a validated subset. ELISPOT on individual peptide pulsed HLA-matched healthy donor PBMCs demonstrated robust IFN-gamma responses. Top 30 peptides with highest ELISPOT signals were selected as vaccine candidates. To check the vaccine efficacy in vivo, mouse TC-1 cells engineered to express E2 and PIK3ca mutations will be used as HPV preclinical animal model. Conclusions: This project will deliver a clinically actionable off-the-shelf vaccine platform that enables early immunologic intervention in HPV16-driven cancers. By priming the immune system ahead of personalized therapy, we aim to reduce time-to-treatment, enhance therapeutic outcomes, and expand access to precision immunotherapy.