Abstract A003: High-throughput TCR sequencing demonstrates induction of long-lasting HPV16-specific T cell responses in VB10.16 vaccinated advanced cervical cancer patients
Authors: Berg Kaja C G , Bousquet Paula , Blaga Milena , Bello Thomas , Arabpour Mohammad , Pedersen Mikkel W , Schjetne Karoline 
Published: December 2023

Abstract
Background: Assessment of vaccine-induced T cell responses is a primary pharmacodynamic readout in cancer vaccine clinical trials. High-throughput sequencing of T cell receptors (TCRs) is emerging as a rapid and scalable method, suitable for late-stage clinical trials, and offers sensitive and accurate quantification of the full T cell repertoire. Here we performed ELISpot and TCR sequencing on serial peripheral blood mononuclear cell (PBMC) samples from a clinical phase 2 trial investigating the therapeutic HPV16 cancer vaccine VB10.16 in combination with atezolizumab in advanced cervical cancer patients (NCT04405349).
Methods: T cell responses were assessed by ex vivo IFN-g ELISpot (n=36). Immunosequencing of the TCRB locus was performed in 10 patients with available PBMCs, representing clinical response, stable disease, and progressive disease as best overall response. Immunosequencing of PBMC-derived gDNA was performed on up to five timepoints per patient, ranging from week 10 to 52. Novel and expanded clones from baseline to on-treatment timepoints were determined by a differential abundance framework, using binomial models in pair-wise comparisons, enabling longitudinal tracking of significantly expanded T cell clones. The sequences were matched and annotated to HPV16-specific TCRs present in a proprietary database of confirmed HLA class I HPV16-specific T cell clones; the database was constructed from querying the T cell repertoires of 92 healthy donors with 146 peptides derived from HPV16 E6 and E7 in MIRA assay.
Results: An increased T cell response was significantly associated with disease control assessed by RECIST1.1 (n=24 patients with disease control vs n=12 patients with progressive disease, p=0.0113) and patients with a &gt;2-fold increase measured by ex vivo IFN-g ELISpot showed a numerically improved progression-free survival (8 vs 3.7 months median PFS). The longitudinal tracking of TCRs provided a detailed insight into the dynamics of the overall TCR repertoire during treatment. Expansion of both pre-existing and newly expanded T cell clones was observed from week 10 and persisted until the end of treatment. Despite the non-exhaustive database, at least one verified HPV16-specific CD8 T cell clone was expanded in 8 out of 10 patients, supporting that the clonotypic expansion is caused by VB10.16. In 5 out of 7 patients with disease control, the breadth of HPV16-specific TCRs increased after vaccination, demonstrating induction of clinically relevant T cell responses.
Conclusions: We demonstrate induction of strong and long-lasting HPV16-specific T cell responses after treatment with VB10.16 and atezolizumab in advanced cervical cancer patients. Induction of HPV16-specific T cell responses was significantly correlated with clinical efficacy. Immunosequencing and HPV16-specific annotation allowed longitudinal tracking of expanded TCRs and demonstrated a potential clinical relevance of increased repertoire diversity of HPV16-specific CD8 T cells in patients.
Citation Format: Kaja C G Berg, Paula Bousquet, Milena Blaga, Thomas Bello, Mohammad Arabpour, Mikkel W Pedersen, Karoline Schjetne. High-throughput TCR sequencing demonstrates induction of long-lasting HPV16-specific T cell responses in VB10.16 vaccinated advanced cervical cancer patients [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A003.