A personalized neoantigen vaccine to reprogram the immune landscape of glioblastoma.

2006 Background: Glioblastoma (GBM) remains uniformly lethal despite standard therapy. An immunosuppressive tumor microenvironment (TME) and limited T cell infiltration pose major barriers to immunotherapy. Personalized neoantigen vaccines offer a strategy to prime tumor-specific T cell responses by targeting patient-specific mutations, driving effector cells into the CNS. Here, we report results from a phase I trial of a personalized neoantigen peptide vaccine combined with pembrolizumab in newly diagnosed GBM. Methods: Patients with newly diagnosed GBM who were not on dexamethasone following gross total resection were enrolled across four cohorts. Up to 20 synthetic long peptides targeting personal neoantigens were selected per patient, and admixed with the adjuvant poly-ICLC (NeoVax). Following radiotherapy, NeoVax was administered subcutaneously as five priming doses followed by two booster doses. MGMT -unmethylated patients (Cohorts 1A-C) received NeoVax plus pembrolizumab without temozolomide (TMZ) and differed by time of pembrolizumab initiation relative to NeoVax priming; MGMT -methylated patients (Cohort 1D) received standard TMZ and pembrolizumab was initiated after NeoVax priming. Immunogenicity was assessed by ex vivo and in vitro IFN-γ ELISpot assays. Single-nucleus/single-cell RNA sequencing and TCR sequencing (snRNA-seq/scTCR-seq) was performed on paired tumor specimens. Results: Of 39 enrolled patients, 37 initiated NeoVax including 35 who completed priming and 2 with ongoing priming. Treatment was well-tolerated with no serious AEs. Median overall survival was 36.9 months for MGMT -methylated patients and 19.0 months for MGMT -unmethylated patients, compared to 25.3 and 16.7 months for propensity score-matched historical controls, respectively. Ex vivo and in vitro neoantigen-specific T cell responses were detected comparably across all cohorts and overall in 65% and 97% of vaccinated patients, respectively. Among all patients, ex vivo immune responders demonstrated improved overall survival compared to non-responders (HR 0.26, 95% CI 0.09-0.77, P = 0.015). Vaccine-reactive clonotypes, defined by in vitro expansion to vaccine peptides, were identified in post-vaccination tumors. snRNA-seq/scTCR-seq revealed increased intratumoral vaccine-specific T effector populations following vaccination. Conclusions: NeoVax generates durable T cell responses that traffic to GBM tumors, with circulating responses associated with improved survival. Ongoing studies are evaluating peripheral clonotype dynamics, remodeling of malignant cell states and the TME, and the spatial distribution of vaccine-reactive clonotypes, which may guide future combinatorial strategies in GBM. Clinical trial information: NCT02287428 .