Clinical trials of self-replicating RNA-based cancer vaccines

Abstract

Therapeutic cancer vaccines, designed to activate immune effectors against tumor antigens, utilize a number of different platforms for antigen delivery. Among these are messenger RNAs (mRNA), successfully deployed in some prophylactic SARS-CoV2 vaccines. To enhance the immunogenicity of mRNA-delivered epitopes, self-replicating RNAs (srRNA) that markedly increase epitope expression have been developed. These vectors are derived from positive-strand RNA viruses in which the structural protein genes have been replaced with heterologous genes of interest, and the structural proteins are provided in trans to create single cycle viral replicon particles (VRPs). Clinical stage srRNA vectors have been derived from alphaviruses, including Venezuelan Equine Encephalitis (VEE), Sindbis, and Semliki Forest virus (SFV) and have encoded the tumor antigens carcinoembryonic antigen (CEA), human epidermal growth factor receptor 2 (HER2), prostate specific membrane antigen (PSMA), and human papilloma virus (HPV) antigens E6 and E7. Adverse events have mainly been grade 1 toxicities and minimal injection site reactions. We review here the clinical experience with these vaccines and our recent safety data from a study combining a VRP encoding HER2 plus an anti-PD1 monoclonal antibody (pembrolizumab). This experience with VRP-based srRNA supports recent development of fully synthetic srRNA technologies, where the viral structural proteins are replaced with protective lipid nanoparticles (LNP), cationic nanoemulsions or polymers.

Fig. 1. Schematic for immune analysis of biopsies and blood samples from safety lead-in cohort form pembrolizumab plus VRP-HER2 trial.

A Biopsies pre- and post-vaccination were digested and single live cells were sorted and were then subjected to single-cell RNA sequencing. B Serum was analyzed for alterations of systemic cytokines. PBMCs were stimulated by an overlapping panel of HER2 peptides and functional cytokine/marker alterations of single cells were assessed by single cell secretome ELISA and Cytometry Time of Flight (CYTOF).

Fig. 2. Interim immune analysis of patients treated with HER2-VRP and pembrolizumab.

A Tumor biopsies were processed fresh for single-cell RNA sequencing of live cells using the 10x Genomics platform. Pre-treatment biopsies from 2 patients and post-treatment biopsies from 3 patients were pooled for analysis of relevant cell populations. B Summary of cellular composition in pre- and post-treatment biopsies. C Serum from patients pre- and post-treatment was analyzed for 22 cytokines using the CodePlex Adaptive Immune chip from Isoplexis. Top hits from a single patient are shown. D Peripheral blood mononuclear cells (PBMCs) were restimulated with pooled HER2 peptides and analyzed for the production of 32 cytokines and chemokines using the Adaptive Immune Single-Cell Secretome chip from Isoplexis. The Polyfunctionality Strength Index for the same patient for C is shown. E PBMCs from patients pre- and post-treatment were stained and analyzed for changes in circulating immune cells by CYTOF. Frequency of select populations from the first 4 patients is shown.