A Genetic Vaccine Encoding Shared Cancer Neoantigens to Treat Tumors with Microsatellite Instability

Abstract

Tumors with microsatellite instability (MSI) are caused by a defective DNA mismatch repair system that leads to the accumulation of mutations within microsatellite regions. Indels in microsatellites of coding genes can result in the synthesis of frameshift peptides (FSP). FSPs are tumor-specific neoantigens shared across patients with MSI. In this study, we developed a neoantigen-based vaccine for the treatment of MSI tumors. Genetic sequences from 320 MSI tumor biopsies and matched healthy tissues in The Cancer Genome Atlas database were analyzed to select shared FSPs. Two hundred nine FSPs were selected and cloned into nonhuman Great Ape Adenoviral and Modified Vaccinia Ankara vectors to generate a viral-vectored vaccine, referred to as Nous-209. Sequencing tumor biopsies of 20 independent patients with MSI colorectal cancer revealed that a median number of 31 FSPs out of the 209 encoded by the vaccine was detected both in DNA and mRNA extracted from each tumor biopsy. A relevant number of peptides encoded by the vaccine were predicted to bind patient HLA haplotypes. Vaccine immunogenicity was demonstrated in mice with potent and broad induction of FSP-specific CD8 and CD4 T-cell responses. Moreover, a vaccine-encoded FSP was processed in vitro by human antigen-presenting cells and was subsequently able to activate human CD8 T cells. Nous-209 is an "off-the-shelf" cancer vaccine encoding many neoantigens shared across sporadic and hereditary MSI tumors. These results indicate that Nous-209 can induce the optimal breadth of immune responses that might achieve clinical benefit to treat and prevent MSI tumors.Significance: These findings demonstrate the feasibility of an "off-the-shelf" vaccine for treatment and prevention of tumors harboring frameshift mutations and neoantigenic peptides as a result of microsatellite instability.

NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes

“…Recently, we and others showed the induction of neoepitope-directed immune responses after vaccination with shared, in silico-predicted neoepitopes in mice (Leoni et al, 2020) and a clinical trial with mismatch repair-deficient patients (Kloor et al, 2020). Moreover, it was shown that T cells, re-activated by immune checkpoint inhibition, target tumor-specific neoepitopes thus further emphasizing the crucial role of HLA class I-presented neoepitopes in immunotherapeutic strategies (Gubin et al, 2014).…”

“…Moreover, InDel neoepitopes have been suggested to possess higher immunogenicity caused by their fundamental difference to endogenous self-antigens originating from wild-type (WT) proteins (Turajlic et al, 2017). Several studies support the presence of InDel neoepitope-specific cytotoxic T cells in both healthy individuals and patients with MSI CRC (Leoni et al, 2020;Roudko et al, 2020;Schwitalle et al, 2008).…”

Mechanisms of Immune Escape and Resistance to Checkpoint Inhibitor Therapies in Mismatch Repair Deficient Metastatic Colorectal Cancers

“…These findings demonstrated that indels generate a higher number of neoantigens than SNVs, thereby increasing the odds of neoantigen-associated immune activation and surveillance of tumor cells. Since every patient can have a peculiar mutational landscape, Leoni and collaborators analyzed 320 MSI tumor biopsies from TGCA, observing that 209 frameshift peptides were shared between patients [ 101 ]. In addition, considering an additional 20 MSI tumor patients, they identified 31 peptides in common with the initial cohort.…”

Microsatellite Instability in Colorectal Cancers: Carcinogenesis, Neo-Antigens, Immuno-Resistance and Emerging Therapies

“…One heavily pretreated patient with bulky metastases showed stable disease over 7 months. A phase I trial with a vaccine encoding various frameshift peptides shared among MSI tumors is ongoing (NCT04041310) [ 111 ]. Vaccines could be combined with ICI such as proposed in phase I KEYNOTE-603 (NCT03313778) testing mRNA-4157 with Pembrolizumab with an acceptable tolerance and 8 out 20 patients experienced disease control.…”