Exploiting the Mutanome for Tumor Vaccination

Abstract

Multiple genetic events and subsequent clonal evolution drive carcinogenesis, making disease elimination with single-targeted drugs difficult. The multiplicity of gene mutations derived from clonal heterogeneity therefore represents an ideal setting for multiepitope tumor vaccination. Here, we used next generation sequencing exome resequencing to identify 962 nonsynonymous somatic point mutations in B16F10 murine melanoma cells, with 563 of those mutations in expressed genes. Potential driver mutations occurred in classical tumor suppressor genes and genes involved in proto-oncogenic signaling pathways that control cell proliferation, adhesion, migration, and apoptosis. Aim1 and Trrap mutations known to be altered in human melanoma were included among those found. The immunogenicity and specificity of 50 validated mutations was determined by immunizing mice with long peptides encoding the mutated epitopes. One-third of these peptides were found to be immunogenic, with 60% in this group eliciting immune responses directed preferentially against the mutated sequence as compared with the wild-type sequence. In tumor transplant models, peptide immunization conferred in vivo tumor control in protective and therapeutic settings, thereby qualifying mutated epitopes that include single amino acid substitutions as effective vaccines. Together, our findings provide a comprehensive picture of the mutanome of B16F10 melanoma which is used widely in immunotherapy studies. In addition, they offer insight into the extent of the immunogenicity of nonsynonymous base substitution mutations. Lastly, they argue that the use of deep sequencing to systematically analyze immunogenicity mutations may pave the way for individualized immunotherapy of cancer patients. Cancer Res; 72(5);

Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy

“…Note that only combinations of adjacent missense mutations supported on the same read of WES data were considered and only neoantigens predicted in four of four biological replicates were included in our analysis. This neoantigen list was combined with a previously published list of neoantigens 24, 36 . Briefly, a list of nanoparticle bound proteins obtained from the mass spec data was run through a python script to find proteins with at least one predicted neoantigen or previously identified neoantigen.…”

Enhancing Efficacy of Anticancer Vaccines by Targeted Delivery to Tumor-Draining Lymph Nodes

“…2). Compared with current published studies, our TRP-2-based therapeutic nanoparticle vaccine is very potent at the low doses used for antigen and adjuvant (18,39,40). Similarly, other studies have shown improved therapeutic outcomes by either conjugating the adjuvant or the antigen onto or into delivery systems, such as poly(lactideco-glycolide) particles and liposomes, but, to our knowledge, this is the first study to show enhanced co-uptake of both adjuvant and antigen by LN-resident APCs after nanoparticle conjugation (14)(15)(16)(17)(18)(19).…”

Long-peptide vaccination with driver gene mutations in p53 and Kras induces cancer mutation-specific effector as well as regulatory T cell responses

“…Most of the latest and more advanced clinical trials for TSA-specific vaccines are based on the administration of Ag cocktails 47,66 . Another recent approach delivers multiple Ags as an individualized neo-antigen mRNA-polytope vaccine 67-69 which represents a promising alternative to administration of antigens via synthetic peptides. Eliciting a broad immune response against several tumor-specific CD4 and CD8 epitopes has major advantages.…”