Neoantigens as potential vaccines in hepatocellular carcinoma

Abstract

BackgroundNeoantigens, new immunogenic sequences arising from tumor mutations, have been associated with response to immunotherapy and are considered potential targets for vaccination. Hepatocellular carcinoma (HCC) is a moderately mutated tumor, where the neoantigen repertoire has not been investigated. Our aim was to analyze whether tumors in HCC patients contain immunogenic neoantigens suitable for future use in therapeutic vaccination.MethodsWhole-exome sequencing and RNAseq were performed in a cohort of fourteen HCC patients submitted to surgery or liver transplant. To identify mutations, single-nucleotide variants (SNV) originating non-synonymous changes that were confirmed at the RNA level were analyzed. Immunogenicity of putative neoAgs predicted by HLA binding algorithms was confirmed by using in vitro HLA binding assays and T-cell stimulation experiments, the latter in vivo, by immunizing HLA-A*02.01/HLA-DRB1*01 (HHD-DR1) transgenic mice, and in in vitro, using human lymphocytes.ResultsSequencing led to the identification of a median of 1217 missense somatic SNV per patient, narrowed to 30 when filtering by using RNAseq data. A median of 13 and 5 peptides per patient were predicted as potential binders to HLA class I and class II molecules, respectively. Considering only HLA-A*02.01- and HLA-DRB1*01-predicted binders, 70% demonstrated HLA-binding capacity and about 50% were immunogenic when tested in HHD-DR1 mice. These peptides induced polyfunctional T cells that specifically recognized the mutated but not the wild-type sequence as well as neoantigen-expressing cells. Moreover, coimmunization experiments combining CD8 and CD4 neoantigen epitopes resulted in stronger CD8 T cell responses. Finally, responses against neoantigens were also induced in vitro using human cells.ConclusionThese results show that mutations in HCC tumors may generate immunogenic neoantigens with potential applicability for future combinatorial therapeutic strategies.

Identification of HLA class I-restricted immunogenic neoantigens in triple negative breast cancer

“…Nevertheless, we have demonstrated that some neoAgs identified in murine vaccination experiments were immunogenic in vitro using human cells from healthy donors. We have recently reported equivalent results for immunogenicity of neoAgs identified in hepatocellular carcinoma patients ( 41 ), demonstrating not only the activity of HLA class I-restricted neoAgs but also for class II binding peptides. Thus, our current results obtained in TNBC patients suggest that the TMB found may originate a sufficient number of neoAgs for vaccination.…”

Engineering neoantigen vaccines to improve cancer personalized immunotherapy

“…Underlying neoantigens produced by nsSNVs in HCC were identified by WES and RNA sequencing. Most predictive peptides bound to HLA-A*02.01 and HLA-DRB1*01 representative class I and class II alleles and enjoyed immunogenicity, providing a novel strategy for HCC treatment 28 . It was noteworthy that nsSNVs and neoantigen loads were associated with checkpoint inhibitor responses.…”

mRNA-Based Approaches to Treating Liver Diseases

“…HCC is a moderately mutated tumor. Recently, Repáraz et al compared the results of whole-exome sequencing and RNAseq analyses performed on malignant and normal tissues obtained from fourteen HCC patients [ 107 ]. A median of 1217 missense somatic single nucleotide variants were identified per patient in malignant tissues; of these, a median of 13 and 5 peptide sequences (neoantigens) per patient were predicted to bind HLA class I and class II molecules, respectively.…”