9 Background: Anti-cancer therapy with immune checkpoint inhibitors demonstrated high efficacy in hypermutated tumors; Food and Drug Administration recently proved PD1/PDL-1 blockade therapy in solid tumors characterized with deficiency of mismatch repair (MMR). However, several malignancies contain less feature of MMR deficiency. Except MMR, it remains uncertain whether mutations of other DNA repair genes are associated with hypermutated status. We aim to analyze the relationship between DNA repair gene-mutation statuses, mutation burden and neoantigen load in breast cancer. Methods: Whole exome sequencing was performed on germline and tumor DNA in 82 patients with early-onset breast cancer (≤ 40 year-old). Calculation of mutation burden includes tumor-specific insertion/deletion (Indel) and single nucleotide variants. Missense mutations, frameshift mutations and uncorrected splicing were considered to generate new peptides (neopeptides). Binding affinity of neopeptide-major histocompatibility complex class I and their immunogenicity were predicted by NetMHC 4.0 and POPI 2.0. Results: A total of 18 pathogenic mutations were found, 4 in ATM (2 germline and 2 somatic), 3 in BRCA1 (germline), 4 in BRCA2 (germline), 1 in BRIP1 (germline), 1 in CHK2 (germline), 1 in ERCC8 (germline), 2 in MSH2 (1 germline and 1 somatic), 1 in RAD51C (somatic) and 1 in OGG1 (germline). The median number of exomic mutations (missense mutations and Indels) were 744 (min. 355; max. 3587) variants per sample. Tumors with mutations of homologous recombination (HR) and MMR genes contained a higher trend of exomic mutations than those without mutation. However, tumors with mutations of HR and MMR genes contained significantly higher numbers of neopeptides with high binding affinity and immunogenicity than those without mutation (p = 0.04). Conclusions: Tumors with mutations of HR and MMR genes contained higher numbers of neoantigens. This study showed that HR and MMR mutation may be a biomarker predicted clinical benefit of immune checkpoint blockade therapy in breast cancer.
DNA Repair Gene Mutations as Predictors of Immune Checkpoint Inhibitor Response beyond Tumor Mutation Burden
