NOT NEOANTIGEN QUANTITY, BUT NEOANTIGEN QUALITY, COPY NUMBER ALTERATIONS AND FUSIONS ARE ASSOCIATED WITH SURVIVAL IN PANCREATIC CANCER

Abstract

Introduction: Immunotherapy has not been effective for pancreatic ductal adenocarcinoma (PDAC). However, factors underlying antitumor immunity in PDAC are poorly understood. We hypothesized that, for PDAC, not the quantity of MHC-binding neoantigens, but neoantigen quality and frequency of both copy number alterations (CNAs) and gene fusions are related to effective immune cell responses and survival. Methodology: We performed extensive genomic and transcriptomic profiling of paired normal and tumor tissue of PDAC patients with distinct survival times (n=13; Table 1, Fig. 1A). Additionally, immunological profiling (CIBERSORTx) was performed. Data was analyzed using Mann-Whitney U, chi2-test and Spearman’s correlation. Results: Mutations or CNAs were most often detected in KRAS, TP53, TTN, ZNF471, ZNF667, and LOC101928982 ($4 patients). MHCI- or MHCII-binding neoantigens most AGA Abstracts S-662 frequently resulted from mutations in KRAS, TP53, TTN, APOB, and COL6A ($3 patients). The range of neoantigen-per-mutation ratios was 0.53-1.85 for MHCI (HLA rank#2) and 0.38-43.02 for MCHII (HLA rank#10). No differences in CD8+ T cell infiltration between survival groups was found (Fig. 1B). However, TCRs of long-term survivors were more polyclonal (TCRa p=0.07; TCRb p=0.03; Fig. 1C, D). Tumor tissue of long-term survivors was rich in plasma cells (P=0.005), CD4+ memory resting T cells (P=0.01), and monocytes (P=0.02). Naive (M0) macrophages (P=0.05) and activated dendritic cells (P=0.03) were more abundant in tumor tissue from short-term survivors (Fig. E-I). The proportion of neoantigens with a low similarity-to-self score was higher in short-term survivors (P<0.0001; Fig L, M), while mutational load, neoantigen burden (Fig. J, K), similarity of neoantigens to known pathogens and neoantigen immunogenicity were not associated with survival or immune cell infiltration, Additionally, the number of CNAs negatively correlated with survival time (r=-0.62), cytotoxic T-lymphocytes (r=-0.64), plasma cells (r=-0.55), follicular helping T-cells (r=-0.73), and monocytes (r=-0.59). Conversely, the number of gene fusions positively correlated with survival time (r=0.62), infiltrating CD4+ resting memory T-cells (r=0.75) and monocytes (r=0.57). As compared to gene mutations, gene fusions less often resulted in MHC-binding neoantigens, with neoantigen-per-fusion ratios of 0.00-0.51 for MHCI and 0-3.08 for MCHII. Conclusion: In contrast to other cancer types, not tumor mutational load or neoantigen quantity, but a low similarity-to-self score, low number of CNAs, and high number of gene fusions were associated with long-term survival and immune cell infiltration. While CD8+ T-cell infiltration did not correlate to survival in our study, plasma cell and macrophage lineage-derived cell infiltration did. More research is required to identify pathways responsible for these correlations.