POLE Proofreading Mutations Elicit an Antitumor Immune Response in Endometrial Cancer

Abstract

Purpose Recent studies have shown that 7-12% of endometrial cancers (ECs) are ultramutated due to somatic mutation in the proofreading exonuclease domain of the DNA replicase POLE. Interestingly, these tumors have an excellent prognosis. In view of the emerging data linking mutation burden, immune response and clinical outcome in cancer, we investigated whether POLE-mutant ECs showed evidence of increased immunogenicity. Experimental design We examined immune infiltration and activation according to tumor POLE proofreading mutation in a molecularly defined EC cohort including 47 POLE-mutant tumors. We sought to confirm our results by analysis of RNAseq data from the TCGA EC series and used the same series to examine whether differences in immune infiltration could be explained by an enrichment of immunogenic neoepitopes in POLE-mutant ECs. Results Compared to other ECs, POLE-mutants displayed an enhanced cytotoxic T cell response, evidenced by increased numbers of CD8+ tumor infiltrating lymphocytes and CD8A expression, enrichment for a tumor-infiltrating T cell gene signature, and strong upregulation of the T cell cytotoxic differentiation and effector markers T-bet, Eomes, IFNG, PRF and granzyme B. This was accompanied by upregulation of T cell exhaustion markers, consistent with chronic antigen exposure. In-silico analysis confirmed that POLE-mutant cancers are predicted to display more antigenic neo-epitopes than other ECs, providing a potential explanation for our findings. Conclusions Ultramutated POLE proofreading-mutant ECs are characterized by a robust intratumoral T cell response, which correlates with, and may be caused by an enrichment of antigenic neo-peptides. Our study provides a plausible mechanism for the excellent prognosis of these cancers.

Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response

“…Somatic POLE mutations in endometrial and colorectal cancers are associated with enhanced tumour immunogenicity and a favourable prognosis 11, 14, 15. We speculated that the early acquisition of somatic POLE mutations would cause rapid acquisition of mutations, some of which would produce neoantigens capable of eliciting an antitumour immune response.…”

“…Fifty‐one formalin‐fixed paraffin‐embedded (FFPE) endometrial cancers carrying known pathogenic somatic POLE mutations identified in our previous studies 12, 14, 26 were reviewed for the presence of a concomitant and spatially discrete area of endometrial intraepithelial neoplasia (EIN) by examination of haematoxylin and eosin (H&E)‐stained slides by two expert gynaecological pathologists (V.S. and T.B.).…”

“…TCGA colorectal (COADREAD) 10 and endometrial (uterine corpus endometrial carcinoma) 8 cancer data were downloaded from the Genomic Data Commons (GDC) Data Portal (https://portal.gdc.cancer.gov; June 2017). An additional series of 78 FFPE endometrial cancers, including 32 cases with pathogenic somatic POLE mutations, were identified from the Leiden University Medical Centre (LUMC) archives (2001–2015) 14. Further details of the cohorts used in this study are provided in supplementary material, Table S1.…”

“…Immunohistochemistry (IHC) for CD8 was performed as reported previously 14. The number of CD8 + cells was quantified for the epithelial and stromal regions of the EIN.…”

“…Somatic POLE exonuclease domain mutations (hereafter simply referred to as POLE mutations) occur in sporadic tumours of the endometrium (7–15% cases) 8, 9, colorectum (1–2%) 10, 11, and, less commonly, in other cancers (although, for reasons that are unclear, somatic POLD1 exonuclease domain mutations are very uncommon). POLE ‐mutant colorectal and endometrial cancers have an excellent prognosis 8, 11, 12, 13, probably owing to a robust antitumour immune response against the multitude of immunogenic neoantigens that they are predicted to harbour 11, 14, 15. Very recent reports have also suggested that these tumours may be highly responsive to immune checkpoint inhibition 16.…”