Genetic intratumour heterogeneity in digestive high-grade neuroendocrine neoplasms

Digestive high-grade neuroendocrine neoplasms (HG-NEN) are rare and heterogeneous tumours with an aggressive biology and limited treatment efficacy. Genetic intratumour heterogeneity (ITH) is a mechanism of progression and treatment resistance in other cancers, yet unexplored in digestive HG-NEN. Next-generation sequencing with a 360-cancer gene panel was performed on 51 digestive HG-NEN, suitable for multiregional sampling. The mutational status of each sample within a patient was assessed to calculate an ITH-index, defined as the average number of discordant mutations across all pair-wise comparisons between samples. An ITH-index based on primary tumour samples was calculated for chemotherapy-naïve cases: 28 neuroendocrine carcinomas (NEC), 9 mixed neuroendocrine-non-neuroendocrine neoplasms (MiNEN) and 3 neuroendocrine tumour grade 3 (NET G3). Median ITH-index in NEC/MiNEN was 5, with a wide range (0-98.8). Greater heterogeneity was associated with right-sided colonic primaries (p = .005) and higher tumour mutational burden (r = 0.74, p < .001). Median overall survival was 7 months longer in NEC/MiNEN with median ITH-index above compared to below median (22.5 vs. 15.5 months, p = .077), driven mostly by patients with locoregional disease. Response to first-line chemotherapy was not influenced by median ITH-index. No heterogeneity was found among driver mutations in BRAF and KRAS. NET G3 displayed low heterogeneity (ITH-index 2-3). Higher ITH-index was not associated with shorter survival or treatment response, suggesting that genetic ITH is not the primary resistance mechanism in digestive NEC/MiNEN. Moving towards targeted treatment strategies, our data indicate that a single biopsy may underestimate ITH. BRAF and KRAS may be favourable targets as they displayed no heterogeneity.