Molecular alterations in high‐grade neuroendocrine tumors of the small intestine

High-grade neuroendocrine tumors of the small intestine are separated into two groups: well-differentiated neuroendocrine tumors (NETs, high-grade) and poorly differentiated neuroendocrine carcinomas (NECs). They represent very rare entities, with few molecular data available, and are very challenging to treat. In this study we aimed to describe the molecular profile of these tumors and their spatial and temporal heterogeneity. We collected a national multicenter cohort of high-grade NETs (14 patients) and NECs (11 patients). DNA and RNA were extracted and somatic point mutations, copy number variations, and gene expression levels were studied using high-throughput sequencing of a panel of 571 genes and RNA sequencing, respectively. Additional samples to study spatial or temporal heterogeneity were available for 12 patients, leading to a total of 42 samples analyzed. Differential diagnostic markers were confirmed by immunohistochemistry. NECs resemble their counterparts in other organs, with a relatively high tumor mutational burden (TMB) and frequent alteration of TP53 and RB1, together with organ-specific alterations such as APC. In contrast, high-grade NETs resemble low-grade NETs, with a low TMB but frequent chromosomic alterations. Transcriptomic analysis confirmed that high-grade NETs and NECs are two distinct entities, with specific drivers. Serotonin pathway markers were the most efficient to discriminate high-grade ileal NETs from NECs. Despite variations in the proliferation index, NETs showed little spatial and temporal heterogeneity, suggesting that epigenetic mechanisms play a crucial role in tumor progression. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.