Background: High-grade gastro-entero-pancreatic neoplasms (H-EP-NENs) are a heterogeneous group of rare neoplasms with a dismal prognosis. H-GEP-NENs can be stratified according to their morphology and Ki-67 into three prognostic classes: neuroendocrine tumors grade 3 (NETs G3), neuroendocrine carcinomas with Ki-67<55% (NECs<55) and NECs with Ki-67≥55% (NECs≥55).
Design: We analyzed a cohort of 49 H-GEP-NENs (21 GEP-NETs G3, 12 GEP-NECs <55% and 16 GEP-NECs ≥55) using targeted Next-Generation Sequencing (TrueSight Oncology 500, Illumina) and comprehensive RNA-seq. The samples were also investigated for immunohistochemical (IHC) expression of p53, Rb1, PD-L1 and SSTR2A.
Results: Frequent genomic alterations were observed in TP53 (26%), APC (20%), KRAS and MEN1 (both 11%). GEP-NET G3 carried a higher frequency of mutations in MEN1 (p=0.02), while GEP-NECs ≥55%, followed by GEP-NECs <55% showed a higher frequency of mutations in TP53 (p=0.001), APC (p=0.002) and KRAS (p=0.02) and were enriched in tumors with TMB>10 muts/Mb
(p=0.01). At the transcriptomic level, GEP-NECs <55% and GEP-NECs ≥55% did not show any differences, while 1129 differentially expressed (DE) genes were identified between GEP-NET G3 and GEP-NECs. When analyzing pancreatic (Pan) and non-pancreatic (NonPan) tumors separately, no transcriptomic differences were found between Pan NET G3 and Pan NECs, while 450 DE genes were identified between Nonpan NET G3 and Nonpan NECs. The immune microenvironment landscape was found to be poor for both groups with a slight enrichment of CD4 and CD8 T cells in GEP-NECs and of CAFs and M2 macrophages in GEP-NET G3. PD-L1 expression was absent across all histologic groups. When comparing NECs from patients who received chemotherapy, an enrichment of pathways implied in replication stress was found in the group with progressive disease. Univariate analysis demonstrated the worst OS for GEP-NECs ≥55%, followed by GEP-NECs <55%. p53 aberrant expression, Rb1 loss, TP53, APC, and KRAS mutations were also associated with worse OS at univariate analysis. At multivariate analysis, histologic type, and Rb1 absence of expression were independent prognostic factors for OS.
Conclusions: H-GEP-NENs are a heterogenous group of neoplasms at the genomic and transcriptomic level. This comprehensive molecular study offered new insights into the biology of H-GEP-NENs and the rationale behind their classification and provided findings with prognostic and therapeutic relevance.
