Comprehensive genomic and transcriptomic characterization of high-grade gastro-entero-pancreatic neoplasms

Abstract

Background: High-grade gastro-entero-pancreatic neoplasms (HG GEP-NENs) can be stratified according to their morphology and Ki-67 values 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).

Methods: We analyzed a cohort of 49 HG GEP-NENs by targeted Next-Generation Sequencing (TrueSight Oncology 500), RNA-seq, and immunohistochemistry for p53, Rb1, SSTR-2A, and PD-L1.

Results: Frequent genomic alterations affected TP53 (26%), APC (20%), KRAS and MEN1 (both 11%) genes. NET G3 were enriched in MEN1 (p = 0.02) mutations, while both NECs groups were enriched in TP53 (p = 0.001), APC (p = 0.002) and KRAS (p = 0.02) mutations and tumors with TMB ≥ 10 muts/Mb (p = 0.01). No differentially expressed (DE) gene was found between NECs <55% and NECs ≥55%, while 1129 DE genes were identified between NET G3 and NECs. A slight enrichment of CD4⁺ and CD8⁺ T cells in NECs and of cancer-associated fibroblasts and macrophages (M2-like) in NET G3. Multivariate analysis identified histologic type and Rb1 loss as independent prognostic factors for overall survival.

Conclusions: This study showed that GEP-NET G3 and GEP-NECs exhibit clear genomic and transcriptomic differences, differently from GEP-NECs <55% and GEP-NECs ≥55%, and provided molecular findings with prognostic and potentially predictive value.

Fig. 1. Morphological and immunohistochemical features of three selected cases of GEP-NET G3, GEP-NEC < 55% and GEP-NEC ≥ 55%.

SYN and MIB are used to prove the neuroendocrine differentiation and discriminate between GEP-NEC < 55% and GEP-NEC ≥ 55%. p53 is aberrant (overexpression) in GEP-NEC < 55% and GEP-NEC ≥ 55%, Rb1 is lost in the GEP-NEC ≥ 55%, and SSTR2A expression is present in the GEP-NET G3. GEP gastroenteropancreatic, NET neuroendocrine tumor, NEC neuroendocrine carcinoma; NEC < 55%, NEC with Ki-67 < 55%; NEC ≥ 55%, NEC with Ki-67 ≥ 55%, E&E hematoxylin and eosin, SYN synaptophysin, MIB antibody for detecting the Ki-67 antigen, p53 tumor suppressor p53, Rb1 retinoblastoma-associated protein, SSTR-2A somatostatin receptor 2A.

Fig. 2. Genetic alterations and molecular signatures of high-grade GEP-NENs.

a Oncoplot summarizing the genomic findings of 46 high-grade neuroendocrine neoplasms according to morphology and Ki-67. b Representation of COSMIC mutational signature analysis performed in 45 high-grade neuroendocrine neoplasms. NET neuroendocrine tumor, NEC neuroendocrine carcinoma.

Fig. 3. Transcriptomic profiling and pathway analysis of high-grade GEP-NENs.

a Differential gene expression analysis of 48 high-grade neuroendocrine neoplasms, divided into neuroendocrine tumors (NET) G3 and neuroendocrine carcinomas (NECs). The expression values of the 1129 genes identified are arranged in rows. b Representation of up- and down-regulated pathways in NET G3 and NECs. Color legend: red and blue indicate high and low expression, respectively.

Fig. 4. Survival outcomes in high-grade GEP-NENs.

a Overall survival according to morphology and Ki-67. b Progression-free survival (PFS) after first-line chemotherapy in colorectal neuroendocrine carcinomas (NECs) vs NECs from other sites.