Molecular features of gastroenteropancreatic neuroendocrine carcinoma: A comparative analysis with lung neuroendocrine carcinoma and digestive adenocarcinomas

Abstract

Objective: There is an ongoing debate about whether the management of gastroenteropancreatic (GEP) neuroendocrine carcinoma (NEC) should follow the guidelines of small-cell lung cancer (SCLC). We aim to identify the genetic differences of GEPNEC and its counterpart.

Methods: We recruited GEPNEC patients as the main cohort, with lung NEC and digestive adenocarcinomas as comparative cohorts. All patients undergone next-generation sequencing (NGS). Different gene alterations were compared and analyzed between GEPNEC and lung NEC (LNEC), GEPNEC and adenocarcinoma to yield the remarkable genes.

Results: We recruited 257 patients, including 99 GEPNEC, 57 LNEC, and 101 digestive adenocarcinomas. Among the mutations, KRAS, RB1, TERT, IL7R, and CTNNB1 were found to have different gene alterations between GEPNEC and LNEC samples. Specific genes for each site were revealed: gastric NEC ( TERT amplification), colorectal NEC ( KRAS mutation), and bile tract NEC ( ARID1A mutation). The gene disparities between small-cell NEC (SCNEC) and large-cell NEC (LCNEC) were KEAP1 and CDH1. Digestive adenocarcinoma was also compared with GEPNEC and suggested RB1, APC, and KRAS as significant genes. The TP53/ RB1 mutation pattern was associated with first-line effectiveness. Putative targetable genes and biomarkers in GEPNEC were identified in 22.2% of the patients, and they had longer progression-free survival (PFS) upon targetable treatment [12.5 months vs. 3.0 months, HR=0.40 (0.21-0.75), P=0.006].

Conclusions: This work demonstrated striking gene distinctions in GEPNEC compared with LNEC and adenocarcinoma and their clinical utility.

Keywords: Neuroendocrine carcinoma; gastroenteropancreatic; genetic alterations; lung; molecular markers.

Figure S1

Overview of flowchart in study inclusion process and pie charts of basic subgroups of NEC. (A) Flowchart of whole study; (B) Primary tumor sites; (C) Detailed primary tumor sites; (D) Pathology subgroups. NEN, neuroendocrine neoplasm; NET, neuroendocrine tumor; NEC, neuroendocrine carcinoma; GEP, gastroenteropancreatic; LNEC, lung NEC; LCNEC, large-cell NEC; SCNEC, small-cell NEC; ENEC, esophagus NEC; GNEC, gastric NEC; DNEC, duodenum NEC; CRNEC, colorectal NEC; PNEC, pancreas NEC; BTNEC, bile tract NEC; UPNEC, unknown primary NEC.

Figure S2

Morphological distinctions between GEPNEC and LNEC. (A) SCNEC of PNEC; (B) SCNEC of lung. GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; LNEC, lung NEC; SCNEC, small-cell NEC; PNEC, pancreatic NEC. Hematoxylin-eosin staining, ×400.

Figure 1

Overview of genomic landscape of whole NEC cohort of GEPNEC and LNEC. NEC, neuroendocrine carcinoma; GEP, gastroenteropancreatic; MiNEN, mixed neuroendocrine-non-neuroendocrine neoplasm; LCNEC, large-cell NEC; SCNEC, small-cell NEC; Unknown, unknown pathological types; CRNEC, colorectal NEC; BTNEC, bile tract NEC; GNEC, gastric NEC; PNEC, pancreas NEC; LNEC, lung NEC; DNEC, duodenum NEC; UPNEC, unknown primary NEC; ENEC, esophagus NEC.

Figure 2

Comparisons of significant gene alteration frequency of GEPNEC and LNEC patients. (A) Oncoprints showing the top most frequent and significant gene alterations between GEPNEC and LNEC; (B) Bar plots of pathway alteration proportions of GEPNEC and LNEC. GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; LNEC, lung NEC. P values were determined using Fisher’s exact test. *, P<0.05; **, P<0.01.

Figure S3

Correlations analysis of co-occurrence genes in GEPNEC and LNEC. (A) Co-occurrence and mutual exclusiveness of gene alteration pattern in GEPNEC patients; (B) Co-occurrence and mutual exclusiveness of gene alteration pattern in LNEC patients. GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; LNEC, lung NEC. Co-occurring mutations are indicated by green squares and mutually exclusive mutations between gene pairs in purple. The color intensity is proportionate the –log10 (P-value). P values were determined using Fisher’s exact test.

Figure S4

Summary of gene pathway analysis of GEPNEC vs. LNEC. (A) Oncoprints of main pathways with alteration frequency among GEPNEC and LNEC patients; (B) Bar plots of pathway alteration proportions of GEPNEC vs. LNEC. GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; LNEC, lung NEC. P values were determined using Fisher’s exact test. *, P<0.05; ***, P<0.001.

Figure S5

CNV analysis between GEPNEC and LNEC. (A) Graphics representing CNV data by sites of origins. The gain or loss of CNV regions in each clade is labeled with colored boxes. Red, gain; blue, loss; (B) Graphics demonstrating CNV data through pathology. GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; LNEC, lung NEC; CNV, copy number variation.

Figure S6

Distinctions of CNV gain/loss between GEPNEC and LNEC. (A,B) Venn plots for CNV gain (A) and CNV loss (B) of genes between GEPNEC and LNEC; (C,D) Bar plots showing quantity analysis of CNV in gene pathway CNV gain (C) and CNV loss (D). CNV, copy number variation; GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; LNEC, lung NEC.

Figure S7

Drivers genes and TMB distributions for GEPNEC of different primary sites. (A) Sankey plots of distinct driver genes of high frequency in GPENEC with different locations; (B) Box plots of TMB of various primary sites of GEPNEC. TMB, tumor mutation burden; GEPNEC, gastroenteropancreatic neuroendocrine carcinoma; LNEC, lung NEC; GNEC, gastric NEC; UPNEC, unknown primary NEC; ENEC, esophagus NEC; DNEC, duodenum NEC; CRNEC, colorectal NEC; BTNEC, bile tract NEC; PNEC, pancreas NEC.

Figure S8

Summary of alteration frequency of SCNEC vs. LCNEC. (A) Oncoprints showing the top most frequent and significant gene alterations between SCNEC and LCNEC; (B) Bar plots of pathway alteration proportions of SCNEC and LCNEC. SCNEC, small-cell neuroendocrine carcinoma; LCNEC, large-cell neuroendocrine carcinoma. P values were determined using Fisher’s exact test. *, P<0.05; **, P<0.01; ns, no significance.

Figure S9

Summary of alteration frequency of GEPSCNEC vs. GEPLCNEC. (A) Oncoprints showing the top most frequent and significant gene alterations between GEPSCNEC and GEPLCNEC; (B) Bar plots of pathway alteration proportions of GEPSCNEC and SCLC; (C) Bar plots of pathway alteration proportions of GEPLCNEC and LCLC. GEPSCNEC, gastroenteropancreatic small-cell neuroendocrine carcinoma; GEPLCNEC, gastroenteropancreatic large-cell neuroendocrine carcinoma; SCLC, small-cell lung cancer; LCLC, large-cell lung cancer. P values were determined using Fisher’s exact test. *, P<0.05; **, P<0.01.

Figure 3

Bar plots of comparisons of significant gene alteration frequency of GEPNEC and local adenocarcinoma patients. GEPNEC, gastroenteropancreatic neuroendocrine carcinoma. *, P<0.05; **, P<0.01.

Figure 4

Survival plots of targetable patients with target therapy and non-targetable patients with other therapies. (A) PFS of patients with/without target therapy (P=0.006); (B) OS of patients with/without target therapy (P=0.020). PFS, progression-free survival; OS, overall survival.