ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup

Abstract

The commonly mutated genes in pancreatic neuroendocrine tumors (PanNETs) are ATRX, DAXX, and MEN1. We genotyped 64 PanNETs and found 58% carry ATRX, DAXX, and MEN1 mutations (A-D-M mutant PanNETs) and this correlates with a worse clinical outcome than tumors carrying the wild-type alleles of all three genes (A-D-M WT PanNETs). We performed RNA sequencing and DNA-methylation analysis to reveal two distinct subgroups with one consisting entirely of A-D-M mutant PanNETs. Two genes differentiating A-D-M mutant from A-D-M WT PanNETs were high ARX and low PDX1 gene expression with PDX1 promoter hyper-methylation in the A-D-M mutant PanNETs. Moreover, A-D-M mutant PanNETs had a gene expression signature related to that of alpha-cells (FDR q-value < 0.009) of pancreatic islets including increased expression of HNF1A and its transcriptional target genes. This gene expression profile suggests that A-D-M mutant PanNETs originate from or transdifferentiate into a distinct cell type similar to alpha cells.

Assessment of ARX expression, a novel biomarker for metastatic risk in pancreatic neuroendocrine tumors, in endoscopic ultrasound fine‐needle aspiration

“…Since reliable cytologic determination of PDX1 is critical to determine the prognostic subgroups as described in Cejas et al, cytologic PDX1 interpretation should be performed with caution, but concerning prognostic value, this study was too limited in size to draw strong conclusions. The high percentage of ARX positive non‐functional PanNETs (17/18) compared to 50% to 60% in recent studies, might be caused by selection bias and reflect more aggressive/faster growing tumors that warranted biopsy.…”

“…PDX1 or double positive expression on the other hand identified a more indolent group, in which only few tumors relapsed . Similarly, Chan et al showed, using RNA sequencing and whole genome methylation, that the ARX positive, PDX1 negative subgroup was often associated with somatic mutations in ATRX , DAXX , or MEN1 and a worse prognosis …”

“…12 Similarly, Chan et al showed, using RNA sequencing and whole genome methylation, that the ARX positive, PDX1 negative subgroup was often associated with somatic mutations in ATRX, DAXX, or MEN1 and a worse prognosis. 13 Thus, ARX and PDX1, in combination with ALT, may be prognostic markers to identify low and high risk subgroups preoperatively on cytology, as staining of these proteins seems to identify these alpha and beta cell-like subgroups robustly. Although, a prerequisite to be able to consider these markers for routine clinical use, is to determine if cytologic material can be reliably used to detect tumor subtype.…”

DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas (PanNECs) and pancreatic neuroendocrine tumors (PanNETs)

“…Samples used for each assay and their characteristics are shown in Figure 1a, further details are depicted in Supplementary Table 1. The cohort includes tumors of grades NET G1 (27) and NET G2 (25) NET G3 (4), and NEC (3), 45 samples were primary PanNENs and 14 were metastases (8 liver, 6 lymph nodes). As healthy control we used matched adjacent healthy (24) or distant healthy tissue (27) or blood (4) from the same patient.…”

“…Comparison of PanNEN MEN1/DAXX/ATRX-mutated and -wildtype subgroups by whole transcriptome profiling revealed a gene expression signature similar to α-cells of the Islets of Langerhans only in the mutant group 27 . The specific signature showed a strong expression of the well-established α-cell-specific transcription factor ARX.…”