DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors

Abstract

Background Pancreatic neuroendocrine neoplasms (PanNENs) fall into two subclasses: the well-differentiated, low- to high-grade pancreatic neuroendocrine tumors (PanNETs), and the poorly-differentiated, high-grade pancreatic neuroendocrine carcinomas (PanNECs). While recent studies suggest an endocrine descent of PanNETs, the origin of PanNECs remains unknown. Methods We performed DNA methylation analysis for 57 PanNEN samples and found that distinct methylation profiles separated PanNENs into two major groups, clearly distinguishing high-grade PanNECs from other PanNETs including high-grade NETG3. DNA alterations and immunohistochemistry of cell-type markers PDX1, ARX, and SOX9 were utilized to further characterize PanNECs and their cell of origin in the pancreas. Results Phylo-epigenetic and cell-type signature features derived from alpha, beta, acinar, and ductal adult cells suggest an exocrine cell of origin for PanNECs, thus separating them in cell lineage from other PanNENs of endocrine origin. Conclusions Our study provides a robust and clinically applicable method to clearly distinguish PanNECs from G3 PanNETs, improving patient stratification.

The role of DNA methylation in human pancreatic neuroendocrine tumours

“…The PNET methylome has been profiled, in 24 studies in a gene specific manner (Dammann et al, 2003, House et al, 2003, Arnold et al, 2007, Malpeli et al, 2011, Muscarella et al, 1998, Serrano et al, 2000, Bartsch et al, 2000, Campana et al, 2018, Chan et al, 2003, Liu et al, 2005, Ohki et al, 2014, Schmitt et al, 2014, Ushiku et al, 2016, Wild et al, 2003, Ban et al, 2022, Conemans et al, 2018, Stefanoli et al, 2014, Liu et al, 2014, Cros et al, 2016, Dejeux et al, 2009, Choi et al, 2007, Zhang et al, 2020, Evans et al, 2022a, Stricker et al, 2012 and subsequently by both global methylation (Marinoni et al, 2017) and hydroxymethylation (Sharma et al, 2022), and by specific CpG site assessment with array-based technologies. (Chan et al, 2003, Boons et al, 2020, Di Domenico et al, 2020, Lakis et al, 2021, Tirosh et al, 2019, Simon et al, 2022, Yachida et al, 2022 Out of the 24 studies looking at a specific subset of genes, 58% (14/24) have used methylationspecific polymerase chain reaction (MSP) to investigate the percentage of methylation present at specific gene promoters. However, the criteria used to classify whether a gene is methylated were not defined in most studies.…”

“…(Di Domenico et al, 2020, Boons et al, 2020, Lakis et al, 2021, Chan et al, 2018, Yachida et al, 2022 Two studies which stratified PNETs from PNECs, reported that PNECs have a similar methylation profile to exocrine pancreatic tissue. (Simon et al, 2022, Yachida et al, 2022 One of these studies used multiomic data to further stratify PNECs into 'ductal' (Retinoblastoma-Associated Protein (RB1) protein loss, Tumour Protein 53 (TP53) mutations and a CpG Island Methylator Phenotype (CIMP) phenotype) and 'acinar' (CDKN2A alterations, deletions or promoter hypermethylation and WNT signalling alterations) subtypes. (Yachida et al, 2022) These studies provide further evidence that PNECs are a distinct biological entity when compared to PNETs, and highlight the importance of accurate tumour diagnosis to ensure that patients receive the appropriate therapies.…”

Epigenetic Regulation in Gastroenteropancreatic Neuroendocrine Tumors

“…performed in-depth genomic analysis of 57 pNENs (43 pNET, 14 pNEC) using DNA sequencing to identify recurrent genetic mutations. From this analysis, the authors identified two groups: Group A included mutations that are often associated with pNETs including MEN1 , DAXX , ATRX , VHL , PTEN and TSC2 , while Group B contained no mutations in DAXX , ATRX or MEN1 but contained KRAS , SMAD4 and TP53 mutations ( 39 ). Allen, et al.…”

“…The Simon et al. study performed DNA methylation profiling of the 57 pNENs (43 pNET, 14 pNEC) and was able to delineate pNET tumors from NEC based on t-distributed stochastic neighbor embedding (tSNE) analysis of methylation profiles ( 39 ).…”

Insights into Epigenetic Changes Related to Genetic Variants and Cells-of-Origin of Pancreatic Neuroendocrine Tumors: An Algorithm for Practical Workup

“…A recent study performed by Simon et al [ 58 ] outlined the importance of finding molecular groups by performing genetic and epigenetic profiling of 57 PanNENs. The molecular classification accurately differentiates PanNECs that may have an exocrine cell-of-origin, from PanNETs’ endocrine cell-of-origin.…”