Epigenetic landscape of pancreatic neuroendocrine tumours reveals distinct cells of origin and means of tumour progression

Abstract

25Recent data suggest that Pancreatic Neuroendocrine Tumours (PanNETs) originate from α-or β-cells of 26 the islets of Langerhans. The majority of PanNETs are non-functional and do not express cell-type 27 specific hormones. We examined whether tumour DNA methylation (DNAme) profiling combined with 28 genomic data could identify cell of origin and reveal pathways involved in PanNET progression. We 29 analysed genome-wide DNAme data of 125 PanNETs and sorted α-and β-cells. To confirm cell identity, 30we investigated ARX and PDX1 expression. Based on epigenetic similarities, PanNETs clustered in α-31 like, β-like and intermediate tumours. The epigenetic similarity to α-cells progressively decreased in the 32 intermediate tumours, which presented unclear differentiation. Specific transcription factor methylation 33 and expression varied in the respective α/β-tumour groups. Depending on DNAme similarity to α/β-34 cells, PanNETs have different mutational spectra, stage of the disease and prognosis, indicating potential 35 means of PanNET progression. 36 Recent studies of gene expression and master regulator analysis alongside investigation of super-53 enhancer signatures have suggested both and -cells as two possible cells of origin for non-54 functioning (NF)-PanNETs5-8. On the other hand, Sadanandam et al. reported that a group of aggressive 55PanNET, namely, "metastasis-like primary", have a phenotype characterised by "stemness" transcripts 56 compared to well differentiated tumours, also suggesting a common progenitor cell origin5. Similarly, 57 based on the identification of master regulator proteins, de-differentiation and acquisition of stem cell 58 characteristics seem to be one of the pathways associated with tumour progression6. 59The cell of origin in cancer refers to the normal cell that acquires the initial cancer-promoting genetic 60 hit(s). During development, cell lineage fate is determined by cell-type specific transcription factor (TF) 61 expression, which in turn is dependent on the type of epigenetic markers that are located at the relative 62 regulatory regions (e.g. super-enhancer activation)9. The five endocrine cell types derive from a common 63 endocrine precursor, which has segregated from a ducto-endocrine bipotent cell population10. The TFs, 64Pax4 (Paired Box 4) and Arx (Aristaless Related Homeobox), are required for β-and α-cell fates, 65respectively. Lineage decision is determined via cross-inhibitory interactions11. Pdx1 (Pancreatic And 66 Duodenal Homeobox 1) expression becomes restricted to cells at the stage of initiating insulin 67 expression and, in the pancreatic islets of Langerhans, remains up-regulated exclusively in β-cells12. 68Integrative analysis of human epigenomes including histone modification patterns, DNA accessibility, 69 DNA methylation and RNA expression has revealed that disease-and trait-associated genetic variants 70 are enriched in tissue-specific epigenomic marks13. In the context of tumour biology, epigenetic states 71 of cell lineages shape the vulnerabilit...

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

“…The largest two groups, Groups A and B, clearly distinguished NECs from the rest of the cohort. Three recent studies have investigated PanNET subgroups at the epigenetic level [17][18][19] . Cejas et al looked at histone acetylation and transcriptomes 17 of NET samples, with two neuroendocrine samples both from the ileum.…”

“…Cejas et al looked at histone acetylation and transcriptomes 17 of NET samples, with two neuroendocrine samples both from the ileum. Di Domenico et al 18 and Lakis et al 19 used 450K methylation profiles from cohorts of well-differentiated PanNET samples. Our work expands the field by including the most aggressive subtypes of PanNENs: NETG3 and NEC tumors, which the aforementioned studies largely excluded (Di Domecio et al included only two NETG3).…”

“…This is due to the epigenetic memory of the cancer's cell of origin, as discovered in several studies 64,65 , most importantly in Cancers of Unknown Primary (CUP) 48,55 . Epigenetic identification of cancer cell-of-origin can determine the diagnosis 18,56 , evolution [66][67][68] and treatment 60,69 of this disease. Our study supports the introduction of methylation analysis in routine diagnosis of high-grade PanNEN tumors.…”

“…PDACs have been shown to originate from normal ductal or acinar cells 15,16 , while G1 and G2 PanNETs have been shown to originate from endocrine cells of the pancreas 17,18,19 . As yet, no study has attempted to identify the origin of PanNECs.…”

Molecular drivers and cells of origin in pancreatic ductal adenocarcinoma and pancreatic neuroendocrine carcinoma

“…Specifically, at least two different progenitor cells can give rise to non-functional PanNETs, the α-cells lineage (ARX +) or β-cells lineage (PDX +) [19]. Global DNAme profiles of the early stage of PanNET show strong similarities with both α-and β-cell DNAme profiles, while late stage tumors show a lower degree of similarities with normal cell types [47]. An additional study confirmed that different molecular subtypes of PanNET arise from different cellular origins, or from mature β-cell lineage, or islet cell precursors [48].…”