Prognostic Relevance of Aberrant DNA Methylation in G1 and G2 Pancreatic Neuroendocrine Tumors

Abstract

Background/Aims: The occurrence and clinical relevance of DNA hypermethylation and global hypomethylation in pancreatic neuroendocrine tumours (PanNETs) are still unknown. We evaluated the frequency of both epigenetic alterations in PanNETs to assess the relationship between methylation profiles and chromosomal instability, tumour phenotypes and prognosis. Methods: In a well-characterized series of 56 sporadic G1 and G2 PanNETs, methylation-sensitive multiple ligation-dependent probe amplification was performed to assess hypermethylayion of 33 genes and copy number alterations (CNAs) of 53 chromosomal regions. Long interspersed nucleotide element-1 (LINE-1) hypomethylation was quantified by pyrosequencing. Results: Unsupervised hierarchical clustering allowed to identify a subset of 22 PanNETs (39%) exhibiting high frequency of gene-specific methylation and low CNA percentages. This tumour cluster was significantly associated with stage IV (p = 0.04) and with poor prognosis in univariable analysis (p = 0.004). LINE-1 methylation levels in PanNETs were significantly lower than in normal samples (p < 0.01) and were approximately normally distributed. 12 tumours (21%) were highly hypomethylated, showing variable levels of CNA. Interestingly, only 5 PanNETs (9%) were observed to show simultaneously LINE-1 hypomethylation and high frequency of gene-specific methylation. LINE-1 hypomethylation was strongly correlated with advanced stage (p = 0.002) and with poor prognosis (p < 0.0001). In the multivariable analysis, low LINE-1 methylation status and methylation clusters were the only independent significant predictors of outcome (p = 0.034 and p = 0.029, respectively). Conclusion: The combination of global DNA hypomethylation and gene hypermethylation analyses may be useful to define distinct subsets of PanNETs. Both alterations are common in PanNETs and could be directly correlated with tumour progression.

Genetic and epigenetic drivers of neuroendocrine tumours (NET)

“…LINE1 hypomethylation significantly correlated with poor prognosis and advanced tumour stage in PanNET (Stefanoli et al 2014). Interestingly, in the same study, the authors found that DAPK1, TIMP3, PAX5, HIC1, CADM1, PYCARD, ESR1, VHL, RARB and WT1 promoters were significantly hyper-methylated in late-stage tumours and in tumours with poor prognosis (Stefanoli et al 2014). However, the majority of the tumours did not show simultaneous global hypomethylation and CpG hypermethylation suggesting that in PanNET the two mechanisms are independent.…”

Acinar Cell Carcinoma of the Pancreas: Overview of Clinicopathologic Features and Insights into the Molecular Pathology

“…Aberrant methylation of CpG islands is a well-known mechanism associated with the silencing of cancer-related genes in several cancers including pancreatic adenocarcinomas (58, 59) and PanNETs (60). In the literature, there is only one study, which, analyzing the promoter methylation status of 34 tumor suppressor genes, evaluated the methylation profile of ACCs (37).…”

“…In general, ACCs showed low levels of hypermethylation and no tumors characterized by concerted hypermethylation at multiple loci were identified among 55 ACC/MANECs investigated. Consequently, the so-called “CpG island methylator phenotype (CIMP)” described not only in colorectal cancers but also in pancreatic ductal adenocarcinomas and PanNETs (60, 61) seems not to be present in pancreatic ACCs. However, some genes, including RASSF1 and APC , frequently were found to be methylated.…”

Unmet Needs in Functional and Nonfunctional Pancreatic Neuroendocrine Neoplasms

“…The recurrence rate postresection in patients with PanNENs varies markedly in different series and, as outlined in a previous paragraph, it is affected by the type of PanNEN included (insulinomas, the most frequent F-PanNEN, have a very low recurrence rate) [61], the tumor grade, the tumor stage, and the pathologic features other than grade/differentiation of the tumors, such as degree of invasion [20, 21, 24-31, 33-36]. In addition, other molecular features of PanNENs have been shown to correlate with tumor aggressiveness/recurrence, including ATRX/DAXX/telomere changes and changes in other chromatin remodeling genes [62], miRNA/mRNA transcriptome profiles [63], methylation status [64], and a number of other alterations [65] (Table 2). Each of the radiologic features discussed above in Possible Unmet Needs Protocol 1 could also be correlated with tumor aggressiveness/recurrence either from preoperative/pretreatment studies or residual tumor.…”