Methylation profiling reveals epigenetic programs associated with chr18 loss in small intestinal neuroendocrine tumors

Abstract

Small intestinal neuroendocrine tumors (SI-NETs) are characterized by a low mutational burden and limited recurrent driver mutations, suggesting that other mechanisms contribute to tumor development. One of the most frequent genomic alterations in SI-NETs is loss of heterozygosity on chromosome 18 (chr18del), which defines a major molecular subtype. However, the epigenetic consequences of this event remain poorly understood. In this study, we used long-read whole-genome sequencing to characterize genome-wide DNA methylation patterns in twelve primary tumors. Native methylation detection and copy-number profiling enabled stratification of tumors according to chromosome 18 status and direct comparison of epigenetic states between chr18del and non-chr18del (diploid) tumors. Chr18del tumors displayed widespread hypomethylation relative to diploid tumors, while chromosome 18 showed spatially structured regional methylation differences, including localized regions of increased methylation. Cross-platform validation using an independent Illumina EPIC methylation cohort confirmed the direction and distribution of many methylation events. Integration with the corresponding transcriptomic dataset revealed that a subset of methylation changes was associated with differential gene expression consistent with established promoter- and gene-body methylation models. Functional categorization of these methylation states revealed regulatory patterns linked to neuronal signaling, intracellular signaling cascades, and interactions with the extracellular matrix. Together, these findings support an association between chromosome 18 status and widespread methylation differences that extend beyond the affected chromosome and are linked to transcriptional programs relevant to neuroendocrine tumor biology.