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Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors
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Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors
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Journal Article
Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors
2025
Overview
The extent of genetic variation and its influence on gene expression across multiple tissue and cellular contexts is still being characterized, with germline Structural Variants (SVs) being historically understudied. DNA methylation also represents a component of normal germline variation across individuals. Here, we combine germline SVs (by short-read sequencing) with tumor DNA methylation across 1292 pediatric brain tumor patients. For thousands of methylation probes for CpG Islands (CGIs) or enhancers, rare and common SV breakpoints upstream or downstream associate with differential methylation in tumors spanning various histologic types, a significant subset involving genes with SV-associated differential expression. Cancer predisposition genes involving SV-associated differential methylation and expression include
MSH2
,
RSPA
, and
PALB2
. SV breakpoints falling within CGIs or histone marks H3K36me3 or H3K9me3 associate with differential CGI methylation. Genes with SVs and CGI methylation associated with patient survival include
POLD4
. Our results capture a class of normal phenotypic variation having disease implications.
The role of germline variation in cancer remains underexplored. Here, the authors investigate the landscape of germline structural variants on tumour DNA methylation across pediatric brain and central nervous system tumour patients and suggest disease implications.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ 45/23
/ Brain
/ Cancer
/ Child
/ DNA
/ Female
/ Gene Expression Regulation, Neoplastic
/ Genes
/ Genetic Predisposition to Disease
/ Genomic Structural Variation
/ Histones
/ Humanities and Social Sciences
/ Humans
/ Male
/ MutS Homolog 2 Protein - genetics
/ MutS Homolog 2 Protein - metabolism
/ Science
/ Tumors
