Abstract
Abstract
Background
EGFR
amplification and/or mutation are found in more than half of the cases with glioblastoma. Yet, the role of chromatin interactions and its regulation of gene expression in
EGFR
-amplified glioblastoma remains unclear.
Methods
In this study, we explored alterations in 3D chromatin organization of
EGFR-
amplified glioblastoma and its subsequent impact by performing a comparative analysis of Hi-C, RNA-seq, and whole-genome sequencing (WGS) on
EGFR
-amplified glioblastoma-derived A172 and normal astrocytes (HA1800 cell line).
Results
A172 cells showed an elevated chromatin relaxation, and unexpected entanglement of chromosome regions. A genome-wide landscape of switched compartments and differentially expressed genes between HA1800 and A172 cell lines demonstrated that compartment activation reshaped chromatin accessibility and activated tumorigenesis-related genes. Topological associating domain (TAD) analysis revealed that altered TAD domains in A172 also contribute to oncogene activation and tumor repressor deactivation. Interestingly, glioblastoma-derived A172 cells showed a different chromatin loop contact propensity. Genes in tumorigenesis-associated signaling pathways were significantly enriched at the anchor loci of altered chromatin loops. Oncogene activation and tumor repressor deactivation were associated with chromatin loop alteration. Structure variations (SVs) had a dramatic impact on the chromatin conformation of
EGFR-
amplified glioblastoma-derived tumor cells. Moreover, our results revealed that 7p11.2 duplication activated
EGFR
expression in
EGFR
-amplified glioblastoma via neo-TAD formation and novel enhancer-promoter interaction emergence between
LINC01446
and
EGFR
.
Conclusions
The disordered 3D genomic map and multi-omics data of
EGFR-
amplified glioblastoma provide a resource for future interrogation of the relationship between chromatin interactions and transcriptome in tumorigenesis.