Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma.
Comput Struct Biotechnol J
; 20: 1967-1978, 2022.
Article
en En
| MEDLINE
| ID: mdl-35521558
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.
3D genomic; Astrocytes; DE, Differentially expressed; FDR, False discovery rate; GBM, Glioblastoma multiform; Glioblastoma; Hi-C; ICE, Iterative correction and eigenvector decomposition; IDE, Distance decay exponent; PCC, Pearson's correlation coefficient; SV, Structure variation; Structure Variation; TAD, Topological associating domain; Tumorigenesis; WGS, Whole-genome sequencing
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Colección:
01-internacional
Banco de datos:
MEDLINE
Idioma:
En
Revista:
Comput Struct Biotechnol J
Año:
2022
Tipo del documento:
Article