A 3D genome atlas of breast cancer progression
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1144432 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A 3D genome atlas of breast cancer progression [Hi-C]
| PRJNA1144436 | ENA
Project description:A 3D genome atlas of breast cancer progression [ChIP-seq]
| PRJNA1144435 | ENA
Project description:During cancer development and progression massive alterations in gene expression have been observed. The regulation of genes occurs within the context of the 3D genome. However, the impact of disease progression on the 3D structure of the genome remains poorly understood. Using breast cancer as a model we have profiled the 3D genome throughout the natural course of the disease; from development to progression. Uniquely, we analysed tumours from the same patients, enabling us to gauge the extent of changes that happen upon metastasis. Our results show that the organization of genome at the level of topologically associating domains (TADs) and compartments upon tumorigenesis and metastasis, is remarkably stable. However, in pleural metastases, representing heavily pretreated progressive disease, the 3D genome is massively affected, and highly heterogeneous between patients, both on the compartment and TAD level. Our data reveal that disease progression in breast cancer is associated with a progressive unravelling of the 3D genome.
2025-06-27 | GSE273998 | GEO
Project description:During cancer development and progression massive alterations in gene expression have been observed. The regulation of genes occurs within the context of the 3D genome. However, the impact of disease progression on the 3D structure of the genome remains poorly understood. Using breast cancer as a model we have profiled the 3D genome throughout the natural course of the disease; from development to progression. Uniquely, we analysed tumours from the same patients, enabling us to gauge the extent of changes that happen upon metastasis. Our results show that the organization of genome at the level of topologically associating domains (TADs) and compartments upon tumorigenesis and metastasis, is remarkably stable. However, in pleural metastases, representing heavily pretreated progressive disease, the 3D genome is massively affected, and highly heterogeneous between patients, both on the compartment and TAD level. Our data reveal that disease progression in breast cancer is associated with a progressive unravelling of the 3D genome.
2025-06-27 | GSE273997 | GEO
Project description:Breast cancer progression entails intricate, multi-level alterations in genome organization and expression. To gain insights into the modifications in chromatin's three-dimensional (3D) structure during breast cancer progression, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observed a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identified a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene becomes inserted into a highly active region on chromosome 10. This insertion event leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing the complex interplay between genomic structure and oncogenic processes.
2024-08-07 | GSE246689 | GEO
Project description:Breast cancer progression entails intricate, multi-level alterations in genome organization and expression. To gain insights into the modifications in chromatin's three-dimensional (3D) structure during breast cancer progression, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observed a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identified a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene becomes inserted into a highly active region on chromosome 10. This insertion event leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing the complex interplay between genomic structure and oncogenic processes.
2024-08-06 | GSE246599 | GEO
Project description:Breast cancer progression entails intricate, multi-level alterations in genome organization and expression. To gain insights into the modifications in chromatin's three-dimensional (3D) structure during breast cancer progression, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observed a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identified a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene becomes inserted into a highly active region on chromosome 10. This insertion event leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing the complex interplay between genomic structure and oncogenic processes.
2024-08-06 | GSE246947 | GEO
Project description:Deterioration of multi-level 3D genome organization during breast cancer progression
| PRJNA1033691 | ENA
Project description:Deterioration of multi-level 3D genome organization during breast cancer progression
| PRJNA1035141 | ENA
Project description:Deterioration of multi-level 3D genome organization during breast cancer progression
| PRJNA1034127 | ENA