A 3D genome atlas of breast cancer progression [ChIP-seq]

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. ChIP-seq has been perfomed on fresh-frozen tissue derived from healthy breast (HB), primary breast cancer (PB), BCa-derived liver metastasis (LM). Immunoprecipitation has been performed for ERa (sc-542, SantaCruz). Raw paired-end fastq.gz files for both immunoprecipitated DNA and input samples are available under controlled access at the EGA database; project number EGAS50000000444 (DataSet: EGAD50000000642) *************************************************************** Raw data are derived from patient data, for this reason we deposited the raw sequences at the EGA (for both datasets). The corresponding EGA study accession number is EGAS50000000444 (https://ega-archive.org/studies/EGAS50000000444). ***************************************************************