Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer

Study ID Alternative Stable ID Type
EGAS00001005071 Other

Study Description

We determine the genome-wide transcriptome, enhancer landscape and transcription factor binding profiles of FOXA1 and GATA3 in luminal and basal subtypes of bladder cancer. Furthermore, we report the first-ever mapping of genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors. We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal-enhancers of luminal and basal bladder cancers. Finally, we identify a novel clinically relevant transcription factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other subtype-specific genes and influences cancer cell proliferation and migration.

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
This contains H3K27ac ChIP-seq, RNA-seq and HiC fastq files.
Illumina Genome Analyzer,Illumina NovaSeq 6000 5

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