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

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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001007052	This contains H3K27ac ChIP-seq, RNA-seq and HiC fastq files.	Illumina Genome Analyzer Illumina NovaSeq 6000	5

Publications	Citations
Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. Iyyanki T, Zhang B, Wang Q, Hou Y, Jin Q, Xu J, Yang H, Liu T, Wang X, Song F, Luan Y, Yamashita H, Chien R, Lyu H, Zhang L, Wang L, Warrick J, Raman JD, Meeks JJ, DeGraff DJ, Yue F. Genome Biol 22: 2021 105	21