Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer
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Published:2021-04-15
Issue:1
Volume:22
Page:
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ISSN:1474-760X
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Container-title:Genome Biology
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language:en
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Short-container-title:Genome Biol
Author:
Iyyanki Tejaswi, Zhang Baozhen, Wang Qixuan, Hou Ye, Jin Qiushi, Xu Jie, Yang Hongbo, Liu Tingting, Wang Xiaotao, Song Fan, Luan Yu, Yamashita Hironobu, Chien Ruby, Lyu Huijue, Zhang Lijun, Wang Lu, Warrick Joshua, Raman Jay D., Meeks Joshua J., DeGraff David J., Yue FengORCID
Abstract
Abstract
Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. Transcriptionally, FOXA1, GATA3, and PPARG are shown to be essential for luminal subtype-specific gene regulation and subtype switching, while TP63, STAT3, and TFAP2 family members are critical for regulation of basal subtype-specific genes. Despite these advances, the underlying epigenetic mechanisms and 3D chromatin architecture responsible for subtype-specific regulation in bladder cancer remain unknown.
Result
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.
Conclusion
In summary, our work identifies unique epigenomic signatures and 3D genome structures in luminal and basal urinary bladder cancers and suggests a novel link between the circadian transcription factor NPAS2 and a clinical bladder cancer subtype.
Funder
National Institute of General Medical Sciences National Human Genome Research Institute National Cancer Institute National Institute of Diabetes and Digestive and Kidney Diseases American Cancer Society
Publisher
Springer Science and Business Media LLC
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