Journal Article

Epigenetic regulation during cancer transitions across 11 tumour types

Puram, Sidharth V., Vij, Ravi, Ma, Cong, Ibrahim, Omar M., Strzalkowski, Alexander, Herndon, John M., Southard-Smith, Austin N., Held, Jason M., Mo, Chia-Kuei, Wyczalkowski, Matthew A., Karpova, Alla, Shinkle, Andrew, Chheda, Milan G., Sarkar, Hirak, DeNardo, David G., Porta-Pardo, Eduard, Cao, Song, DiPersio, John F., Pachynski, Russell, Mudd, Jacqueline, Ding, Li, Iglesia, Michael D., Kim, Albert H., Wendl, Michael C., Fuh, Katherine C., Sato, Kazuhito, Li, Yize, Caravan, Wagma, Liang, Wen-Wei, Terekhanova, Nadezhda V., Gillanders, William E., Jayasinghe, Reyka G., Schwarz, Julie K., Liu, Jingxian, Fields, Ryan C., Naser Al Deen, Nataly, Chasnoff, Sara E., Chen, Siqi, Chen, Feng, Raphael, Benjamin J., Liu, Xiuting, Houston, Andrew, Song, Yizhe, Lu, Rita Jui-Hsien

2023

Overview

Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis 1 – 4 . Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA ; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19 , ASAP2 and EN1 , and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial–mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions. A pan-cancer epigenetic and transcriptomic atlas identifies epigenetic drivers associated with cancer transitions.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 13/51 / 38/1 / 45/23 / 45/91 / 631/114 / 631/67/69 / 631/80 / 64/60 / Accessibility / ATP-Binding Cassette, Sub-Family C Proteins / Cancer / Cell Hypoxia / Cell Nucleus / Cells / Chromatin / Chromatin - genetics / Chromatin - metabolism / Cooperation / Enhancer Elements, Genetic - genetics / Epigenesis, Genetic - genetics / Epigenetics / Epithelial-Mesenchymal Transition / Estrogens / Estrogens - metabolism / Fibroblast Growth Factors / GATA6 Transcription Factor / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Neoplastic / GTPase-Activating Proteins - metabolism / Homeodomain Proteins / Humanities and Social Sciences / Humans / Hypoxia / Keratin / Metastases / Metastasis / multidisciplinary / Mutation / Neoplasm Metastasis / Neoplasms - classification / Neoplasms - genetics / Neoplasms - pathology / Nuclei (cytology) / p53 Protein / Pancreatic cancer / Proto-Oncogene Proteins / Regulatory sequences / Regulatory Sequences, Nucleic Acid - genetics / Science / Science (multidisciplinary) / Signal transduction / Single-Cell Analysis / Transcription Factors - metabolism / Transcriptomics / Tumor Suppressor Protein p53 / Tumors / Vascular Endothelial Growth Factor A