An integrative ENCODE resource for cancer genomics

• Published in: Nature communications Vol. 11; no. 1; pp. 3696 - 11
• Main Authors: Zhang, Jing, Lee, Donghoon, Dhiman, Vineet, Jiang, Peng, Xu, Jie, McGillivray, Patrick, Yang, Hongbo, Liu, Jason, Meyerson, William, Clarke, Declan, Gu, Mengting, Li, Shantao, Lou, Shaoke, Xu, Jinrui, Lochovsky, Lucas, Ung, Matthew, Ma, Lijia, Yu, Shan, Cao, Qin, Harmanci, Arif, Yan, Koon-Kiu, Sethi, Anurag, Gürsoy, Gamze, Schoenberg, Michael Rutenberg, Rozowsky, Joel, Warrell, Jonathan, Emani, Prashant, Yang, Yucheng T., Galeev, Timur, Kong, Xiangmeng, Liu, Shuang, Li, Xiaotong, Krishnan, Jayanth, Feng, Yanlin, Rivera-Mulia, Juan Carlos, Adrian, Jessica, Broach, James R, Bolt, Michael, Moran, Jennifer, Fitzgerald, Dominic, Dileep, Vishnu, Liu, Tingting, Mei, Shenglin, Sasaki, Takayo, Trevilla-Garcia, Claudia, Wang, Su, Wang, Yanli, Zang, Chongzhi, Wang, Daifeng, Klein, Robert J., Snyder, Michael, Gilbert, David M., Yip, Kevin, Cheng, Chao, Yue, Feng, Liu, X. Shirley, White, Kevin P., Gerstein, Mark
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29.07.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 45/15; 45/23; 45/47; 45/91; 49/15; 49/47; 631/114/2114; 631/114/2401; 631/208/69; Annotations; Cancer; Cell Line, Tumor; Cell Transformation, Neoplastic - genetics; CRISPR; Crosstalk; Databases, Genetic; Datasets; Encyclopedias; Gene Regulatory Networks; Genomes; Genomics; Hierarchies; Humanities and Social Sciences; Humans; multidisciplinary; Mutation - genetics; Myc protein; Neoplasms - genetics; Regulators; Reproducibility of Results; RNA-binding protein; Science; Science (multidisciplinary); siRNA; Transcription factors; Transcription Factors - metabolism; Tumorigenesis; Tumors; Workflow
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-14743-w

ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource. ENCODE is a resource comprising thousands of functional genomic datasets. Here, the authors present custom annotation within ENCODE for cancer, highlighting a workflow that can help prioritise key elements in oncogenesis.