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Title: Profiling of 3D genome organization in nasopharyngeal cancer needle biopsy patient samples by a modified Hi-C approach
Authors: Animesh, Sambhavi
Choudhary, Ruchi
Wong, Bertrand Jern Han
Koh, Charlotte Tze Jia
Ng, Xin Yi
Tay, Joshua Kai Xun
Chong, Wan-Qin
Jian, Han
Chen, Leilei
Goh, Boon Cher
Fullwood, Melissa Jane
Keywords: Science::Biological sciences
Issue Date: 2021
Source: Animesh, S., Choudhary, R., Wong, B. J. H., Koh, C. T. J., Ng, X. Y., Tay, J. K. X., Chong, W., Jian, H., Chen, L., Goh, B. C. & Fullwood, M. J. (2021). Profiling of 3D genome organization in nasopharyngeal cancer needle biopsy patient samples by a modified Hi-C approach. Frontiers in Genetics, 12, 673530-.
Project: NRF-NRFF2012-054 
Journal: Frontiers in Genetics 
Abstract: Nasopharyngeal cancer (NPC), a cancer derived from epithelial cells in the nasopharynx, is a cancer common in China, Southeast Asia, and Africa. The three-dimensional (3D) genome organization of nasopharyngeal cancer is poorly understood. A major challenge in understanding the 3D genome organization of cancer samples is the lack of a method for the characterization of chromatin interactions in solid cancer needle biopsy samples. Here, we developed Biop-C, a modified in situ Hi-C method using solid cancer needle biopsy samples. We applied Biop-C to characterize three nasopharyngeal cancer solid cancer needle biopsy patient samples. We identified topologically associated domains (TADs), chromatin interaction loops, and frequently interacting regions (FIREs) at key oncogenes in nasopharyngeal cancer from the Biop-C heatmaps. We observed that the genomic features are shared at some important oncogenes, but the patients also display extensive heterogeneity at certain genomic loci. On analyzing the super enhancer landscape in nasopharyngeal cancer cell lines, we found that the super enhancers are associated with FIREs and can be linked to distal genes via chromatin loops in NPC. Taken together, our results demonstrate the utility of our Biop-C method in investigating 3D genome organization in solid cancers.
ISSN: 1664-8021
DOI: 10.3389/fgene.2021.673530
Schools: School of Biological Sciences 
Organisations: National University of Singapore
Rights: © 2021 Animesh, Choudhary, Wong, Koh, Ng, Tay, Chong, Jian, Chen, Goh and Fullwood. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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