Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach

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...

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Bibliographic Details
Published in:Frontiers in genetics 2021-09, Vol.12, p.673530-673530
Main 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
Format: Article
Language:English
Subjects:
3D genome organization
Biop-C
chromatin organization
Genetics
Hi-C
nasopharyngeal cancer
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Summary: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
1664-8021
DOI:10.3389/fgene.2021.673530