Research reveals the relationship between the genome, three-dimensional genome and transcriptome of clinical samples of lung cancer

Chromatin folds into a highly complex three-dimensional structure in the cell nucleus, and is dynamically regulated during cell differentiation and proliferation

In this study, the researchers first demonstrated the feasibility of using a small number of cells (1×10^4) Hi-C experiments to study the three-dimensional genome of clinical lung cancer samples (Figure 1)

▲Figure 1: Comparison of TAD detection in Hi-C experiments with different cell amounts in A549 cell line and 5534T clinical samples (Image source: Contributed by Professor Li Cheng's research group)

Through multi-omics data integration and analysis of genomic changes at different levels, we found:

(1) The topological domains (TADs) and chromatin loops (loops) structure in clinical lung cancer samples have undergone significant changes

(2) Hi-C technology can be used not only to detect the three-dimensional structure of chromatin, but also to infer copy number variation (CNV) (Figure 2) and point mutations (SNV) in cancer

▲Figure 2: Identification of CNVs from Hi-C data

(3) The authors obtained the three-dimensional genome structure, CNV and mutation information of clinical lung cancer patients through Hi-C data, and integrated analysis with RNA-seq data to explore how genomic mutations affect transcriptional regulation through three-dimensional genomes

(4) This study emphasizes the importance of 3D genomics in clinical cancer sample research, and provides a data integration analysis process for future cancer 3D genomics research

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