3D chromatin structure in colon cancer. 3D chromatin structure in colon cancer

We report the application of in situ Hi-C technology to 40 colorectal cancer patients and 10 paired-normal tissue to identify CRC specific changes in 3D chromatin structure. The chromatin contact matrices were generated by the sequencing data and image processing/deep learning-based algorithm was proposed to identify long-range abnormal chromatin interaction patterns in the contact matrices. The tumor specific 3D chromatin structure changes and the enhancer-promoter rewiring mediated by the identified chromatin structure changes were analyzed. The complex chromosome-wide rearrangements such as chromothripsis and its effect to 3D chromatin structure were also observed. Overall design: This study contains in situ Hi-C data for colorectal cancer patient samples. Additional processed data is available at: http://junglab.kaist.ac.kr/Dataset/Kim_et_al_2023 Online tissue slide data repository is available at: http://junglab.kaist.ac.kr/Dataset/CellReports_tissueData.html

本研究采用原位Hi-C（in situ Hi-C）技术，对40名结直肠癌患者及10例配对正常组织样本进行检测，以鉴定结直肠癌（Colorectal Cancer，简称CRC）特异性的三维染色质结构改变。研究人员基于测序数据生成了染色质接触矩阵，并提出了基于图像处理与深度学习的算法，用于识别该矩阵中的远距离异常染色质互作模式。本研究进一步分析了肿瘤特异性三维染色质结构改变，以及由此类结构改变介导的增强子-启动子重编程事件。此外，本研究还观测到了染色体碎裂（chromothripsis）等全染色体复杂重排事件，及其对三维染色质结构的影响。整体实验设计：本数据集包含结直肠癌患者样本的原位Hi-C数据。额外的已处理数据可通过以下链接获取：http://junglab.kaist.ac.kr/Dataset/Kim_et_al_2023；组织切片在线数据仓库可访问：http://junglab.kaist.ac.kr/Dataset/CellReports_tissueData.html