Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
BMC Biol. 2021 Sep 21;19(1):207. doi: 10.1186/s12915-021-01147-5.
Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate cancer development are useful for controlled serial time sampling.
We performed single-cell exome and transcriptome sequencing of 200 cells to investigate how ITH is generated in a mouse colorectal cancer model. In the model, a single normal intestinal cell is grown into organoids that mimic the intestinal crypt structure. Upon RNAi-mediated downregulation of a tumor suppressor gene APC, the transduced organoids were serially transplanted into mice to allow exposure to in vivo microenvironments, which play relevant roles in cancer development. The ITH of the transcriptome increased after the transplantation, while that of the exome decreased. Mutations generated during organoid culture did not greatly change at the bulk-cell level upon the transplantation. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes after the transplantation. Analyses of colorectal cancer data from The Cancer Genome Atlas revealed a high proportion of metastatic cases in human subjects with expression patterns similar to the new cell subpopulations in mouse. These results suggest that the birth of transcriptional subpopulations may be a key for adaptation to drastic micro-environmental changes when cancer cells have sufficient genetic alterations at later tumor stages.
This study revealed an evolutionary dynamics of single-cell RNA and DNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer.
肿瘤内异质性（ITH）包含肿瘤内的细胞差异，与药物耐药等临床结果相关。然而，由于缺乏单细胞水平的时间序列分析，对 ITH 的动态变化知之甚少。重现癌症发展的小鼠模型有助于进行受控的连续时间采样。
我们对 200 个细胞进行了单细胞外显子组和转录组测序，以研究 ITH 如何在小鼠结直肠癌模型中产生。在该模型中，单个正常肠细胞生长成类器官，模拟肠隐窝结构。在用 RNAi 下调抑癌基因 APC 后，转导的类器官被连续移植到小鼠体内，以使其暴露于在癌症发展中起相关作用的体内微环境中。在移植后，转录组的 ITH 增加，而外显子组的 ITH 减少。在移植时，在类器官培养过程中产生的突变在细胞群体水平上并没有发生很大变化。RNA ITH 的增加是由于新转录亚群的出现。与最初表达间充质标志物基因的细胞相反，新亚群在移植后抑制了这些基因。对癌症基因组图谱中结直肠癌数据的分析显示，在人类受试者中，具有与小鼠新细胞亚群相似表达模式的转移性病例比例较高。这些结果表明，转录亚群的出现可能是当癌细胞在后期肿瘤阶段具有足够的遗传改变时适应剧烈的微环境变化的关键。
本研究揭示了肿瘤进展中单细胞 RNA 和 DNA 异质性的进化动态，深入了解了结直肠癌中肿瘤细胞的间质上皮转化。
