DNA methylome profiling of circulating tumor cells in lung cancer at single base-pair resolution

DNA methylation plays a pivotal role in regulating cellular processes, and altered DNA methylation pattern is a general hallmark of cancer. However, DNA methylome in circulating tumor cells (CTCs) is still a mystery due to the lack of proper analytical techniques. We introduced an efficient workflow, LCM-mu WGBS, which can efficiently profile the DNA methylation of microdissected CTC samples. LCM-mu WGBS combines the laser capture microdissection (LCM)-based CTC capture method and whole-genome bisulfite sequencing in very small CTC population (mu WGBS) to gain insight into the DNA methylation landscape of CTCs. We herein profiled the DNA methylome of CTCs from lung cancer patients. Deriving from a comprehensive analysis of CTC methylome, a unique CTC DNA methylation signature that is distinct from primary lung cancer tissues was identified. Further analysis showed that promoter hypermethylation of epithelial genes is a hallmark of stable epithelial-mesenchymal transition process. Moreover, it has been suggested that CTCs are endowed with a stemness-related feature during dissemination and metastasis. This work constitutes a unique DNA methylation analysis of CTCs at single base-pair resolution, which might facilitate to propose noninvasive CTC DNA methylation biomarkers contributing to clinical diagnosis.

Automated summary

In this study, an efficient workflow LCM-mu WGBS was introduced to profile the DNA methylome of circulating tumor cells from lung cancer patients. A unique DNA methylation signature of CTCs distinct from primary lung cancer tissues was identified, with promoter hypermethylation of epithelial genes as a hallmark of stable epithelial-mesenchymal transition. Furthermore, CTCs may exhibit a stemness-related feature during dissemination and metastasis, providing potential noninvasive CTC DNA methylation biomarkers for clinical diagnosis.