Low-dose DNA demethylating therapy induces reprogramming of diverse cancer-related pathways at the single-cell level

Clinical Epigenetics

Satoshi Yamashita¹  Mika Wakabayashi¹  Naoko Hattori¹  Hideyuki Takeshima¹  Toshikazu Ushijima¹  Yukie Yoda² 

[1] Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan;Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan;Department of Surgery, Faculty of Medicine, Saga University, Saga, Japan;

关键词: Epigenetics;    DNA methylation;    Epigenetic therapy;    Single cell analysis;   

DOI  :  10.1186/s13148-020-00937-y

来源: Springer

【 摘 要 】

BackgroundEpigenetic reprogramming using DNA demethylating drugs is a promising approach for cancer therapy, but its efficacy is highly dependent on the dosing regimen. Low-dose treatment for a prolonged period shows a remarkable therapeutic efficacy, despite its small demethylating effect. Here, we aimed to explore the mechanisms of how such low-dose treatment shows this remarkable efficacy by focusing on epigenetic reprograming at the single-cell level.MethodsExpression profiles in HCT116 cells treated with decitabine (DAC) were analyzed by single-cell RNA-sequencing (scRNA-seq). Functional consequences and DNA demethylation at the single-cell level were analyzed using cloned HCT116 cells after DAC treatment.ResultsscRNA-seq revealed that DAC-treated cells had highly diverse expression profiles at the single-cell level, and tumor-suppressor genes, endogenous retroviruses, and interferon-stimulated genes were upregulated in random fractions of cells. DNA methylation analysis of cloned HCT116 cells revealed that, while only partial reduction of DNA methylation levels was observed in bulk cells, complete demethylation of specific cancer-related genes, such as cell cycle regulation, WNT pathway, p53 pathway, and TGF-β pathway, was observed, depending upon clones. Functionally, a clone with complete demethylation of CDKN2A (p16) had a larger fraction of cells with tetraploid than parental cells, indicating induction of cellular senescence due to normalization of cell cycle regulation.ConclusionsEpigenetic reprogramming of specific cancer-related pathways at the single-cell level is likely to underlie the remarkable efficacy of low-dose DNA demethylating therapy.

【 授权许可】

CC BY