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

Hideyuki Takeshima1, Yukie Yoda1,2, Mika Wakabayashi1

  • 1Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.

Clinical Epigenetics
|September 22, 2020
PubMed
Abstract

Insights

Low-dose decitabine (DAC) therapy shows remarkable cancer treatment efficacy by reprogramming specific cancer-related pathways at the single-cell level. This epigenetic reprogramming, observed via single-cell RNA-sequencing, reveals diverse cellular responses and targeted gene demethylation.

Area of Science:

  • Cancer Biology
  • Epigenetics
  • Genomics

Background:

  • DNA demethylating drugs offer promising cancer therapy, with efficacy dependent on dosing.
  • Low-dose, prolonged treatment exhibits significant therapeutic effects despite minimal DNA demethylation.
  • Understanding single-cell epigenetic reprogramming mechanisms is key to optimizing this therapy.

Purpose of the Study:

  • To investigate the mechanisms behind the efficacy of low-dose DNA demethylating therapy.
  • To analyze epigenetic reprogramming at the single-cell level in response to decitabine (DAC).

Main Methods:

  • Single-cell RNA-sequencing (scRNA-seq) to analyze gene expression profiles in HCT116 cells treated with DAC.
  • DNA methylation analysis of cloned HCT116 cells post-DAC treatment to assess demethylation.
  • Functional analysis of cellular consequences, including cell cycle regulation and senescence.

Main Results:

  • scRNA-seq showed highly diverse single-cell expression profiles with upregulated tumor-suppressor genes, endogenous retroviruses, and interferon-stimulated genes in random cell fractions.
  • DNA methylation analysis revealed complete demethylation of specific cancer-related genes (cell cycle, WNT, p53, TGF-β pathways) in a clone-dependent manner.
  • A clone with complete CDKN2A (p16) demethylation showed increased tetraploidy, indicating cellular senescence due to normalized cell cycle regulation.

Conclusions:

  • Epigenetic reprogramming of specific cancer-related pathways at the single-cell level underlies the efficacy of low-dose DNA demethylating therapy.
  • Single-cell analysis provides crucial insights into the heterogeneous responses to epigenetic drugs in cancer.
Keywords:
DNA methylationEpigenetic therapyEpigeneticsSingle cell analysis

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