Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding

Cell. 2019 Jan 10;176(1-2):98-112.e14. doi: 10.1016/j.cell.2018.11.046.


The ability of circulating tumor cells (CTCs) to form clusters has been linked to increased metastatic potential. Yet biological features and vulnerabilities of CTC clusters remain largely unknown. Here, we profile the DNA methylation landscape of single CTCs and CTC clusters from breast cancer patients and mouse models on a genome-wide scale. We find that binding sites for stemness- and proliferation-associated transcription factors are specifically hypomethylated in CTC clusters, including binding sites for OCT4, NANOG, SOX2, and SIN3A, paralleling embryonic stem cell biology. Among 2,486 FDA-approved compounds, we identify Na+/K+ ATPase inhibitors that enable the dissociation of CTC clusters into single cells, leading to DNA methylation remodeling at critical sites and metastasis suppression. Thus, our results link CTC clustering to specific changes in DNA methylation that promote stemness and metastasis and point to cluster-targeting compounds to suppress the spread of cancer.

Keywords: RNA sequencing; bisulfite sequencing; circulating tumor cell clusters; circulating tumor cells; drug screen; proliferation-associated transcription factors; single cell sequencing; stemness-associated transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • Cell Differentiation
  • Cell Line, Tumor
  • Cell Proliferation
  • DNA Methylation / physiology
  • Disease Models, Animal
  • Female
  • Humans
  • Mice
  • Mice, Inbred NOD
  • Nanog Homeobox Protein / metabolism
  • Neoplasm Metastasis / genetics*
  • Neoplasm Metastasis / physiopathology
  • Neoplastic Cells, Circulating / metabolism
  • Neoplastic Cells, Circulating / pathology*
  • Octamer Transcription Factor-3 / metabolism
  • Repressor Proteins / metabolism
  • SOXB1 Transcription Factors / metabolism
  • Sin3 Histone Deacetylase and Corepressor Complex


  • NANOG protein, human
  • Nanog Homeobox Protein
  • Octamer Transcription Factor-3
  • POU5F1 protein, human
  • Repressor Proteins
  • SIN3A transcription factor
  • SOX2 protein, human
  • SOXB1 Transcription Factors
  • Sin3 Histone Deacetylase and Corepressor Complex