Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding

• Published in: Cell 2019-01, Vol.176 (1-2), p.98-112.e14
• Main Authors: Gkountela, Sofia, Castro-Giner, Francesc, Szczerba, Barbara Maria, Vetter, Marcus, Landin, Julia, Scherrer, Ramona, Krol, Ilona, Scheidmann, Manuel C., Beisel, Christian, Stirnimann, Christian U., Kurzeder, Christian, Heinzelmann-Schwarz, Viola, Rochlitz, Christoph, Weber, Walter Paul, Aceto, Nicola
• Format: Article
• Language: English
• Subjects: Animals; bisulfite sequencing; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Cell Differentiation; Cell Line, Tumor; Cell Proliferation; circulating tumor cell clusters; circulating tumor cells; Disease Models, Animal; DNA Methylation - physiology; drug screen; 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; proliferation-associated transcription factors; Repressor Proteins - metabolism; RNA sequencing; single cell sequencing; SOXB1 Transcription Factors - metabolism; stemness-associated transcription factors
• ISSN: 0092-8674; 1097-4172
• 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. [Display omitted] •Binding sites for OCT4, SOX2, NANOG, and SIN3A are hypomethylated in CTC clusters•CTC cluster hypomethylation profile correlates with a poor prognosis in breast cancer•Treatment with FDA-approved Na+/K+-ATPase inhibitors dissociates CTC clusters•Dissociation reverts the methylation profile of CTC clusters and suppresses metastasis A comparative analysis of the methylation landscape of single and clusters of circulating tumor cells reveals patterns of similarity to embryonic stem cells and identifies pharmacological agents that can target clustering, suppress stemness, and blunt metastatic spreading.