Single cell transcriptional profiling reveals developmental mimicry in latent metastasis
Ashley Laughney Bakhoum1*, Ambrose Carr2, Juozas Nainys2, David van Dijk12, Vaidotas Kiseliovas2, Samuel F. Bakhoum3, Dana Pe’er2, Joan Massagué1
1Cancer Biology and Genetics Program, 2Computational Biology Program, 3Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, NY, USA
Most cancer deaths are caused by metastasis—recurrence of disease in distant organs, which is seeded by disseminated tumor cells (DTCs). The invasion-metastasis cascade releases large numbers of DTCs throughout the body, even during the early stages of tumor growth. A minority survives as potential seeds for future metastatic outbreaks (latency competent cells, LCC). They often evade immune surveillance and resist anti-cancer therapies, which primarily target dividing cells. The biology underlying these adaptive abilities remains poorly understood. We exploited the droplet-based barcoding technology, inDrop, to transcriptionally profile >50,000 single cells in latent metastases to identify networks that maintain latency and regulate its phenotypic switch from quiescence to a proliferative, immune-exposed state. We compared the development of LCC trapped in a quiescent state to those that drive metastatic outbreak, either spontaneously or upon depletion of Natural Killer cells, using PhenoGraph clustering, imputation of drop-out noise, and identification of diffusion trajectories. Our data show that a minority of LCC pre-exists in the parental cell line, and these precursors recapitulate normal lung epithelial development. Quiescent LCCs freshly harvested from mice with no sign of metastasis show a striking, differentiated state. However, those that escape immune surveillance and form an outbreak, emerge from a bi-potent progenitor state.Our data suggests that latent DTCs exist in a state of extended differentiation diapause, and successful metastatic outbreak is driven by proliferation of LCCs that remained in or reacquired a progenitor-like state.
Funding:Burroughs Wellcome Fund, NIH Cancer Systems Biology Consortium, MSKCC Center for Metastasis and Tumor Ecosystems Research