Time-resolved lineage recording reveals a pre-existing, heritable cell state underlying metastatic potential

Abstract

Metastasis causes most cancer deaths1,2, yet no recurrent mutation specifically drives it3,4, raising the possibility that metastatic potential is a non-genetic yet heritable cell state. Classic experiments established that metastatically predisposed subclones pre-exist within a tumor and that these predispositions are inherited over many cell divisions5, but what molecular states or factors underlie this predisposition remain unknown. While previous lineage recording studies6,7 mapped how tumors disseminate, their recording sites saturate too quickly to resolve when a lineage branched, or to attribute a state to its founder. Here we show, using a DNA Typewriter lineage recorder8 with nearly 1,000 recording sites in lung cancer cells, that metastatic potential is already present before dissemination, with colonization predicted by a pre-existing glycolytic state and further spread by expression of ENO1, a glycolytic enzyme that also moonlights as a cell-surface plasminogen receptor9. Profiling the pre-transplant cells and the post-transplantation tumors for both their transcriptomes and their lineage recordings, we reconstructed time-resolved lineage trees across three orthotopically transplanted mice. These trees trace each liver metastasis to a single founder of known pre-transplant state, dating each dissemination event from the primary lung. When every clone was scored before transplant against 349 genes recurrently heritable in vitro, both that set and the glycolytic state independently shifted a clones odds of colonizing the lung. At the gene level, sixteen genes were both heritable and predictive of colonization, and ENO1 alone also predicted which established clones spread further. Hypoxia, the program most strongly associated with phylogenetic fitness within the metastases, did not predict colonization when scored before transplant, separating niche-selected traits from the inherited cell state. Metastatic potential in this system is therefore transmitted along the lineage rather than acquired after seeding. Looking forward, we anticipate that time-resolved lineage recorders will enable the separation of the heritable and acquired components of the cellular heterogeneity seen in single-cell studies of tumor progression and drug tolerance.