Life history enlightened therapies: cell cycle mapping to identify molecular targets to prevent hepatocellular carcinoma

Life history enlightened therapies (LHETs) were originally developed in cancer to combat therapeutic resistance by targeting pathological cell state transitions that enable evolutionary rescue and adaptation to therapy. In this paper we expand the scope of LHETs to cancer prevention, namely metabolic dysfunction-associated steatohepatitis (MASH)-induced hepatocellular carcinoma (HCC) initiation. We focus on endocycling, a process wherein cells undergo whole-genome duplication via mitotic skipping, as a keystone life history transition that promotes HCC initiation. A key obstacle to LHET translation is the lack of systematic methods that capture cellular life histories and their molecular drivers. To address this gap, we introduce cell cycle mapping, a technique that integrates in situ multiplexed immunofluorescence imaging with manifold learning to visualize the life history of proliferating cells and proteins involved in transitions to pathological cell states. Mathematical modeling demonstrated how endocycling can create an environment that promotes HCC initiation and revealed the potential for endocycle-targeting therapies to prevent HCC. Using cell cycle mapping on human MASH liver tissues, we identified the molecular factors that drive pathological endocycling (Wee1, CDK2, and RAIDD), providing new therapeutic targets for pre-clinical investigation. This application illustrates how cell cycle mapping can uncover key proteins that drive disease-associated cell state transitions and broaden the scope of LHETs from therapy resistance to cancer prevention. More broadly, our study establishes a generalizable pipeline for inferring the life history of cells in diseased tissues and potential interventions for disease management.