A disease dynamics atlas forecasts patient states and maps molecular programs in ALS

Abstract ALS progression is multidimensional, yet fragmented records and scalar outcomes obscure how patients move through disease states and how those states relate to molecular variation. MEDSTREM converts patient-held medical-record images into standardised longitudinal data, enabling bottom-up cohort construction. Using MEDSTREM-structured records from more than 8,000 AskHelpU participants together with PRO-ACT and Answer ALS, we developed DynaALS, the ALS Disease Dynamics Atlas. DynaALS represents ALS as a dynamic patient-state manifold that captures distinct directions of deterioration and patient movement between them over time. DynaALS retrieved population-referenced future states and decoded them into multidimensional clinical profiles without requiring patient-specific longitudinal histories. Motor-neuron RNA and chromatin profiles linked DynaALS states to developmental and regulatory programs, while neuromuscular-organoid single-cell multi-omics converged on a neural-developmental Netrin-DCC signalling axis across interacting cell types. By coupling MEDSTREM-enabled data construction to dynamic state modelling, DynaALS establishes a transferable patient-state engine for predictive and biologically interpretable disease models.