Interactome-based deep learning and path-level decomposition reveal TGFβ-IFNα competition in MASH

Dysregulated signaling drives Metabolic Dysfunction-Associated Steatohepatitis (MASH) through a complex crosstalk between pro- and anti-fibrotic cues. We previously observed potential competition between IFNα-mediated JAK-STAT signaling and TGFβ in modulating MASH fibrosis, but the precise mechanism of that competition, and whether it can act directly on hepatocytes, is yet unknown. We used DT-LEMBAS, an interactome-based deep learning framework, training an ensemble of 50 models on drug-induced transcriptomics from primary human hepatocytes. The ensemble captured transcriptional changes induced by simulated receptor knockouts and aligned predicted profiles with known TGFβ- and IFNα-induced phenotypes. Systematic simulations demonstrate their competitive modulation of MASH phenotype scores benchmarked against human cohorts. To extract mechanistic insights, we developed a gradient-based approach, where we computed the Jacobian of the used recurrent signaling network and applied chain rule decomposition to identify a four-node module of SMAD3, TP63, STAT2, and STAT3. Mechanistic hypotheses involving these canonical and non-canonical TF mediators were experimentally validated in primary hepatocyte spheroids. This work establishes a generalizable and scalable approach to decode large signaling neural networks into interpretable biological subnetworks.