Integrating Mechanistic Modeling and Machine Learning to Study CD4+/CD8+ CAR-T Cell Dynamics with Tumor Antigen Regulation

Abstract

Chimeric antigen receptor (CAR) T cell therapy has shown remarkable success in hematological malignancies, yet patient responses remain highly variable and the roles of CD4+ and CD8+ subsets are not fully understood. We present an extended mathematical framework of CAR-T cell dynamics that explicitly models CD4+ helper and CD8+ cytotoxic lineages and their interactions with tumor antigen burden. Building on the Kirouac et al. (2023) model of antigen-regulated memory-effector-exhaustion transitions, our system of differential equations incorporates CD4-mediated modulation of CD8+ proliferation, cytotoxicity, and memory regeneration through biologically grounded, saturating interactions. Sensitivity analyses identify effector proliferation, antigen turnover, and CD8+ expansion rates as dominant drivers of treatment outcome. Virtual patient simulations recover reported qualitative trends in CAR-T composition, including enhanced expansion and tumor clearance for defined CD4:CD8 products relative to CD8-only formulations, while also revealing inter-patient variability and time-dependent effects. To assess the practical limits of patient-level prediction under parameter uncertainty, we introduce controlled noise into key parameters and show that direct mechanistic classification rapidly degrades. We then demonstrate that a simple feed-forward neural network can partially recover predictive signal from noisy inputs, outperforming a naive baseline while remaining consistent with mechanistic sensitivities. This work positions the extended model as a hypothesis generator, and illustrates how data-driven methods can complement mechanistic modeling when parameter uncertainty constrains predictive confidence.