A Hallmark-Integrated, Agent-Based Framework for Intratumor Heterogeneity in Melanoma Evolution

Abstract

Advances in multiregion sequencing have revealed extensive intratumor heterogeneity (ITH) - the presence of genetically distinct subclones within a single tumor. ITH profoundly influences tumor behavior, including well-accepted hall-marks of cancer such as sustained proliferation, resistance to apoptosis, and immune evasion, and the emergence of therapeutic resistance. In this work, we introduce a hallmark-integrated branching evolution process agent-based model (BEP-HI) to study the emergence of intratumor heterogeneity (ITH) in melanoma under coupled genetic, immune, and spatial selection pressures. Using this model, we identify three distinct evolutionary ITH modes and demonstrate a mechanistic decoupling between tumor growth kinetics and heterogeneity. We further show that immune recruitment exerts the strongest influence on ITH through nonlinear immune-editing feedback, while motility of melanoma cells shapes complex morphologies in different ITH modes as observed in clinical SSM tumors. This work provides a biologically grounded and adaptable computational framework for exploring how hallmark interactions shape ITH evolution and for generating virtual tumor cohorts that link genetic diversity with tumor behavior, morphology, and treatment resistance.