T-SCAPE: T-cell Immunogenicity Scoring via Cross-domain Aided Predictive Engine

Abstract

T-cell immunogenicity, the ability of peptide fragments to elicit T-cell responses, is a critical determinant of the safety and efficacy of protein therapeutics and vaccines. While deep learning shows promise for in silico prediction, the scarcity of comprehensive immunogenicity data is a major challenge. We present T-SCAPE, a novel multi-domain deep learning framework that leverages adversarial domain adaptation to integrate diverse immunologically relevant data sources, including MHC presentation, peptide-MHC binding affinity, TCR-pMHC interaction, source organism information, and T-cell activation. Validated through rigorous leakage-controlled benchmarks, T-SCAPE demonstrates exceptional performance in predicting T-cell activation for specific peptide-MHC pairs. Remarkably, it also accurately predicts the ADA-inducing potential of therapeutic antibodies without requiring MHC inputs. This success is attributed to T-SCAPEs biologically grounded and data-driven multi-domain pretraining. Its consistent and robust performance highlights its potential to advance the development of safer and more effective vaccines and protein therapeutics.