Gene Program Negotiation Defines Cellular Identity in Single-Cell Transcriptomes

Abstract

Single-cell transcriptomics has transformed the characterization of cellular heterogeneity by enabling systematic analysis of biological gene programs. However, existing computational approaches primarily quantify the activity of individual programs independently and therefore provide limited insight into how multiple simultaneously active programs collectively determine cellular identity. Here we present Gene Program Negotiation (GPN), a graph-based computational framework that models regulatory decision-making among concurrently active biological programs. GPN reconstructs cell-specific program interaction networks from local transcriptional neighborhoods and quantifies regulatory organization using the Gene Program Coherence Index (GPCI) together with measures of local regulatory conflict, program diversity, and dominance. These graph-derived properties enable the classification of individual cells into five regulatory decision states: Consensus, Competition, Negotiation, Dominance, and Low activity. Applying GPN to gastric cancer single-cell transcriptomes revealed that cells sharing the same dominant biological program frequently occupied distinct regulatory decision states, demonstrating that dominant program identity alone does not uniquely define cellular regulatory organization. Competition states consistently exhibited elevated local regulatory conflict and were preferentially enriched among transition-like cells, indicating that regulatory competition is closely associated with transcriptional plasticity. Independent validation using glioblastoma single-cell transcriptomes reproduced these regulatory patterns without modification of the computational framework, supporting the robustness and generalizability of the approach across biologically distinct malignancies. These findings establish regulatory negotiation as an additional layer of cellular organization beyond conventional gene-program activity analysis. By explicitly modeling interactions among simultaneously active biological programs, GPN provides a general computational framework for investigating regulatory coordination, cellular plasticity, and dynamic cell-state organization in single-cell transcriptomic data.