Transcription factor-driven metabolic stratification reveals glycolytic and lipogenic subtypes with distinct prognostic and functional features in pancreatic cancer

Abstract

Pancreatic ductal adenocarcinoma (PDAC) exhibits profound molecular and metabolic heterogeneity associated with distinct phenotypic states. However, the contribution of transcription factor (TF)-driven regulatory programs to metabolic subtype stratification remains poorly understood. This study aims to determine whether TF-based classification can identify prognostically relevant glycolytic and lipogenic PDAC subtypes. Bulk transcriptomic data from multiple PDAC cohorts and single-cell RNA sequencing data were integrated to characterize TF-associated metabolic heterogeneity. Metabolic signatures and TFs were quantified using single-sample gene set enrichment analysis (ssGSEA) and AddModule Score (AMS). Differential expression, enrichment analysis, integrative bulk and single-cell transcriptomic analysis, and deep neural network-based metabolic flux modeling were performed to investigate metabolic programs and functional differences between TF-defined subtypes. Additionally, RNA interference, RT-qPCR, lipid droplets staining, lactate assay, and transwell assays were used to evaluate the roles of TP63 in metabolic regulation. Glycolytic and lipogenic TF-defined metabolic subtypes were identified across multiple independent PDAC cohorts. These subtypes exhibited distinct metabolic programs, differentiation states, and prognostic outcomes. The glycolytic TF-defined subtype was associated with worse prognosis and differentiation, whereas the lipogenic TF-defined subtype exhibited more favorable clinical features. Integration of public bulk and single-cell transcriptomic analyses, together with deep neural network-based metabolic flux modeling, revealed consistent metabolic heterogeneity at both cellular and functional levels. Notably, TP63 was identified as a potential regulator of glycolytic-lipogenic metabolic reprogramming in PDAC. TF-based classification delineates glycolytic and lipogenic subtypes in PDAC, underscoring the critical role of TF-regulated metabolic programs in patient stratification. These findings highlight the prognostic significance of glycolytic and lipogenic metabolic heterogeneity and support the development of metabolism-targeted therapeutic strategies.