Multi-omics profiling identifies a metabolic and energetic signature associated with neuronal dENL/AF9 suppression in aged flies

Abstract Maintenance of neuronal function during aging requires metabolic adaptation, yet how metabolite-sensitive chromatin regulators contribute to this process remains unclear. YEATS-domain proteins, including ENL and AF9, recognize histone acylation marks and are positioned at the interface between cellular metabolism and transcriptional regulation. We previously showed that pan-neuronal suppression of dENL/AF9 , the single Drosophila orthologue of mammalian ENL and AF9, extends lifespan, preserves healthspan, and enhances oxidative-stress resistance. Here, we used multi-omics and biochemical analyses to define the molecular state associated with neuronal dENL/AF9 suppression. Transcriptomic profiling revealed a markedly stronger response in aged than young male fly heads, with prominent enrichment of fatty-acid degradation and several intermediary metabolic pathways in the aged dataset. Guided by this age-related transcriptional response, we focused subsequent profiling on aged heads, where independent molecular layers converged on a distinct metabolic and energetic signature. Lipidomics identified reduced abundance of multiple triglyceride-related and fatty acid derivatives, while metabolomics revealed changes in central-carbon/TCA-, nicotinamide-, and purine-associated features. Proteomics implicated mitochondrial and ATP-associated processes, accompanied by increased ATP abundance and a higher NAD/NADH ratio. Matched lipidome-metabolome integration further identified citrate as a cross-omics feature inversely associated with altered triglyceride and ceramide species, linking central-carbon and lipid-associated components of the molecular signature. Together, these findings identify a stronger transcriptional response to neuronal dENL/AF9 suppression in aged flies and a distinct metabolic and energetic molecular signature in aged fly heads, providing candidate molecular correlates of the previously established longevity phenotype and a framework for studies of neuronal aging biology. Graphical abstract