An atlas of transcriptomic changes in human immune cells driven by 364 endogenous and gut-microbiota-derived metabolites

Metabolites, particularly those derived from gut microbiota, play crucial roles in modulating immune responses, but the impact of most metabolites on immune cells remains unexplored. To systematically investigate the effect of metabolites on immune cells, we treated peripheral blood mononuclear cells (PBMCs) with 364 endogenous and gut microbiota metabolites and analyzed their impact on the PBMC transcriptome using RNA sequencing (RNA-seq). Clustering analysis revealed three distinct metabolite groups (Cluster 0, 1, 2), each exerting unique immunomodulatory effects. Cluster 1 metabolites, enhanced inflammatory pathways (e.g., cytokine signaling, neutrophil migration) and suppressed ferroptosis, potentially prolonging immune cell activity. In contrast, Cluster 0 metabolites promoted antigen presentation and extracellular matrix repair, while Cluster 2 metabolites upregulated autophagy-related pathways (e.g., GTPase signaling, ubiquitin-protein regulation), suggesting anti-inflammatory and tissue-homeostatic functions. Immune deconvolution highlighted Cluster 1-driven monocyte-to-M0 macrophage differentiation and elevated activated dendritic/mast cells, aligning with pro-inflammatory outcomes. Metabolites in Clusters 0/2 were enriched in the TCA cycle and alanine/aspartate metabolism, whereas Cluster 1 metabolites correlated with beta-alanine and branched-chain amino acid pathways. Gut microbiota analysis identified 23 species overrepresented in Cluster 1, linking dysbiosis to inflammatory metabolite profiles. Together, this high-throughput atlas elucidates how bloodborne metabolites shape PBMC function, offering insights into metabolic-immune crosstalk and potential therapeutic targets for inflammatory and autoimmune disorders.