Transcriptomic features associated with tumoral metabolites characterizing the immune microenvironment in clear cell renal cell carcinoma

Abstract: Objectives: Previous studies have demonstrated that the metabolic milieu plays a pivotal role in shaping the immunological landscape of cancer tissues. This study aimed to characterize the immune microenvironment of clear cell renal cell carcinoma (ccRCC) in relation to intratumoral metabolite levels. Methods: Metabolomic and transcriptomic analyses were performed on frozen tumor samples and their paired formalin-fixed paraffin-embedded (FFPE) specimens from 31 ccRCC surgical cases. Five metabolites previously implicated in immune modulation-lactate, glutamine, adenosine, arginine, and tryptophan-were quantified and compared against transcriptomic profiles using pre-ranked gene set enrichment analysis (GSEA). The analysis incorporated hallmark gene sets (h.all.v2025.1.Hs.symbols) and immune-related gene sets (c7.immunesigdb.v2025.1.Hs.symbols). Results: Lactate levels positively correlated with gene sets related to glycolysis , hypoxia , interferon gamma response , and unfolded protein response , as well as immune signatures derived from monocytes and dendritic cells stimulated by influenza A virus and HPV antigens. Negative correlations were observed with mitotic spindle and oxidative phosphorylation pathways. Glutamine showed positive associations with glycolysis , RORgammat-deficient CD4+ T cells under Th17-polarizing conditions , SPHK1 knockout inflammatory responses , and type I interferon-treated endothelial cells , while negatively correlating with coagulation . Adenosine was positively linked to glycolysis , hypoxia , xenobiotic metabolism , mTORC1 signaling , and reactive oxygen species pathways , as well as immune signatures involving memory CD4+ T cells, IL-4 stimulation, and monocyte activation. Negative correlations included mitotic spindle , FOXP3-mutant Tconv cells , and plasmacytoid dendritic cell responses . Arginine was positively associated with gene sets reflecting monocyte culture dynamics, memory CD8+ T cell differentiation, and thymocyte maturation. Conclusions: These findings highlight distinct transcriptomic programs associated with specific metabolites in ccRCC, suggesting that intratumoral metabolic states-particularly elevated lactate and adenosine-are linked to immunosuppressive and inflammatory transcriptional profiles. The enrichment of immune gene sets derived from viral stimulation contexts implies that tumor metabolism may mimic or modulate immune activation pathways typically seen in infection. Overall, this integrative metabolomic-transcriptomic approach provides insight into how metabolic reprogramming in ccRCC contributes to shaping the immune microenvironment, with potential implications for immunotherapeutic strategies and metabolic targeting.