Multi-omics analysis reveals dynamic proteomic remodeling and metabonomic dysregulation underlying cytokine release syndrome in CAR-T-treated B-ALL.

CAR-T therapy has transformed B-cell acute lymphoblastic leukemia (B-ALL) treatment, but predictive biomarkers for efficacy and toxicity remain limited. Through liquid chromatography-tandem mass spectrometry (LC-MS/MS) profiling of 19 B-ALL patients across four treatment phases. Proteomic analysis revealed dynamic alterations in immune response, inflammatory regulation, complement activation, and cellular metabolism during treatment. Cytokine release syndrome (CRS)-associated differentially expressed proteins predominantly involved complement and coagulation cascades, cell adhesion molecules, and phagosome pathways. Metabonomic profiling demonstrated enrichment in taurine and hypotaurine metabolism, primary bile acid biosynthesis, and steroid hormone biosynthesis pathways during CAR-T therapy. Stage-specific metabolites of CRS revealed escalating arginine and proline metabolism dysregulation and nicotinate-nicotinamide metabolism activation, correlating with inflammatory escalation and multi-organ injury. Cox regression analysis was used to screen 6 protein [(SCRN2, OAF, SBSN, ERP44, TWF2 and ENSA) and 7 metabolic (pseudouridine, 3-methylglutarylcarnitine, 3-(2-hydroxyphenyl) propanoic acid, N-acetylthreonine, PC(18:1(9Z)/16:0), PE(P-18:0/20:4(5Z,8Z,11Z,14Z)), and Cer(d18:1/24:1(15Z)] markers, which showed good predictive ability and provided potential biomarkers for CRS monitoring and survival prediction.