Nucleic acid turnover and lipid remodeling distinguish T cell activation and exhaustion states via label-free Raman spectroscopy

Abstract

T cell exhaustion impairs immune control of chronic diseases including tuberculosis, HIV, malaria, and cancer. Its clinical implications are vast, predicting HIV-associated malignancy and treatment response and limiting the efficacy of cell therapies. Despite the advantages of monitoring and removing exhausted T cells, current detection methods require expensive antibody labeling, destructive workflows, or days-long functional assays. Here, we introduce Raman spectroscopy as a label-free assay for distinguishing T cell states directly from culture while preserving viability for downstream use. We achieve >97% accuracy in discriminating unstimulated, activated, and exhausted T cells across three donors and multiple hardware setups. We identify vibrational modes associated with nucleic acid turnover and lipid remodeling as key features that distinguish T cell activation and exhaustion. In heterogeneous populations, we quantify exhaustion percentage with R2= 1 and strong correlation to adenine (r= -0.91) and amide II protein (r= 0.94) vibrational modes. This work establishes vibrational fingerprinting as a direct measure of T cell exhaustion beyond surface marker expression towards scalable immune diagnostics, in-line monitoring, and selective immunopheresis.