Stage-Specific Gene Expression Profiles in Multiple Sclerosis Cortical Lesions Identified via Spatial Transcriptomics

Background and Objectives Multiple sclerosis (MS) is a chronic inflammatory disease characterized by demyelinating lesions in the central nervous system. While animal models have provided valuable insights into lesion development, human-based studies—particularly those focusing on gray matter—remain limited. This study aimed to investigate the molecular landscape of gray matter lesions at different stages of development using spatial transcriptomics. Methods We applied spatial transcriptomics to post-mortem cortical tissue from MS patients to examine gene expression within the spatial context of gray matter lesions. Seven fresh-frozen tissue blocks were analyzed: five from MS patients and two from neurologically healthy controls. Lesions were classified as early active, chronic active, or chronic inactive based on myelin integrity and macrophage/microglia activity. Results We identified distinct gene expression signatures across lesion stages. Early active lesions showed increased astrocytic and microglial activation, and enrichment of immune-related and tissue remodeling genes. Chronic active lesions exhibited sustained immune activation, extracellular matrix reorganization, and metabolic stress signatures. Chronic inactive lesions displayed low inflammatory activity, partial remyelination, and upregulation of stress response and repair-associated genes. Control samples showed preserved neuronal and myelin gene expression, with enrichment of synaptic and homeostatic processes. Conclusion These findings provide new insights into the molecular mechanisms underlying MS lesion progression. The gene expression profiles identified may serve as a valuable source of candidate biomarkers for future studies at both the gene and protein levels.