Fig. 5: Spatial transcriptomics mapping of MS brain tissue.

a Overview of the study design. Multimodal data were imputed in each spot, including gene expression, definition of microenvironments/niches (unsupervised and/or manual clustering), snRNA-seq informed spot’s cell-type deconvolution, and ligand-receptor pair-based cell communication. Created in BioRender. Absinta, M. (2025) https://BioRender.com/d0hxq2g. b Pie chart showing the percentage of spots by anatomo-pathological niches (total number of spots = 45,335; Supplementary Data 4 for a detailed description of each sample and identification number). c Violin plots showing the number of gene counts by niches for each location and pathological stage. d Heatmap showing the deconvoluted cell-type proportion by niches (asterisks identify conditions with more than 15% of total deconvoluted cells). e Representative example of the comprehensive spatial transcriptomic analysis of a CAL (woman with progressive MS in her 40 s). By histology, CAL are demyelinated lesions with an inflammatory edge of MHCII⁺ myeloid cells. A 6.5-mm² of tissue (white square) was processed for spatial transcriptomics using the 10× Visium platform. Both manual and unsupervised clustering are shown. The unsupervised clustering identified transcriptional microenvironments (CAL edge, core, WM periplaque, and cortex; red spots) overlaid onto the LFB-stained tissue. These microenvironments are in line with the pathological tissue staging. f Enhanced spatial gene expression of SPP1, CHIT1, FTL, APOE, and C1QB that are the among top differentially expressed genes at the CAL edge. g Spatially-resolved microglia subclustering (red spots) after deconvolution of the snRNAseq dataset from Absinta et al.⁸ are overlaid onto the LFB-stained tissue. The previously described MIMS-iron and MIMS-foamy are microglia clusters located at the CAL edge. Stressed microglia are sparsely seen in the CAL core, edge, and periplaque. Homeostatic microglia are rarely located in the periplaque WM only. WM white matter, CAL chronic active lesion, CI chronic inactive lesion, LFB-PAS luxol fast blue-periodic acid-Schiff.