Extended Data Fig. 3: Cortical neuron and lymphocyte subtype analysis in MS lesions.

a, t-SNE plots for neuron subtype specific expression of RORB, THY1, NRGN, SST, SV2C and PVALB (left). LAST (control, n = 5) showing layer-specific expression of neuronal RORB in intermediate cortical layer 4 and widespread expression of pyramidal neuron marker THY1 with enrichment in layer 5; note that SST-expressing INs preferentially map to deep-cortical layers. Co-expression studies (control, n = 5) with SYT1 confirm neuronal expression of RORB, THY1 and SST (black arrowheads). b, Heat map with hierarchical clustering of lymphocyte-associated transcripts allowing subclustering of lymphocytes in T cells, B cells and plasma cells based on marker gene expression (top left). t-SNE plots for typical B cell (plasma cell) and T cell marker genes enriched in lymphocyte clusters (top right). Immunohistochemistry for T cell adapter protein SKAP1 (black arrowheads mark SKAP1⁺ T cells) together with spatial transcriptomics for B-cell-associated IGHG1 encoding immunoglobulin G1 (IgG1) (magenta arrowheads; bottom left); note increased expression of the plasma cell-associated marker gene MZB1 (top left) and preferential enrichment of MZB1⁺ and IGHG1-expressing plasma cells (white arrowheads, bottom right) in inflamed meningeal tissue versus mixed T and B cell infiltration in perivascular cuffs of subcortical lesions (bottom). One caveat to these findings is the relatively small number of MS tissue samples, which limited our ability to cluster T cell populations. For t-SNE plots (a, b) and hierarchical clustering (b), data are shown from 9 control and 12 MS samples. For t-SNE plots, data shown for all 48,919 nuclei; for hierarchical clustering, data are shown from 53 nuclei in the B cell cluster. For in situ hybridization and immunohistochemistry experiments in b, representative images shown from individual tissue sections (control, n = 4; MS, n = 7).