Fig. 4: IL-12 signaling promotes neuronal survival, homeostasis and trophic support to oligodendrocytes in the inflamed murine CNS.

Nuclei were isolated from pooled cerebellum, brainstem (dissected from one brain hemisphere) and cervical spinal cord from Il12rb2^fl/fl and Nestin^Cre/+Il12rb2^fl/fl male mice (n = 4 per genotype) at the onset of EAE (10 d.p.i.). Nuclei were lysed, purified by FANS selecting for the Hoechst⁺ fraction and used for snRNA-seq. a, snRNA-seq clustering of 133,151 nuclei by cell type labeled on the basis of known lineage markers and visualized as a UMAP. Each dot corresponds to a single nucleus and each color to a cell-type cluster. b–d, Mean frequencies of cell clusters (b), average fold change of cluster abundance (c) and number of DEGs per cluster (d) between Nestin^Cre/+Il12rb2^fl/fl and Il12rb2^fl/fl mice. e,f, Dot plots showing differential expression of hallmark genes across neurons and oligodendrocytes. Dot size indicates significance and color indicates log fold change between Nestin^Cre/+Il12rb2^fl/fl and Il12rb2^fl/fl mice in the respective cell types. g,h, Average fold change of manually selected gene signatures for hyperinflammation and neuroprotection (Supplementary Table 2) between Nestin^Cre/+Il12rb2^fl/fl and Il12rb2^fl/fl mice across cell types. i, Schematic of the receptor–ligand interaction analysis (NicheNet; created with BioRender.com). Senders were defined by their ability to sense IL-12 (expression of Il12rb1 and/or Il12rb2 transcripts) and the magnitude of their differential gene expression (cutoff > 35 DEGs). Both autocrine and paracrine ligand–receptor interactions were considered. j, Circos plots showing links between unique ligands from senders (ribbon color indicates subcluster of origin for each ligand; multiple sender cells are indicated by black ribbon) and predicted associated DEGs in granule cells. Transparency indicates interaction strength, and the ribbon thickness is proportional to the ligand’s regulatory potential. Heatmap (right) displaying potential receptors expressed in granule cells associated with each predicted ligand. Differential gene expression in e–h was tested using a two-sided Wilcoxon rank-sum test and applying a Benjamini–Hochberg correction and is presented in Supplementary Table 1. OPC, oligodendrocyte progenitor cell; VLMC, vascular and leptomeningeal cell. UBC, unipolar brush cells.