Fig. 3: Distinct late fibroblast states include lymphocyte-interactive fibroblasts associated with T cell persistence.

a, Fibroblast cluster abundance over time, with corresponding early and late spatial signatures. b, Co-expression of pial, arachnoid and dural genes³⁵ among corresponding clusters. c, snRNA-seq signatures of meningeal fibroblast subsets mapped onto spatial transcriptomic data. d,e, Fluorescence microscopy (d) and cartoon (e) of late fibroblast subset topography and protein expression. Scale bars: 500 μm (main images), 100 μm (enlarged views). f, Gene set enrichment analysis among lymphocyte-interactive fibroblasts. g, Heat map of chemokines expressed in ≥0.5% of any cluster; lymphocyte-interactive fibroblasts are highlighted (blue). h–j, Total T cells (h; CD3ε⁺), CD4⁺ and CD8⁺ T cells (i) and or T_H1 (TBET⁺), T helper type 2 (T_H2; GATA3⁺) and T helper type 17 (T_H17; RORγt⁺) CD4⁺ T cells (j; 14 dpi) after PT injury (cortical flow cytometry). Rest: n = 5, contralateral: n = 46, 7 dpi: n = 6, 14 dpi: n = 38, 21 dpi: n = 18, 60 dpi: n = 11 mice (h); n = 18 mice per time point (i); n = 15 mice (j). k,l, Native microscopy (k; 21 dpi) and time course of T cell surfaces (l; Cd4^cre; Rosa26^tdT+; Cd3e⁺) near fibroblast-rich lesions (ER-TR7⁺). Scale bars: 50 μm (k), 500 μm (l). m, Schematic of proximity analysis between T cells (CD4^cre; Rosa26^tdT+; Cd3e⁺) or myeloid cells (IBA1^hi, macrophages and reactive microglia) and fibroblast ECM (ER-TR7) or astrocytes (GFAP). n,o, Median T cell distance from nearest fibroblast ECM or astrocyte surface (n) and T cell or myeloid cell distance from nearest fibroblast surface (o). 21 and 60 dpi. n = 5 mice per time point (2 slices per mouse; lighter green or grey dots and P values represent tissue slices; darker dots and P values are per mouse). p,q, Image (p; 21 dpi) and quantification (q) of T cell proximity to CD80⁺ lymphocyte-interactive fibroblasts at 14, 21 and 60 dpi. n = 5 mice per time point (2 slices per mouse). Scale bar, 50 μm. r,s, Schematic for ex vivo lesional coculture (r) and quantification of T cell survival (s; 21 dpi lesions). Alone: n = 36, contralateral: n = 34, 21 dpi lesion: n = 44, beads: n = 33 wells. t, T cell survival after coculture with dural or lung fibroblasts. T cells alone (T alone): n = 3, T cells plus meningeal fibroblasts (men. fib.): n = 3, lung: n = 4 wells. Over-representation test (one-sided Fisher’s exact test, FDR-adjusted) (f); one-way ANOVA, Tukey post-test (h,q,s,t); multiple two-way t-tests, Holm–Sidak correction (i; paired per point, unpaired per slice (n,o)); one-way repeated-measures ANOVA, Tukey post-test (j). Slice thickness, 14 μm. Images represent two or more mice.

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