Extended Data Fig. 3: Gene expression programs delineate three ThyMC subsets in human and mouse.
From: Mesenchymal thymic niche cells enable regeneration of the adult thymus and T cell immunity
(A) Dot plots displaying genes differentially expressed across human and mouse thymic ThyMC subsets. (B) Expression of marker genes CD248, PENK, COL15A1, POSTN that define each ThyMC subtype in human (left) and mouse (right). Presented as UMAP embeddings and bar graphs displaying expression in each cell type. Statistical significance is based on a two-sided DESeq2-based Wald test with Benjamini-Hochberg FDR control of these comparisons. (human n = 3, mouse n = 4, mean ± SEM). Human samples: CD248 CD248+ ThyMC vs. POSTN+ ThyMC **** p = 1.6×10−16. CD248+ ThyMC vs. COL15A1+ ThyMC **** p = 5.5×10−7. COL15A1 COL15A1+ ThyMC vs. POSTN+ ThyMC **** p = 3.2×10−16. COL15A1+ ThyMC vs. CD248+ ThyMC **** p = 1.1×10−16. POSTN POSTN+ ThyMC vs. COL15A1+ ThyMC **** p = 4.6×10−13. Mouse samples: Cd248 Cd248+ ThyMC vs. Postn+ ThyMC **** p = 7.9×10−36. Cd248+ ThyMC vs. Penk+ ThyMC **** p = 1.9×10−17. Penk Penk+ ThyMC vs. Cd248+ ThyMC *** p = 3.3×10−4. Penk+ ThyMC vs. Postn+ ThyMC * p = 1.9×10−2. Postn Postn+ ThyMC vs. Penk+ ThyMC **** p = 2.7×10−5. Postn+ ThyMC vs. Cd248+ ThyMC **** p = 1.9×10−11. (C) Normalized enrichment score for GSEA pathways specific to mouse Postn+ ThyMC presented as UMAP. (D) Expression of Ccl19, Flt3l, and Il15 across ThyMC subsets and other stromal cell types. (n = 4, mean ± SEM). Statistical significance is based on a two-sided DESeq2-based Wald test with Benjamini-Hochberg FDR control of these comparisons. Ccl19: Postn+ ThyMC vs. EC **** 1.49×10−8, Postn+ ThyMC vs. Cd248+ ThyMC **** p = 7.2×10−10, Postn+ ThyMC vs. vSMC **** p = 6.8×10−8, Postn+ ThyMC vs. PC ** p = 6.9×10−3, Postn+ ThyMC vs. Lrrn4+ **** p = 5.8×10−6, Postn+ ThyMC vs. Tuft cells **** p = 1.5×10−8. Flt3l: Postn+ ThyMC vs. EC **** p = 1.1×10−5, Postn+ ThyMC vs. Cd248+ ThyMC **** p = 2.6×10−6, Postn+ ThyMC vs. Penk+ ThyMC ** p = 6.9×10−3, Postn+ ThyMC vs. vSMC **** p = 5.6×10−6, Postn+ ThyMC vs. PC ** p = 5.0×10−3, Postn+ ThyMC vs. Lrrn4+ ** p = 2.4×10−3, Postn+ ThyMC vs. cTEC/mTECi **** p = 7.6×10−8, Postn+ ThyMC vs. mTECm ****p = 3.8×10−4, Postn+ ThyMC vs. Tuft cells ****p = 3.5×10−5. Il15 Postn+ ThyMC vs. Cd248+ ThyMC **** p = 1.1×10−9, Postn+ ThyMC vs. Penk+ ThyMC **** p = 3.7×10−5, Postn+ ThyMC vs. vSMC *** p = 9.3×10−4, Postn+ ThyMC vs. PC * p = 1.2×10−2, Postn+ ThyMC vs. Lrrn4+ *** p = 2.6×10−3, Postn+ ThyMC vs. cTEC/mTECi *** p = 4.3×10−4. Postn+ ThyMC vs. Tuft cells ****p = 1.6×10−4.
