Extended Data Fig. 7: Thymus stroma compositional changes with transplantation, IL7R KO, and aging.
From: Mesenchymal thymic niche cells enable regeneration of the adult thymus and T cell immunity
(A) UMAP embedding showing stromal cell (Cd3e-, Cd4-, Cd8a-, Ptprc-) compositional differences between Control (n = 4, total number of stromal cells=5451), Transplantation (n = 3, total number of stromal cells=8057), IL7RKO (n = 4, total number of stromal cells=4551) and Aging (n = 4, total number of stromal cells=16178) samples. (B) Bar graphs comparing proportional shifts of different stromal cell subsets between Control, Transplantation, IL7RKO and Aging samples as determined by scRNAseq. (Control n = 4, Transplantation n = 3, IL7RKO n = 4, Aging n = 4, mean ± SEM). NCs were excluded from this analysis due to the populations small size (6.5 cells per sample in Controls). Statistical significance is using a two-sided Beta regression-based Wald test with Benjamini-Hochberg FDR control of these comparisons. EC: Control vs. Aged ** p = 7.1×10−3. PC: Control vs. IL7R KO ** p = 3.1×10−3, Control vs. Aged ** p = 1.7×10−3. vSMC: Control vs. Aged ** p = 6.0×10−3. (C) Dot plot showing expression of neural crest-like (NC) cell marker genes (rows) across different stress states (columns). Total number of NCs per condition noted in parenthesis. (D) Expression of marker genes defining mouse osteogenic smooth muscle cells (oSMC) presented as dot plot. (E) Bar graphs showing the difference in proportions within the MC population of Penk+ ThyMCs in Control, Transplantation, and Aging samples as determined by scRNAseq. (Control n = 4, Transplantation n = 3, Aging n = 4, mean ± SEM). Statistical significance is using a two-sided Beta regression-based Wald test with Benjamini-Hochberg FDR control of these comparisons. Control vs. Transplant **** p = 2.0×10−28, Control vs. Aged **** p = 3.0×10−8. (F) Bar graphs showing Postn and Ccl19 expression as determined by qPCR on sorted CD248- ThyMC 2 months and 22-27 months old mice (n = 4, mean ± SEM). Statistical significance was calculated by unpaired two-tailed student’s t-test. Postn: Control vs. Aged **p = 9.9×10−3. Ccl19: Control vs. Aged ** p = 8.4×10−3.
