Fig. 4: Signalling pathways active during positive selection of T cells.

a The heatmap shows the normalised enrichment of the signalling pathways that are active within the cortical niches across the thymus ages. b The dot plot shows the gene expression of selected ligands and receptors in the cell types found in scRNA-seq data. c Spatial co-localisation of the LRP1 and MDK and the cell type involved, like fibroblasts, is marked by COL1A1 in the fetal 17w thymus. d The spatial co-localisation of CXCL12, CXCR4, and the cell type involved, like cTECs, is marked by PRSS16. e Immunostaining of human thymic slides (P:1 y) revealed cortical enrichment of CXCL12/CXCR4 pathway. Co-staining of CXCL12 and CXCR4 showed preferential expression in cortex rather than in medulla. Two representative regions are shown from four independent regions. f Immunostaining of human thymic slides (P:7w) revealed co-expression of Col-I (fibroblast marker) and CXCL12, especially at the capsule layer, as indicated by white arrows, thus supporting cortical fibroblasts as another source for CXCL12 in cortex. Two representative regions were shown from three independent regions. g Immunostaining of human thymic slides (P:1 yr) showed co-expression between PSMB11 (cTEC marker) and CXCL12, as indicated by white arrows, thus supporting cTECs as a source for CXCL12 in cortex. Two representative regions are shown from three independent regions. h Immunostaining of human thymic slides (P:1 yr) of T cell marker CD3 with CXCR4 showed their co-expression, supporting T cells as a source for CXCR4 in cortex. Two representative regions are shown from three independent regions. F fetal, P paediatric.