Fig 1: NOD2 limits thymus regeneration by inhibiting the production of regenerative factors(A and B) Thymuses were pooled from 6-week-old C57BL/6 mice, and transcriptome analysis was performed on fluorescence-activated cell sorting (FACS)-purified ECs (A) or DCs (B) isolated from either untreated mice (d0) or 4 days after TBI (550 cGy, d0, n = 3; d4, n = 2; each n pooled from 5 mice). (A) Gene ontology (GO) pathway analysis was performed on upregulated genes in ECs at day 4 after SL-TBI using DAVID, and the top-ten pathways by FDR are displayed. Red bars represent pathways involved with immune function; dashed line at p = 0.05. Top-ten genes in ECs are shown by frequency of representation among all GO pathways with an FDR <0.05. (B) Gene ontology (GO) pathway analysis was performed on upregulated genes in DCs at day 4 after SL-TBI using DAVID, and the top-ten pathways by FDR are displayed. Red bars represent pathways involved with immune function; dashed line at p = 0.05. Top-ten genes in DCs are shown by frequency of representation among all GO pathways with an FDR <0.05.(C–I) 6- to 8-week C57BL/6 WT or Nod2-/- mice were given a sublethal dose of TBI (550 cGy), and the thymus was harvested and analyzed at the indicated time points. (C) Total thymic amounts of BMP4, IL-23, and IL-22 were assessed by ELISA at day 7 after SL-TBI (n = 4/group from a representative experiment of at least two independent experiments). (D) Total thymic cellularity at days 7 and 14 after SL-TBI (d7, n = 11–15; d14, n = 6–10; combined from two independent experiments). (E) Concatenated flow plots showing CD4 and CD8 expression at days 7 and 14 after SL-TBI. (F) Total number of CD4+CD8+ DP, CD4+CD3+ SP4, or CD3+CD8+ SP8 thymocytes (d7, n = 11–15; d14, n = 6–10; combined from two independent experiments). (G) Number of CD45+MHCII+CD11c+CD103+ cDC1 and CD45-EpCAM-CD31+PDGFRa- ECs at day 7 after SL-TBI (n = 11–15/group across two independent experiments). (H) Number of CD45–EpCAM+MHCII+UEA1loLy51hi cTECs and CD45-EpCAM+MH-CII+UEA1hiLy51lo mTECs at day 7 after SL-TBI (n = 11–15/group across two independent experiments). (I) Total thymic cellularity and absolute number of thymocyte subsets at day 150 after SL-TBI (n = 3–5). Graphs represent mean ± SEM; each dot represents a biologically independent observation. See also Figures S1 and S2.