Mesenchymal niche alterations in adult Lama4^−/− mouse BM. BM MSCs, MPCs, and ECs from 3 to 4 month-old Lama4^+/+ and Lama4^−/− mice were analyzed. Data are from 3 to 7 independent experiments. (A) A representative FACS profiles showing gating strategy for sorting the MSCs, MPCs, and ECs. (B) Frequency of MSCs, MPCs, and ECs within total BM MNCs at steady-state. (C) CFU-Fs in BM of Lama4^+/+ and Lama4^−/− mice during steady-state and postirradiation (IR). (D-E) Q-PCR of HSC niche factors in Lama4^+/+ and Lama4^−/− BM MSCs, MPCs, and ECs at steady-state (D) and 6 weeks after sublethal irradiation (E). Data are mean ± SD from 3 independent experiments. (F) Volcano plot showing adjusted P value (padj) vs log₂fold changes [Log2(FC)] of each gene tested between Lama4^−/− and Lama4^+/+ BM MPCs from RNA sequencing data. The MPCs were sorted from Lama4^+/+ and Lama4^−/− mice at 6 weeks post–sublethal irradiation. Genes with padj <0.05 and Log2(FC) >1 are partly highlighted and annotated. (G) GSEA reveals the gene sets enriched in Lama4^+/+ and Lama4^−/− BM MPCs. False discovery rate (FDR)-q value (adjusted P value) and gene set sizes are indicated by the red color and the size of the circles. NES, Normalized enrichment scores. (H) Relative expression of the genes of ECM molecules and inflammatory cytokines in the Lama4^−/− BM MPCs compared with Lama4^+/+ MPCs 6 weeks post–sublethal irradiation. The P values in the panels were determined by unpaired 1-tailed or 2-tailed parametric Student t test depending on the data distribution. See also supplemental Figures 7-9.