FL macrophage function is impaired in Mrc1 ^Cre Xpr1 ^fl/fl embryos. (A) Representative flow cytometry plots and frequencies (mean ± SD) of liver macrophages extracted from E15.5 Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl embryos (pre-gated on CD45⁺Lin⁻ cells). n = 11 per group, pooled from three independent experiments. Statistical analysis was performed using the Student’s t test. (B) Graphs showing Xpr1 expression in sorted macrophages (CD45⁺F4/80⁺), endothelial cells (CD45⁻CD31⁺), and monocytes (CD11b⁺Ly6C^hiCD64⁺) extracted from livers of E15.5 Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl embryos. n = 3–11 per group. Statistical analysis was performed using the Student’s t test. (C) Immunohistochemistry of E15.5 Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl livers and corresponding quantification of pyrenocyte-containing CD64⁺ cells. Insets show magnification of the outlined regions and expression of DAPI (white) and CD64 (green). Yellow arrows point to CD64⁺ cells containing pyrenocytes. Images are representative of at least five embryos per group. n = 5–7 per group, pooled from three independent experiments. Scale bars are 500 µm. Statistical analysis was performed using the Student’s t test. (D) Graph showing Dnase2a expression in sorted macrophages from livers of E15.5 Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl embryos. Data shown are n = 4 samples per group. Statistical analysis was performed using the Student’s t test. (E–H) RNA-seq data of CD11b^intF4/80⁺ FL macrophages sorted from E15.5 Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl embryos. n = 4–5 samples per group. (E) PCA of Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl FL macrophages. Percentages shown indicate the proportion of variance explained by PC1 and PC2. (F) Volcano plot of DEGs between Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl FL macrophages. (G) Heatmap of core KC-gene signature from Bonnardel et al. (2019) applied to the RNA-seq data of Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl FL macrophages. (H) Heatmap of the top 50 EBI-Mac genes (Li et al., 2019) applied to the RNA-seq data of Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl FL macrophages. (I) Representative flow cytometry plots, frequencies, and numbers (mean ± SD) of liver macrophages from adult Xpr1^fl/fl and Mrc1^CreXpr1^fl/fl mice (pre-gated on Live CD45⁺Lin⁻ cells). Data show n = 7–8 per group and are pooled from three independent experiments. Statistical analysis was performed using the Student’s t test. *P < 0.05, **P < 0.01, and ****P < 0.0001. ns, not significant.