Figure 6.
Donor-derived macrophages remain a transcriptionally and functionally distinct cell type in the CNS. (A) Schematic of transplantation regime for the identification of donor macrophages and host microglia. Lethally irradiated DBA2xF1.Csf1r-eGFP (H2b/d) mice received 5 × 106 TCD BM with no T cells or with 0.5 × 106 CD3+ T cells from C57Bl/6.Csf1r-mApple (H2b) donors to induce low-grade nonlethal cGVHD. (B) Heatmap of log2 counts-per-million (logCPM) values for differentially expressed genes (false discovery rate, <0.05) from bulk RNA-seq analysis of sort-purified infiltrating donor BMDMs compared with host microglia from GVHD brains at day 80 after transplant. Expression across each gene has been scaled so that mean expression is 0 and standard deviation is 1. Plotted alongside is the z score of the same genes from TCD host microglia (GVHD donor, n = 6; GVHD host, n = 4; TCD host, n = 3). (C) Heatmap of logCPM values from RNA-seq analysis data showing expression of genes related to characteristic cellular markers of GVHD donor BMDMs, GVHD host microglia, and TCD host microglia. Color key also applicable to panels E and G. (D) Representative histograms and enumeration of the mean fluorescence intensity of characteristic markers CX3CR1 and P2RY12 on donor BMDMs and host microglia at day 70 (n = 6 mice per group). (E) Dot plot of Gene Ontology terms from the Biological Process ontology enriched in GVHD donor BMDMs compared with GVHD host microglia. (F) Heatmap based on RNA-seq analysis data showing differentially expressed genes related to extracellular matrix (ECM) degradation and the CD300 family in GVHD donor BMDMs, GVHD host microglia, and TCD host microglia. (G) Differentially expressed genes related to IFN-γ signaling, response, and induction in GVHD donor BMDMs and host microglia from GVHD and TCD mice. (H) LogCPM values for selected cytokines from isolated cell populations in panel B. Data presented as mean ± standard error of the mean. Statistical analysis performed with unpaired Student t test (D) or using the glmLRT() function in R for all possible group comparisons (H). **P < .01, ****P < .0001.

Donor-derived macrophages remain a transcriptionally and functionally distinct cell type in the CNS. (A) Schematic of transplantation regime for the identification of donor macrophages and host microglia. Lethally irradiated DBA2xF1.Csf1r-eGFP (H2b/d) mice received 5 × 106 TCD BM with no T cells or with 0.5 × 106 CD3+ T cells from C57Bl/6.Csf1r-mApple (H2b) donors to induce low-grade nonlethal cGVHD. (B) Heatmap of log2 counts-per-million (logCPM) values for differentially expressed genes (false discovery rate, <0.05) from bulk RNA-seq analysis of sort-purified infiltrating donor BMDMs compared with host microglia from GVHD brains at day 80 after transplant. Expression across each gene has been scaled so that mean expression is 0 and standard deviation is 1. Plotted alongside is the z score of the same genes from TCD host microglia (GVHD donor, n = 6; GVHD host, n = 4; TCD host, n = 3). (C) Heatmap of logCPM values from RNA-seq analysis data showing expression of genes related to characteristic cellular markers of GVHD donor BMDMs, GVHD host microglia, and TCD host microglia. Color key also applicable to panels E and G. (D) Representative histograms and enumeration of the mean fluorescence intensity of characteristic markers CX3CR1 and P2RY12 on donor BMDMs and host microglia at day 70 (n = 6 mice per group). (E) Dot plot of Gene Ontology terms from the Biological Process ontology enriched in GVHD donor BMDMs compared with GVHD host microglia. (F) Heatmap based on RNA-seq analysis data showing differentially expressed genes related to extracellular matrix (ECM) degradation and the CD300 family in GVHD donor BMDMs, GVHD host microglia, and TCD host microglia. (G) Differentially expressed genes related to IFN-γ signaling, response, and induction in GVHD donor BMDMs and host microglia from GVHD and TCD mice. (H) LogCPM values for selected cytokines from isolated cell populations in panel B. Data presented as mean ± standard error of the mean. Statistical analysis performed with unpaired Student t test (D) or using the glmLRT() function in R for all possible group comparisons (H). **P < .01, ****P < .0001.

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