Fig. 5

SuperMApo treatment reprograms macrophages among CD11b⁺ myeloid cells toward a pro-tolerogenic profile at the epigenetic level. a Gene expression (log2 FPKM transformed) ordered based on their fold change: i, in orange 357 genes with a change in expression of 1.5-fold or more, (ii, in light blue, 569 genes with a fold change of 0.67 or below, iiii, in red, 214 genes expressed only in CD11b⁺ cells from SuperMApo-treated mice and iv, in dark blue, 241 genes expressed only in CD11b⁺ cells from vehicle-treated mice. b Expression (log2 FPKM transformed, normalized, mean centered) of all 12,049 genes in mouse CD11b⁺ cells, clustered from lowest to highest fold change. c Network analysis of gene-ontology pathway enrichment on all 357 genes with a fold change of 1.5 or more and all 214 genes only expressed in CD11b⁺ cells from SuperMApo-treated mice with a P < 0.05. d Expression (log2 FPKM transformed, normalized, mean centered) of genes corresponding to selected pathways found in the network analysis enrichment on all 357 genes with a fold change of 1.5 or more and all 214 genes only expressed in CD11b⁺ cells from SuperMApo-treated mice. e Network analysis of gene-ontology pathway enrichment on all 569 genes with a fold change of 0.67 or below and all 241 genes only expressed in CD11b⁺ cells from vehicle-treated mice. f Expression (log2 FPKM transformed, normalized, mean centered) of selected genes corresponding to selected pathways found in the network analysis enrichment on all 569 genes with a fold change of 0.67 or below and all 241 genes only expressed in CD11b⁺ cells from vehicle-treated mice. Data obtained from 2 independent experiments from a pool of 5 mice per condition. g Total level of 5-methylcytosine observed in CD11b⁺ cells sorted from mice 72 h post-treatment. TET activity (h), de maintenance (i) and de novo (j) methyltransferase activity in CD11b⁺ cells from g. k TET conversion activity in respective CD11b⁺ cells. l Expression of miRNA-155, -127, -146a and -223 in CD11b⁺ cells from g. m Levels of methylation of genes coding for miR-223 (left) and miR-127 (right) in CD11b⁺ cells from g. n CTCF enrichment on region 1 of miR-127 promoter from g. Data pooled from three independent experiments expressed as mean ± sem, 5 mice per group. ** = p < 0.01, *** = p < 0.001, unpaired two-tailed Student’s t test