Extended Data Fig. 5. DNMT3A mediates efferocytosis and resolution in vivo. Related to Fig. 6. a.

BMDMs were pretreated with vehicle or a TGFβ1R inhibitor for 2 h and with vehicle or recombinant TGFβ1 for 1 h, as indicated. The macrophages were then incubated with PKH26-labeled ACs for 45 mins, followed by rinsing and quantification of percent PKH26-AC⁺ macrophages of total macrophages, n=4 biological replicates. b-f, Wildtype (WT) C57BL/6J mice were transplanted with bone marrow from control or H-DNMT3A-KO mice and, after 4 weeks, injected with PBS or dexamethasone (DEX). After 18 h, the thymi were weighed, n= 7 and 9 mice for PBS and DEX groups respectively (b); immunostained for DAPI, TUNEL, and Mac2 (c); assayed for F4/80⁺ cells, n=5 mice per group (d); and assayed for TNF-a, n=3 and 5 mice for PBS and DEX groups respectively and IL-6 by ELISA, n=3 and 4 mice for PBS and DEX groups respectively (e-f). The image in b illustrates thymic macrophages with cytoplasmic TUNEL as an example of efferocytosing thymic macrophages. Scale bar, 100 μm. g, The peritoneal exudates were assayed for Ly6G⁺ polymorphonuclear cells (PMN) 18 hours after Zymosan A1 injection, n=3 mice per group. h, Wild-type mice received 200 ng/mL recombinant TGFβ1 i.p. or vehicle control 15 and 20 hours after Zymosan injection and then assayed for the number of PMNs 4 hours later, n=3 mice/group. i, Ldlr^−/− (LDLR-KO) mice were transplanted with bone marrow from control or H-DNMT3A-KO mice and, after 4 weeks, fed a western-type diet (WD) for 12 weeks. Aortic root sections were quantified for lesional area, n=8 mice/group. Values are means ± SEM; n.s., not significant (P > 0.05). Two-sided P values were determined by the Student’s t-test for two groups or one-way ANOVA with Fisher’s LSD posthoc analysis for three or more groups.