Efferocytosis activates a DNMT3A-mediated oxidized DNA repair pathway to enable tissue resolution

Efferocytosis, the clearance of apoptotic cells by macrophages, promotes tissue resolution. Efficient resolution requires efferocytosis-induced macrophage proliferation (EIMP) to expand pro-resolving macrophages. Here, we show that efferocytosis activates base excision repair (BER) to remove 8-OHdG from DNA, enabling EIMP. Mechanistically, efferocytosis promotes poly(ADP-ribose) polymerase 1 (PARP1) chromatin binding and PARylation to facilitate DNA repair complex assembly and increases nuclear MutT homolog 1 (MTH1) (gene NUDT1), which hydrolyzes 8-OHdG. Both processes require DNA-methyltransferase-3A (DNMT3A), which is activated during efferocytosis. Using a model in which dexamethasone-induced thymocyte apoptosis triggers efferocytosis-mediated thymic repair, we showed that DNMT3A was required for increases in nuclear PARP1/MTH1, oxidized DNA suppression, EIMP in thymic macrophages, and thymic repair. We next studied a human-relevant model of atherosclerosis regression, whereby efferocytosis drove protective lesional fibrous cap thickening. We compared WT mice with a model of DNMT3A clonal hematopoiesis (CH), in which loss-of-function DNMT3A mutations promoted atherosclerotic disease. Atherosclerosis regression in WT mice led to decreased nuclear 8-OHdG and increased nuclear PARP1/MTH1 and EIMP in lesional macrophages and fibrous cap thickening, all of which were impaired in DNMT3A-CH regression. These findings reveal that efferocytosis initiates a BER pathway to allow macrophage proliferation for tissue resolution, with possible therapeutic relevance to atherosclerosis regression and DNMT3A-CH.