The RNA modification N6-methyladenosine restrains SIRPα to license myeloid efferocytosis in atherosclerosis

Background: Macrophages participate in atherosclerotic plaque development, progression and resolution, integrating lipid and inflammatory cues to balance tissue damage and repair. Despite considerable understanding of macrophage function in atherosclerosis, the underlying regulatory mechanisms governing these responses continue to evolve. Emerging evidence implicates epitranscriptomic gene regulation by the RNA modification N6-methyladenosine (m6A) in control of context specific immune responses, but its role in atherosclerosis is not well-defined. Methods: We integrated m6A quantitative trait loci (m6A QTLs) with Coronary Artery Disease (CAD) GWAS summary statistics. Using Oxford Nanopore direct RNA sequencing and MeRIP-seq, we constructed a high-resolution map of m6A modifications in macrophages. To determine the functional consequences of myeloid m6A loss in-vivo, we generated a myeloid-specific loss-of-function mouse model of m6A (Mettl14f/f LysMCre) and performed atherosclerosis studies using bone marrow transplantation into irradiated Ldlr-/- mice. Atherosclerosis lesions were analyzed using light microscopy and immunofluorescence imaging, with complementary in-vitro mechanistic studies performed in murine bone marrow derived macrophages (BMDMs). Results: m6A quantitative trait loci (m6A-QTLs) were enriched in CAD GWAS loci relevant to immune and lipid function, implicating m6A regulation in human CAD genetics. Using Oxford Nanopore direct RNA sequencing in conjunction with public MeRIP-sequencing data, we generated a single-base resolution, stoichiometric map of m6A modification in macrophages, nominating genes central to macrophage biology in atherosclerosis as high-confidence m6A targets. Myeloid specific deletion of the m6A "writer" complex subunit Mettl14 drove the development of larger, more necrotic and unstable atherosclerotic plaques on an Ldlr-/- background compared with Mettl14f/f controls, establishing an atheroprotective role for myeloid m6A. Loss of myeloid Mettl14 impaired macrophage efferocytosis in atherosclerotic plaques, in a dexamethasone-induced apoptosis in the thymus and in-vitro. Molecularly, m6A methylation of the "don't eat me" antiphagocytic receptor SIRP RNA suppressed its protein expression. Conclusions: These findings identify the myeloid m6A - SIRP axis as a novel homeostatic regulator of efferocytosis and establish epitranscriptomic remodeling as a crucial layer of macrophage regulation in atherosclerosis.