*Purpose: Bronchiolitis obliterans (BOS) remains a major cause of death for lung transplant recipients, and the mechanisms that drive BOS remain poorly understood. It is known that genetically encoded deficiencies in mitophagy, a specialized form of autophagy which targets the removal of damaged mitochondria, promote disease but it is unclear if they play a role in BOS. Prior work has shown that the rs2241880 mutation in ATG16L1, an autophagy related protein, leads to protein instability resulting in deficiency of ATG16L1 in monocyte-derived (Mo-cells) macrophages. We previously observed that human lung recipient carriers of rs2241880 had accelerated BOS. Therefore, we analyzed the effects of ATG16L1 deficiency in Mo-CD11c⁺ cells in a mouse orthotopic lung transplant model of BOS.

*Methods: CD11cCreATG16L1^flox/flox (ATG16L1^Δ/Δ) and control CD11cCre recipients received major MHC-mismatched FVB lungs, with immunosuppression to induce acceptance. Following induced epithelial injury, allografts were assessed for obliterative airway lesions for up to 28 days. Intragraft Mo-CD11c⁺ cells were analyzed for bulk RNA sequencing and by FACS for mitochondrial mass and ROS production. Mitophagic flux was visualized by confocal microscopy using Mt-kiema mitophagy reporter mice. Metabolic activity was characterized using a Seahorse XF analyzer. Alloimmunity was examined via T cell proliferation assays and ELISA.

*Results: ATG16L1^Δ/Δ recipients showed severe and accelerated OB compared to controls. RNAseq analysis of ATG16L1^Δ/Δ deficient intra-graft Mo-derived cells demonstrated a loss of transcripts that encode subunits of mitochondria electron complex I, II and V. Confocal and FACS revealed higher MHCII⁺, attenuated mitophagic flux, high mitochondrial mass and elevated ROS production in ATG16L1^Δ/Δ. In line with these observations were decreased maximal mitochondrial respiratory capacity, lower mitochondrial ATP production and increased utilization of glycolysis; as well as increased T cell proliferation and higher IL1-β suggesting metabolic adaptation of an M1 inflammatory phenotype.

*Conclusions: These data reveal a new role for ATG16L1 as a regulator of mitochondrial quality control and alloimmunity with implications for lung recipients that carry the ATG16L1 rs2241880 mutation.

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