The renal tubules are a major site of mammalian mitophagy in vivo. (A) Tile scan showing parasagittal view of a representative adult kidney section from a mito-QC reporter mouse. Dashed lines demarcate macro-anatomical regions of the kidney, (lateral-medial from left-right). Bar, 200 µm. (B) 3D projection showing the spatial distribution of mitolysosomes within renal cortical tubules in vivo. Image acquired using iDISCO from an intact, cleared, and nonimmunolabeled mito-QC adult kidney with multiphoton microscopy. Arrows depict long stretches of cortical tubules with mitophagy, whereas arrowheads depict more restricted zones of mitophagy within tubules. Bar, 50 µm. (C) Representative Airyscan images from LAMP1 immunostained adult mito-QC kidney sections. Arrows highlight lysosomes containing degraded mitochondria. Bar, 5 µm. (D) Image showing adult mito-QC kidney sections immunolabeled with antibodies to the DCT marker, NCC. NCC-positive DCTs are demarcated by dashed lines, whereas arrows highlight NCC-immunonegative PCTs exhibiting pronounced apical mitophagy. DAPI is shown in blue. Bar, 20 µm. (E) Sample semiquantitative analysis of mitophagy in renal cortical tubules of mito-QC adult littermate kidneys. Data represent mean number of total and NCC-positive mitolysosomes, generated from a single kidney from two individual animals, with 15 fields analyzed per animal. Data from these kidneys were also used for Fig. 5 D.