Cell-Type Resolved Protein Atlas of Brain Lysosomes Identifies SLC45A1-Associated Disease as a Lysosomal Disorder

Description

Methods

U2OS cells (50x10³) were grown on autoclaved coverslips and were placed individually in 12-well plates. Transient transfection was performed by pre-mixing 1 µg DNA and 3 µg PEI (polyethylenimine, MW 25 kDa) in 100 µl OptiMEM (without serum and antibiotics). The transfection mix was incubated for 15 min at RT and 30µl were added dropwise to the wells. Transfection incubation time was 16 h and then media was replaced by DMEM high glucose media and incubated further for 48 h (exception for ENPP5, 12h transfection, without further incubation). Prior fixation, the U2OS cells were incubated with 300 nM MitoTracker (Orange CMTMRos) for 45 min at 37°C for co-staining for Mitochondria. Cells were washed three times with PBS, fixed in 4% formaldehyde (v/v) in PBS for 10 min and incubated 5 min with DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride, 0.02 μg/μl in PBS) at RT, then washed 3 times with PBS. Coverslips were mounted in Permafluor mounting medium using glass slides and dried at RT overnight. All samples were stored at 4°C in the dark until further analysis by microscopy.

SIM imaging (structured illumination microscopy) was performed using a Zeiss Elyra 7 lattice SIM system (Zeiss, Germany) equipped with a 63x/1.4NA oil objective and an additional 1.6x Optovar magnification, resulting in a final optical pixel size of 62 nm. Multicolor z-stacks were acquired with a physical step size of 110 nm according to Nyquist sampling. Each 3D SIM volume was recorded using Zeiss’s lattice SIM mode, with each optical plane reconstructed from 13 raw phase images acquired with an exposure time of 250 ms each. A quad-band dichroic mirror and emission filter (LBF 405/488/561/642) enabled detection of multiple fluorophores. SIM reconstruction was carried out using Zeiss Zen Black software (v3.0) with default settings and the ‘precise’ reconstruction mode and a resulting pixel size of 32.24 nm. No baseline cut was applied. Subsequent post-processing, contrast adjustment, and image export were performed in ImageJ/Fiji.