Ethical statement regarding the use of animals. Mice were bred at the Animal Experimentation Unit of the University of Córdoba, and all protocols were approved by the Bioethics Committee of the University of Córdoba in accordance with the Spanish legislation (RD53/2013). DJ-1 knockout mice were generously donated by Juan Pedro Bolaños (Institute of Functional Biology and Genomics, Salamanca, Spain) (28); back-crossed for at least eleven generations with C57Bl/6J WT mice for the experiments and bred under homozygosis.
Cell cultures. Cortical neurons in primary culture were prepared from foetal (E15.5) dj1-/- (DJ-1 KO) and dj1+/+ (WT) offspring. Cells were seeded at 1.8 x 105 cells cm-2 in cell culture plastic dishes previously coated with poly-D-lysine (15 µg ml-1) in neurobasal medium containing 2% of B-27 supplement (Gibco Brl-Life Technologies, Grand Island, NJ, USA) and 2mM L-glutamine. Neurons were incubated at 37 °C in a humidified 5% CO2-containing atmosphere; at second day, the medium was replaced, and neurons were used on the seventh or eighth day in vitro.
Sample preparation. Cortical neurons grown for 7-8 days were harvested and lysed in 100mM Tris-HCl buffer, pH 7.5, using a homogenization pestle for 1.5 mL tubes. The extracts were centrifuged, and the supernatants stored at −80 °C until use for mass spectrometry or western blot analysis. For the determination of proteasome activity the neuron pellet was homogenized with sea-sand in Tris-HCl buffer (0.5mM EDTA, 1mM PMSF, 100mM Tris-HCl, pH 7.5). The samples were centrifuged, and the supernatant fraction was collected for analysis.
Mass spectrometry.
Sample preparation, digestion and nLC-MS2 analysis. Samples from supernatants were prepared and analyzed in the Proteomics Facility at Research Support Central Service (SCAI), University of Cordoba. Protein extracts were cleaned-up in 10% 1D SDS-PAGE. The gel was stained with Coomassie Blue and protein bands were cut off, diced and kept in water until digestion. Gel dices were firstly distained and protein resuspended and reduced by addition of 20mM dithiothreitol. The mixture was cooled down to room temperature and alkylatated by addition of 40mM iodoacetamide. Proteolytic digestion was performed by addition of Trypsin (Promega, Madison, WI) and stopped by addition of trifluoroacetic acid, the digested samples were finally Speedvac dried. Nano-LC was performed in a Dionex Ultimate 3000 nano UPLC (Thermo Scientific) as described previously (29).
Data analysis. MaxQuant (v1.5.7.0) (30) and Perseus (v1.5.6.0) (31) software were used to analyze the different MSe runs in triplicate. Proteins were identified by searching raw data against the mouse UniprotKB/Swiss-Prot protein database (February 2018 version). Carbamidomethylation of cysteines as fixed modification, and oxidation of methionine and phosphorylation (ST) (Y) as variable modifications, were set for the study. Cleavage specificity was by trypsin, allowing for a maximum of one missed cleavage, a mass tolerance of 10 ppm for precursors and 0.01 Da for fragment ions. The false discovery rate (FDR) cut-off for protein identification was 1%. Enabling the “match between runs” option allowed for identification transfer between samples. Similar proteins were grouped, and only unique peptides were used for quantification. Identified from reverse database or contaminant hit proteins were removed prior to further analysis. Finally, the resultant list was analyzed according to the instructions of the software developers (31). The criteria for considering a differentially expressed protein were that it was identified and quantified using at least two unique peptides and had a P≤0.05 value. (Supplementary Tables S1 and S2). The same criteria were used to identify peptide phosphorylation including a value of posterior error probability (PEP)≤0.05 (Supplementary Table S3). Functional enrichment analysis was carried out using Ingenuity Pathways Analysis tool (IPA-Ingenuity Systems, www.ingenuity.com) and the results compared with other tools such as GOrilla, David and String (32-34).
Western blot. Cells were lysed in 50mM Tris-HCl buffer, pH 7.5 supplemented with 2% sodium dodecyl sulphate (SDS), 2mM EDTA, 2mM EGTA, , phosphatase inhibitor (50mM NaF) and protease inhibitors (100 mM phenylmethylsulphonyl fluoride, 50 µg ml-1 amastatin and 50 µg ml-1 leupeptin), stored on ice for 30 min and boiled for 10 min. Extracts (25–100 μg) were subjected to SDS–PAGE and blotted onto nitrocellulose membrane (GE Healthcare Life Sciences). After electrotransfer, membranes were blocked for 1 h with 5% non-fat milk (BioRad) solubilized in TBS-T (150mM NaCl, 50mM Tris, pH 7.5, 0.05% Tween-20). Primary antibodies were anti-AGEs (1:100; ab23722; Abcam), anti-mTOR Pathway Antibody Sampler Kit (1:1000; Cell Signalling), anti-Akt (1:1000; sc-5298; Santa Cruz Biotechnology), anti-p-Akt (1:1000; 4060S; Cell Signalling), anti-DJ-1 (1:2000; PA1-46262, Invitrogen), and anti-b-actin (1:2000; sc-47778; Santa Cruz Biotechnologies);. Secondary antibodies were anti-rabbit (1:4000) and anti-mouse (1:8000) IgG-peroxidase conjugates (Sigma). Incubations were carried out overnight and for 2 h, respectively. Signal detection was performed with an enhanced chemiluminescence kit (ECL Plus Western blotting detection reagent from GE Healthcare). Western blots were done at least in triplicate and represent independent replicate experiments. The protein abundances were measured by densitometry of the bands on the membranes using ImageJ 1.48u4 software (National Institutes of Health, USA), and normalized against the corresponding b-actin band.
Proteasome activity assay. Cells from three independent experiments were lysed as described above. The proteasomal activity was measured using the 20S Proteasome Activity Assay kit according to the manufacturer's instructions (APT280, Chemicon, Millipore). Proteasome activity is expressed as AMC (7-amino-4-methylcoumarin) relative fluorescent units (RFU) with the signal of the fraction inhibited with Lactacystin, an inhibitor of the 20S proteasome β5subunit provided in the kit, as a reference.
Protein determination. Protein concentrations were determined in the lysates or in parallel cell culture incubations after solubilization with 0.1 M NaOH. Protein concentrations were determined using a Pierce BCA Protein Assay kit (Thermo Scientific, Milan, Italy) with bovine serum albumin as a standard.
Statistical analysis. All measurements in cell culture were carried out, at least, in triplicate, and the results are expressed as the mean ± SEM values from at least three different culture preparations. Two groups were compared and statistical analysis of the results was performed by one-way analysis of variance (ANOVA), followed by the Student's t test. In all cases, p<0.05 was considered significant.