Cell lines and culture conditions
Human neuroglioma H4 cells stably expressing GFP-LC3 and human osteosarcoma U2OS cells stably expressing RFP-FYVE (Zhang et al. 2007) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) high glucose, pyruvate (Gibco, D6546-500 mL) supplemented with 10% heat-inactivated fetal bovine serum (SIGMA, F7524 500 mL), 10 mM HEPES buffer (GIBCO 15630056), 2 mL of penicillin (10 U/ml) and streptomycin (100 μg/mL) (GIBCO, SV30010), and 500 μg/mL G418. Human dopaminergic neuroblastoma SH-SY5Y, stable ATG5 knockdown SH-SY5Y, and mouse neuroblastoma Neuro-2a (N2a) cells were collected in RPMI medium (HyClone 1640) supplemented with 10% heat-inactivated fetal bovine serum (SIGMA, F7524-500 mL), 200 mM l-glutamine, and 0.04 mg/mL gentamicin (Gibco 15750037). Wild-type (WT) and atg5 knockout embryonic mouse fibroblasts (MEFs) were maintained in DMEM (SIGMA, D6546-500 mL) supplemented with 10% heat-inactivated BGS (HyClone, sh30541.3), 200 mM l-glutamine, and 10 U/mL penicillin and streptomycin (100 μg/mL) (GIBCO, SV30010). The cells were cultured in 75 or 150 tissue culture flasks (Thermo Scientific™ 130190) and maintained in 5% CO2/95% air at 37°C under saturating humidity. Cells were passaged every 24–48 h.
Reagents and chemical treatment
Cells grown to 75% confluency were seeded in 6-, 24-, or 96-well plates. After 24 h, cells were treated with QBA (#cay10976-500 mg, Vitro) and HDA (#379700, Sigma-Aldrich) at different concentrations for 2–4 h. We used serum-free Earle’s balanced solution salt (EBSS, #E2888, Sigma-Aldrich), rapamycin (RAPA, 1 μM, #R-5000, LcLabs), or resveratrol (RES, 2 μM, #1418, Tocris) for 4 h to induce autophagy and 3-methyladenine (3-MA) for 1 h (10 mM, #m9281, Sigma-Aldrich), bafilomycin A1 (BAF.A1,100 nM, #b1080, LcLabs), or LY294002 (10 μM, #1130, Biogen) for 4 h to inhibit autophagy. Cells were treated with EX527 for 4 h (2 μM, #E7034, Sigma-Aldrich) to inhibit the protein deacetylase SIRT. 6-Hydroxydopamine (6-OHDA, 35 μM, #H116, Sigma-Aldrich) was added to the medium for 20 h and Trichostatin A (TSA, 1 μM, #T8552, Sigma-Aldrich) was added to the medium for 4 h to the inhibition of class I and II HDACs.
Protein isolation and Western blotting analysis
To isolate proteins, cells were collected and lysed in a buffer containing 0.5% NP-40, 100 mM Tris HCl, 300 mM NaCl, 1% SDS, and protease (#11836170001, Roche) and phosphatase inhibitors (PhosSTOP (#4900837001, Roche). The tissue samples were lysed with lysis buffer containing 150 mM NaCl, 7.5 mM Tris HCl pH 7.5, 1 mM EDTA and complemented with protease and phosphatase inhibitors. Total protein concentration was measured by the bicinchoninic acid assay (#B9643-1L, Sigma-Aldrich) according to the manufacturer’s instructions. Protein samples (20 μg for each samples) were subjected to an electrophoresis on 12% Tris-Glycine Mini-PROTEAN TGXTM gels (10 or 15 well, Bio-Rad) or Criterion TGX Gels (18 well, Bio-Rad) and electrotransferred onto PVDF membranes (#1620177, Bio-Rad). Later, membranes were blocked (1h at RT) with 10% (w/v) fat-free milk in Tris-buffered saline (10 mM Tris/HCl pH 7.5, 150 mM NaCl) containing 0.2% Tween-20 (#P5927, Sigma-Aldrich) (TBST). Membranes were washed with TBST 1X and incubated overnight at 4°C with the corresponding primary antibodies specific to AcK (#9441, Cell Signaling Technologies), ATG5 (#1672630s Cell Signaling Technologies), ACTB (#ab49900, Abcam), BECN1 (#sc-11427, clone H-300, Santa Cruz Biotechnology Inc), Cathepsin B (#ab58802, Abcam), cleaved caspase-3 (Asp175, #9661, Cell Signaling Technologies), cleaved PARP (Asp214, #9541, Cell Signaling Technologies), GAPDH (NG1740950, Millipore), GFP (#29565, Cell Signaling Technologies), LAMP2 (sc18822, Santa Cruz Biotechnology Inc.), LC3-B (#L7543, Sigma-Aldrich), PARP (#9542, Cell Signaling Technologies), p62/SQSTM1 (#H00008878-MO1, Abnova), pS6 ribosomal protein (Ser235/236, #4858, Cell Signaling Technologies), pSIRT1 (Ser 47, #2314, Cell Signaling Technologies), pS6 kinase (Thr389, #9205 Cell Signaling Technologies), S6 ribosomal protein (#2317, Cell Signaling Technologies), S6 kinase (#9202, Cell Signaling Technologies), SIRT1 (#9475, Cell Signaling Technologies), and TSC2 (#3612, Cell Signaling Technologies). After several washing steps in TBST 1X, the membranes were incubated with their respective HRP-conjugated secondary antibodies (1:10000) (#170–6515 and #170-5047, Bio-Rad, for rabbit and mouse antibodies, respectively) for 1h at room temperature. Immunoreactive bands were visualized with ECL substrate (ThermoScientific, 32106) and chemiluminescence images were captured by an Amersham Imager 600 (GE Heathcare). Band intensities were quantified using ImageJ software (NIH), establishing ACTB, GAPDH, or tubulin protein levels as a loading control.
RNA interference
Once cells reached 50% confluence, cells were transfected with siRNAs targeting BECN1 (siBECN1, 50 UUCCGUAAGGAACAAGUCGGdTdT-30), SIRT1 (siSIRT1, #AM16708, Ambion), and TSC2 (siTSC2, #5269468, Invitrogen-Life) using HiPerfect Transfection Reagent (#509301704, Qiagen) according to the manufacturer’s instructions. An irrelevant siRNA duplex (siUNR (Ambion, L/N 1602012)) was employed as a negative control. Forty-eight hours later, transfection efficiency was determined by Western blotting.
Expression analysis by real-time RT-PCR
Total RNA was extracted using an RNeasy mini kit (#74104, Qiagen). Genomic DNA contamination was eliminated from total RNA samples using an RNase-Free DNase kit (#AMPD1-1KT, Sigma-Aldrich). RNA purity and quantity were checked with a NanoDrop. A total of 500 ng of total RNA was reverse transcribed into complementary DNA (cDNA) via QuantiTect reverse transcription (#205311, Qiagen) in a 20-μL reaction according to the manufacturer’s protocol. The resulting cDNA was amplified by real-time RT-PCR and SIRT mRNA expression was measured by a KAPA SYBR® Fast kit (#KK4601, Kapa Biosystems) using the following primers from IDT®: GAPDH (5′-AGCCACATCGCTGAGACA-3′) and SIRT1(5′-TGCGGGAATCCAAAGGATAATTCAGTGTC-3′). The expression of the housekeeping gene GAPDH was used to normalize the result. The expression levels were determined by the 2(−ΔΔCt) ratio.
Automated fluorescence microscopy
GFP-LC3 H4 and RFP-FYVE U2Os cells were plated on 96-well TC-treated Imaging Microplates (BD Falcon, Sparks, MD, USA) and cultured for 24 h. After treatments, cells were washed in PBS, fixed (for 15 min at RT) with 4% PFA, and stained with 2 μM Hoechst 33342 (#B2261, Sigma-Aldrich). After several washing steps with PBS (#mb18201, Nzytech), cells were permeabilized with 0.1% Triton X-100 (#T9284, Sigma-Aldrich) for 10 min RT and blocked (for 1 h at RT) with bovine serum albumin (BSA)/PBS solution (1 mg/mL). Thereafter, cells were incubated with the specific primary antibody overnight at 4°C followed by incubation with appropriate rabbit or mouse Alexa Fluor® 568 (Thermo Scientific, A11004) or 488 (Thermo Scientific, A11008)-conjugated secondary antibodies (for 1 h at RT). Image acquisition was done with a Cellsens IX83 molecular inverted microscope. The presence of cytoplasmic GFP-LC3+ and RFP-FYVE+ dots was assessed using Ifdotmeter® software (Rodriguez-Arribas et al. 2016).
Confocal microscopic analysis
GFP-LC3 H4 cells were seeded in 96-well TC-treated Imaging Microplates (BD Falcon, Sparks, MD, USA) 24 h before stimulation. After experimental treatments, cells were fixed with 4% PFA supplemented with DAPI (ThermoFisher, P36966). Fluorescence images were visualized using an A1 confocal imaging system mounted on an inverted Eclipse Ti microscope (Nikon Corp., Tokyo, Japan A1). LC3 and lysotracker or SQSTM1 cytoplasmic colocalization data were analyzed with the JACoP plugin of ImageJ software with preprogrammed macros. At least 100 hundred cells were analyzed in every experiment.
Immunoprecipitation assay
For acetylation analysis, whole-cell extracts were lysed with cell lysis reagent (CelLyticTM M, c2978, Sigma-Aldrich) supplemented with 10% deacetylase inhibitor cocktail (#sc362323, Santa Cruz Biotechnology Inc., Santa Cruz, CA, USA) and 10 μM anacardic acid (#A7236, Sigma-Aldrich). Two hundred micrograms of protein was incubated with Dynabeads protein G (#1007D, Novex) for 90 min. Once the beads attached to the nonspecificities were discarded, samples were incubated with Ac-K antibody overnight at 4°C in agitation. Proteins were then reincubated with Dynabeads for 150 min. Immunoprecipitated proteins were washed three times with lysis buffer and eluted with Laemmli 2x and SDS loading buffer 5x for 1 min at 95 °C.
Mouse experiments
ICR mice were kept under controlled conditions with food and water ad libitum. Four-week-old male animals were injected intraperitoneally with either 10 mg/kg QBA or 10 mg/kg HDA or an equivalent volume of vehicle. Four hours later, mice were euthanized. To induce autophagy, animals were starved overnight. To analyze autophagic flux, mice received an intraperitoneal injection of QBA, and 2 h later, mice were again injected intraperitoneally with 15 mg/kg leupeptin (in 150 mM NaCl) or an equivalent volume of vehicle and were sacrificed 2 h later. Thereafter, organs were collected and processed for immunoblotting detection of LC3 lipidation. All animal experiments were approved by the Committee for Animal Experimentation of the Universidad de Extremadura and were performed in accordance with its guidelines.
In 6-OHDA studies, C57BL/6 male mice, 2 to 3 months of age, were maintained on a 12-h light/dark cycle with access to food and water ad libitum. The animal protocols used in this study were performed in accordance with institutional guidelines (Institutional Animal Care and Use Committee guidelines) and approved by the “Ethics committee for Animal Experimentation” of the Instituto de Investigaciones Biomédicas (CSIC-UAM). Animals (four mice per experimental group) were anesthetized with a mixture of ketamine (60 mg/kg)/medetomidine (5 μg/kg) and placed in a stereotaxic apparatus (Koft Instruments, CA). Mice were then injected with either 1 μg of 6-OHDA dissolved in 2.5 μL of PBS or QBA (11 μg in 2.5 μL of PBS) or the same dose of 6-OHDA in combination with QBA (11 μg in 2.5 μL of PBS) into the right side of the SNpc at the following coordinates: posterior −3.2 mm, lateral +2.0 mm, and ventral +4.7 mm relative to Bregma and according to the atlas of Paxinos and Watson (Paxinos 1998). Parallel injections of 2.5 μL of PBS served as controls for the 6-OHDA-treated animals. To analyze the effect of autophagy inhibition, mice were anesthetized and injected with 6-OHDA (1 mg in 2.5 mL of PBS) or 6-OHDA in combination with QBA (11 μg in 2.5 μL of PBS) as described previously. After different treatments, mice were housed individually to recover and sacrificed 7 days after lesioning.
Histology and immunohistochemistry
Mice were anesthetized and transcardially perfused with ice-cold PBS and 4% paraformaldehyde (PFA). Brains were harvested, postfixed in 4% PFA at 4°C overnight, cryoprotected in 30% sucrose, and stored at −80°C. Brain tissue was cut into 30-μm-thick sections using a cryostat (Cryocut 1900, Leica) and stored in a solution containing 30% ethylene glycol, 30% glycerol, and 40% phosphate buffer 0.1 M at −80°C until use. For immunohistochemistry, sections were permeabilized and blocked with 0.1% Triton X-100 and 3% goat serum in PBS for 1 h at room temperature followed by overnight incubation with primary antibodies against monoclonal mouse tyrosine hydroxylase (TH) (T2928, Sigma-Aldrich) and polyclonal rabbit Iba1 (011-27991, Wako). After several washing steps, all sections were incubated for 1 h at RT with a secondary Alexa-Fluor 488 goat anti-rabbit or Alexa-Fluor 647 goat anti-mouse antibodies (1:500, Jakcson ImmunoResearch) and washed, and nuclei were stained with DAPI for 15 min at room temperature. Finally, coverslips were mounted in Vectashield H-1000 (Vector Laboratories). Images were acquired under a fluorescence microscope (Nikon 90i).
D. melanogaster studies
w1118, Mhc-Gal4 >UAS-GFP:Atg8a, Atg5d[04577] lines were obtained from the Bloomington Drosophila Stock Center (Indiana University, Bloomington, IN, USA). Mhc-Gal4 flies were described previously (Marek et al. 2000). Flies were maintained at 25 °C with standard fly food. For oral administration of QBA, a maximum of 25 1-day-old adult flies was collected in tubes containing standard food supplemented with QBA (0.16–161 μM). Flies were transferred to tubes containing fresh food every 2–3 days. GFP (11814460001, Sigma-Aldrich) and α-tubulin (clone 12G10, Developmental Studies Hybridoma Bank) immunodetection in protein extracts and GFP:Atg8 in fly thoraces was performed as previously described (Bargiela et al. 2015).
D. melanogaster lifespan analyses
A total of 90–100 newly emerged flies were collected in freshly prepared tubes containing standard nutritive medium with QBA (concentrations ranging from 0.16 to 161 μM), rapamycin (50 μM), or DMSO as vehicle. Males and females were kept in different tubes at 29°C. The number of dead flies was scored daily. Flies were transferred to new tubes twice a week. Survival curves were obtained using the Kaplan-Meier method and were statistically compared according to the Gehan-Breslow-Wilcoxon test (α=0.05).
Flow cytometry assay
Cells were seeded in 24-well plates and cultured for 24 h. After experimental interventions, cells were collected in FACS tubes (51031, Enzo laboratories) and stained with Annexin V-FITC (Immunostep, ANXVF-200T) for 15 min at 37°C and after propidium iodide (0.1 mg/mL) (PI, Sigma-Aldrich, P4170) was added to each tube to detect either the percentage of PI- or Annexin-positive cells using a Beckman Coulter FC500-MPL.
Degradation of long-lived proteins
Cells were seeded in 6-well plates and cultured for 24 h. After treatments, cells were maintained with 0.2 lCi/mL [14C]-valine (NEC291EU050UC, PerkinElmer) for 18 h at 37°C. After several washing steps in PBS (pH 7.4), the medium with the isotope-labeled amino acid was changed for a cell culture medium with l-valine (V0153, Sigma-Aldrich), first for 1h (prechase), and then in combination with several experimental treatments (chase) for 4 h. Thereafter, proteins were precipitated with 10% (v/v) trichloroacetic acid (TCA) (T9159, Sigma-Aldrich), separated from the soluble radioactive fraction by centrifugation at 6000 g for 20 min and then dissolved in 0.2 N NaOH. Finally, the long-lived protein degradation was measured by adding a small quantity of each sample into a scintillation liquid and measuring the radioactive activity with a liquid scintillation counter.
Statistical analyses
Data are expressed as the mean ± SD of triplicate determinations. Experiments were repeated at least three times, yielding similar results. Unless otherwise indicated, comparisons among groups used unpaired Student’s test, one-way ANOVA, or two-way ANOVA with the Sidak or Tukey posttest.