Gabarapl1

Ammonium chloride (NH₄Cl, A0171, Sigma-Aldrich, St. Louis, MI, USA), Earl’s balanced salt solution (EBSS, E3024, Sigma-Aldrich), TGFβ (100-21, PeproTech, Rocky Hill, NJ, USA), TNF-α (300-01A, PeproTech), and SIS3HCl (521984-48-5, CliniSciences, Nanterre, France) were used. For the Western blotting experiments, the following antibodies were used: GABARAPL1 (26632S, Cell Signaling, Saint-Cyr-L’École, France), LC3 (LB8918, Sigma, Saint-Quentin-Fallavier, France), N-cadherin (D4R1H, Cell Signaling), E-cadherin (610181, BD Biosciences, Le Pont de Claix, France), SNAI1 (C15D3, Cell Signaling), SMAD2 (5339T, Cell Signaling), SMAD3 (9523T, Cell Signaling), SMAD4 (38454T, Cell Signaling), β-actin (A5060, Sigma-Aldrich), anti-rabbit (BI2413C, P.A.R.I.S, Diagenode), and anti-mouse (BI2407, P.A.R.I.S). For IHC experiments, the following antibodies were used: vimentin (#7902917, Ventana Medical Systems, Illkirch-Graffenstaden, France), GABARAP (SAB1302861, Sigma-Aldrich), and GABARAPL1 (11010-1-AP, ProteinTech, Manchester, UK). For confocal microscope experiments, actin was labeled using phalloidin (P1951, Sigma-Aldrich), and the following antibodies were used: SMAD2 (5339T, Cell Signaling), SMAD2/3 (sc-133098, Santa Cruz Biotechnology, Heidelberg, Germany), and Alexa Fluor 488 goat anti-rabbit (Life Technologies, Rockville, MD, USA, A-11008, 1:500).

After incubation cells were lysed directly into sample buffer (50 mm Tris-HCl buffer pH 6.8, 2% SDS, 10% glycerol, 0.005% bromophenol blue) containing 100 mm maleimide to preserve protein oxidation. Protein samples were resolved on SDS-PAGE gels and then transferred to polyvinylidene difluoride membranes by western blotting (TransBlot Turbo, Bio-Rad). Membranes were blocked in milk dissolved in phosphate-buffered saline (PBS) supplemented with 1% Tween before incubation with primary antibodies. Membranes were developed using enhanced chemiluminescence substrate (ThermoFisher) and detected using photographic film, which was developed using an automatic processor (Fuji RG II). Samples were immunoblotted for LC3 (1:1000, Cell Signaling), Atg3 (1:5000, Abcam), Atg7 (1:1000, Cell Signaling), Actin (1:10,000, Sigma), Atg5 (1:1000, Cell Signaling), Atg12 (1:1000, Cell Signaling), Atg4B (1:1000, Cell Signaling), Atg10 (1:1000, Abcam), GABARAPL1 (1:1000, Cell Signaling), GABARAPL2 (1:1000, Cell Signaling), cGMP-dependent protein kinase (PKG, 1:1000, ENZO Life Sciences), Myc-tag (1:1000, Cell Signaling), p62 (1:500, Cell Signaling), caspase-3 (1:1000, Abcam), peroxiredoxin-SO3 (1:500, AbFrontier) and GFP (1:2000, Miltenyi Biotec). All uncropped western blots can be found in Supplementary Fig. 6.