DM and endothelial cells were stripped off freshly dissected corneas and homogenized in Tissue Protein Extract Reagent (Thermo Fisher Scientific, Rockford, IL) supplemented with 1% protease inhibitor cocktail (Sigma, St. Louis, MO), 1 PhosSTOP Phosphatase Inhibitor Cocktail Tablet (Roche, Mannheim, Germany), and 1% EDTA (Sigma). All protein samples consisted of 2 corneas from the same animal; however, due to low abundance of LC3A/B, pooling of 6 corneas from 3 different mice of the same genotype and age was necessary for that particular target. MCF7 cell extracts (sc-2206; Santa Cruz Biotechnology, Santa Cruz, CA) were used as side-by-side positive controls for UPR markers, BiP (GRP78), and GADD153 (CHOP). Hela cell extracts (ab29545; Abcam, Cambridge, MA) were used as a positive control for LC3A/B. Samples were centrifuged at 12,000
g for 10 minutes at 4°C and the protein concentration of the supernatant was quantified using the Pierce Bicinchoninic Acid Protein Kit (Thermo Fisher Scientific). Equal aliquots of protein were mixed with 4× NuPage loading dye (Life Technologies) with 2-mercaptoethanol (Sigma) and heated for 5 minutes. Samples then were loaded into a 4% to 20% Mini-PROTEAN TGX Gel (BioRad, Hercules, CA) and subjected to SDS-PAGE separation for 30 minutes at 200 V. Proteins were transferred to a polyvinylidene fluoride (PVDF) membrane and incubated in SuperBlock Blocking Buffer (Thermo Fisher Scientific) for 1 hour. Membranes then were incubated in primary antibodies: BiP (1:500, #3183; Cell Signaling, Danvers, MA), GADD153 (1:1000, sc-793; Santa Cruz Biotechnology), LC3A/B (1:500, #4108; Cell Signaling), ATG12 (1:500, #2011; Cell Signaling), and COL8A2 (1:2000; courtesy of Paul Davis, PhD, Wellington, NZ) diluted in blocking buffer for 1 hour at room temperature. Details regarding secondary antibody, membrane stripping, β-actin loading controls, and densitometry analysis are as described previously.
16 Low abundance proteins were detected using SuperSignal West Dura (Thermo Fisher Scientific), and higher abundance proteins were detected using HyGlo Quick Spray (Denville Scientific, Metuchen, NJ).