12 In selected experiments (see below), hepatocytes were cultured in minimal essential medium (MEM, Invitrogen, Breda, The Netherlands). Hepatocyte AUY-922 nmr viability and purity were over 90%. Primary rat hepatocytes were plated at a density of 1.0 × 105 cells/cm2. After a 24-hour attachment period, cells were incubated with 25, 100, or 300 μM [2,2,4,4-D]Cholic acid (D4CA; isotopic purity

98%, ISOTEC, Miamisburg, OH) for 0 to 24 hours. For taurine or glycine conjugation preference assays, hepatocytes were cultured in MEM, supplemented with 666 μM glycine (Sigma-Aldrich, St. Louis, MO) and/or 666 μM taurine (Sigma-Aldrich) in the presence of 100 μM D4CA. At indicated timepoints, media and cells were collected followed by subcellular fractionation or immediate storage at −20° C. The subcellular fractionation and isolation of peroxisomes from

rat liver was performed essentially as described13 using PEG1500-containing homogenization buffer (isolation medium-3). Peroxisomes were purified from the 500g supernatant (postnuclear supernatant [PNS]) using Nycodenz density gradient centrifugation according to the method described by Verheyden et al.14 Twelve mL PNS was loaded on top of a discontinuous Nycodenz gradient (2 mL 56%, 3 mL 45%, 15 mL 30%, and 5 mL 18%) and EPZ-6438 cell line spun in a vertical rotor (Sorvall, SV288, Thermo Fisher Scientific, Waltham, MA) at 20,000 rpm for 2 hours Phosphatidylethanolamine N-methyltransferase at 4°C in a slow acceleration/deceleration mode. Equal volumes of all supernatants, pellets, and gradient fractions were analyzed by western blotting or were further purified for mass spectrometry. Digitonin assays were performed essentially as described,11 with the basic difference that digitonin treatments were performed on rat hepatocytes attached to collagen-coated culture discs instead of treated in suspension. Equal volumes of supernatant and pellet fractions were analyzed by western blotting or further processed for mass spectrometry. Apoptotic cell death was visualized

by acridine orange nuclear staining15 and quantified by determining caspase-3 activity.16 The arbitrary fluorescence unit (AFU) was corrected for the amount of total protein in the cell lysate. Necrotic cell death was quantified by determining lactate dehydrogenase (LDH) leakage17 and Sytox green (Invitrogen) according to the supplier’s protocol. Protein samples were separated by SDS-PAGE and analyzed by western blotting according to established procedures.11 Protein concentrations were determined using the Bio-Rad Protein Assay system (Bio-Rad, Hercules, CA) using bovine serum albumin as standard. Primary antibody dilutions used in this study are shown in Supporting Table S1. Proteins signals were detected and quantified in a ChemiDoc XRS system (Bio-Rad). Protein band intensities were quantified using Quantity One software (Bio-Rad). Media samples (0.1-1.