The autophagy genes ATG5 and ATG7 contribute to delayed cell death elicited by VX-680. (A) Depletion of Atg5 and Atg7 by their cognate RNAi. RPE-MYC cells were infected with either pLKO.1-puro control lentiviral particles or lentiviral particles encoding shRNA against either ATG5 or ATG7, selected with 0.5 μg/mL of puromycin for 2 d, and subjected to Western blot analysis for Atg7 and Atg5, which are found mainly as Atg5–Atg12 conjugates. Actin was used as a loading control. (B) Suppression of autophagy by depletion of either Atg5 or Atg7. RPE-MYC cells were stably transfected with Cherry-LC3, infected with the indicated RNAi viruses, treated with 300 nM VX-680 for 3 d, and then transferred into drug-free medium. Quantification of autophagy with Cherry-LC3 was performed 2 d after withdrawal of VX-680. Cells that had more than 40 Cherry-LC3 puncta per cell were scored as positive. Each column, here and in ensuing panels, represents the average of three independent experiments, and each experiment was done in triplicate. Error bars represent SD. (C and D) Depletion of autophagy proteins suppresses delayed cell death, but not early death. RPE-MYC cells were infected with the indicated RNAi lentiviruses, treated with 300 nM VX-680 for 3 d, and then transferred into drug-free medium. Cells were harvested at 0, 3, and 6 d after initiation of VX-680 administration and assayed for viability by the trypan blue exclusion assay. (C) Delayed death was calculated using the following formula: percentage of dead cells = [(live cell number at day 3 − live cell number at day 6)/(live cell number at day 3)] × 100. (D) Early death was expressed as the percentage of dead cells at day 3. (E and F) Absence of atg5 protects cells against delayed death, but not against early death. atg5+/+ and atg5−/− MEF cells were infected with either a control virus (pMig) or a Myc-expressing virus (pMigMyc). The infected cells were then treated with DMSO or 300 nM VX-680 for 3 d and transferred into drug-free medium. Cells were harvested at 0, 3, and 6 d after initiation of treatment with VX-680 and assayed for viability by the trypan blue exclusion assay. Early death (E) and delayed death (F) were calculated as described for C and D. #Cells below the limit of detection. In the experiment represented by the hatched column, 100 μM z-VAD-fmk was included in the medium during the delayed cell death assay.