Figure 12. Saponin extraction allows quantification of LC3-II fluorescence by FACS. (A) Schematic diagram of the effects of the saponin wash. Due to the reorganization of the EGFP-LC3 reporter protein, induction of autophagosome formation does not change the total levels of fluorescence in EGFP-LC3-transfected cells. However, extraction of EGFP-LC3-I with saponin results in a higher level of fluorescence in cells with proportionally higher levels of EGFP-LC3-II-containing autophagosomes. This figure was previously published in reference 236 (B) Saponin extraction can also be used to measure flux of endogenous LC3 protein. Human osteosarcoma cells were starved of amino acids and serum by incubation in EBSS, for the indicated times in the presence or absence of a 1 h chloroquine (50 µM) treatment. Cells were then washed with PBS containing 0.05% saponin and processed for FACS analysis for endogenous LC3. These data are provided by K.E. Eng and G.M. McInerney.