a, Immunofluorescence staining of MHC-I after shRNA-mediated ATG3 knockdown. Scale bars, 50 μm. b, Representative flow cytometry plots for PaTu8902 cells after knockdown of ATG3 (related to Fig. 2b) and ATG7 (see also d). Representative plots from d and Fig. 2b are shown. c, Effect of ATG7 knockdown on MHC-I (HLA-A, -B, -C) expression in PaTu8902 cells. d, Flow cytometry-based quantification of plasma membrane levels of MHC-I (HLA-A, -B, -C) after ATG7 knockdown (n = 9 replicates from three independent experiments). e, Immunofluores-cence staining of MHC-I following ATG7 knockdown. Scale bars, 50 μm. f, g, Surface MHC-I levels after knockdown of ATG3 (f) or ATG7 (g) in mouse PDAC cells. Left, knockdown efficiency was confirmed by immunoblots. Middle, cell surface levels of MHC-I (H-2Kb/Db) measured by flow cytometry (n = 8 replicates from two independent experiments). Right, representative flow cytometry plots are shown. h, Treatment of KP4 cells with 150 nM BafA1 for the indicated times causes an increase in levels of HLA-A, -B. i, Flow cytometry-based quantification of plasma membrane MHC-I in the indicated cell lines after treatment with BafA1 for 16 h (n = 9 replicates from three independent experiments). j, Surface MHC-I (H-2) levels measured by flow cytometry. Mouse PDAC organoids were established from Atg5+/+ and Atg5−/− KPC cells. n = 4 biological replicates. Data are representative of three independent experiments. Right, representative flow cytometry plots. k, Effect of BafA1 treatment on the expression levels of antigen presentation machinery. l, Quantitative proteomics analysis of Panc1 cells that were treated with chloroquine (10 μM) for the indicated periods. n = 3 biological replicates. m, Effect of BafA1 treatment on expression levels of MHC-I in the indicated cell lines. Cell lines denoted in green show a significant change across all HLA isoforms after BafA1 treatment. n, o, Effect of ATG3 knockdown in H441 cells on total MHC-I (n) and plasma membrane MHC-I (o) as measured by flow cytometry-based quantification (n = 9 replicates from three independent experiments). A representative of at least two independent experiments is shown in a–c, e–h, j, k, m, n. Data are mean ± s.d. P values were determined by unpaired two-tailed t-tests. See Supplementary Fig. 1 for gel source data. Source Data