Fig. 8: ER-phagy receptor remodelling of the ER proteome landscape and ER-phagy receptor cargo specificity during iNeuron differentiation.

a, Top 25 accumulated and bottom five depleted ER proteins ranked on WT to DKO β-coefficient values (left panel), QKO to PKO β-coefficient values (middle panel) or on log₂FC (ATG12^−/−/WT). b, ER-associated, ER-membrane or ER-lumenal distribution and predicted TM character of ER proteins with significant β-coefficient values (*adjusted P value < 0.05) in WT to DKO (111 up, 4 down), TKO to QKO (1 down) and QKO to PKO (39 up, 5 down). Zero proteins were significant in DKO to TKO. Each protein name is coloured based on whether there is a significant change in these steps in the allelic series, as shown in the legend. The corresponding β-coefficient value heatmap for each protein is coloured in if there is a significant change and left blank if there is no significant change at that step in the allelic series (see legend). P values for the β values extracted from the linear model are calculated with a Student’s t-test (two-sided), and multiple hypothesis correction using the Benjamini–Hochberg method. c, Examples of ER-shaping proteins with significant β coefficients that accumulate at one or more steps in the allelic series. β-coefficient values (top panels) and log₂FC (lower panels) are shown for single proteins, including RTN1-C, RTN3 and REEP5. d, Keima-REEP5 flux measurements in WT, ATG12^−/− and PKO iNeurons (day 12) using acidic/neutral ratios in the presence of BAFA for normalization. e, As in c, but for proteins REEP1 and REEP3 (ER-shaping proteins with significant β coefficients that decrease). f, As in c and e, but for VAPA (an ER-membrane protein that forms contact sites with other organelles). g, Autophagic flux assay for Keima-VAPA in WT, ATG12^−/− or PKO iNeurons (day 12). For the individual protein plots in c, e and f, the green asterisks in the top panels indicate a significant change (*adjusted P value < 0.05) in β coefficients for each mutant, Student’s t-test (two-sided), with multiple hypothesis correction using the Benjamini–Hochberg method. For autophagic flux experiments using Keima-REEP5 and Keima-VAPA, n = 3, data are presented as mean values ± s.d. *P < 0.05; **P < 0.01; Brown–Forsythe and Welch one-way ANOVA and Dunnett’s T3 multiple comparisons test.