Identification of both ATG conjugation system–dependent and ATG conjugation system–independent TFEB regulation during lysosomal damage. (A and B) Representative snapshots of time-lapse imaging of TFEB::mNG in WT (left) and ATG7 KO (right) HeLa cells. Cells were treated with 1 mM LLOMe (A) or 100 μM MK-683 (B) for the indicated times. Arrowheads indicate nuclear-localized TFEB::mNG. (C) Venn diagram showing the overlap among five sets of DEGs: (1) down- or up-regulated genes in WT cells under LLOMe treatment relative to WT cells under control conditions (black circle), (2) down- or up-regulated genes in TFEB KO cells under LLOMe treatment relative to WT cells under LLOMe treatment (purple circle), (3) down- or up-regulated genes in TFEB KO cells under control conditions relative to WT cells under control conditions (yellow circle), (4) down- or up-regulated genes in ATG7 KO cells under LLOMe treatment compared with WT cells under LLOMe treatment (yellow-green circle), and (5) down- or up-regulated genes in ATG7 KO cells under control conditions compared with WT cells under control conditions (green circle). This analysis identified 147 genes as TFEB-dependent targets during lysosomal damage (pink circle) and 128 genes as ATG7-dependent targets during lysosomal damage (light blue circle). 115 genes were regulated by TFEB but not ATG7, corresponding to Mode I TFEB targets (orange). 32 genes were regulated by TFEB and ATG7, corresponding to Mode Il TFEB targets (blue). All DEGs are listed in Table S1. (D) GO enrichment analysis of Mode I and Mode II TFEB target genes using Metascape. The y- and x-axes show enriched terms and enrichment with the top biological process terms plotted according to −log₁₀ P value, respectively. The numbers of genes in each terms are shown. Gene lists for each GO term are shown in Table S2. Scale bars, 20 µm (A and B).