Fig. 3: LAMs in ATG4B, EHMT2, BRAF, and STBD1 found in cancer patients impair their interactions with ATG8.

a The association of LAM-containing LIRCPs and human cancer at SNV, RNA-seq, and DNA methylation levels. b The expression levels of LAM-containing ATG proteins and autophagy regulators across different cancer types. c Mutated EGFR is associated with a shorter survival rate. d Low DNA methylation level of ATG4B is associated with a longer survival rate. e High mRNA expression level of STBD1 is associated with a longer survival rate. f Low DNA methylation level of STBD1 is associated with a longer survival rate. In c–f, significance (p value) is determined by a two-sided log-rank test. g HEK293T cells were co-transfected with Flag-tagged ATG4B wild-type (WT) or Y8C and GFP-tagged LC3B for 24 h. All ATG4B plasmids were made in the F349A/F388A background to minimize the roles of LIR2 and LIR3. Control cells were transfected with an empty vector. One-tenth of the cell lysate was prepared as input, and the rest was used for immunoprecipitation with anti-Flag Sepharose 4B gel followed by immunoblotting with indicated antibodies. The band of LC3B was quantified by Image J and normalized to the level of ATG4B WT, and labeled below the blots. Schematic representation of human ATG4B with red fonts indicating the LIR motif. *IgG heavy chain. h, i HEK293T cells were co-transfected with Flag-tagged EHMT2 (160–360 aa) or BRAF and GFP-tagged LC3B or GABARAPL1 for 24 h. Control cells (vector) were transfected with an empty vector. One-tenth of the cell lysate was prepared as input, and the rest was used for immunoprecipitation (IP) with anti-Flag Sepharose 4B gel followed by immunoblotting with indicated antibodies. Schematic representation of human EHMT2 and BRAF with red fonts indicating the LIR motif. j HEK293T cells were co-transfected with Flag-tagged STBD1 WT or W203C and GFP-tagged GABARAPL1 for 24 h. Control cells (vector) were transfected with an empty vector. One-tenth of the cell lysate was prepared as input, and the rest was used for immunoprecipitation with anti-Flag Sepharose 4B gel followed by immunoblotting with indicated antibodies. Schematic representation of human STBD1 with red fonts indicating the LIR motif. Experiments g–j were performed in triplicate.