mTOR directly controls the development of multiple autophagy-related complexes, such as the ULK1 and VPS34 complexes, and the levels of important autophagy-related proteins, such as TXNIP, AMPK, UVRAG, and p53, to regulate autophagy, thus affecting the development of NAFLD and HCC. This evidence concerns the gene PIK3C3 and metabolic dysfunction-associated steatotic liver disease.