Bulk RNA analysis of 98 samples from three datasets (GSE15653, GSE89632, and GSE24807) revealed four genes—CX3CR1, IRAK3, JUNB, and TNFRSF1A—as diagnostic biomarkers associated with autophagy and endoplasmic reticulum stress in T2DM and MAFLD. This evidence concerns the gene CX3CR1 and type 2 diabetes mellitus.