In conclusion, 5 Hypo­HGs (HOXD9, RAI2, ADPRHL1, C12orf42, and PCDHB16) and 13 Hyper-LGs (EPCAM, GNG4, SLFN13, USH1C, SPINT1, SLC39A4, LYZ, SPARCL1, DGKK, WNK2, DNAH9, STRA8, and ST8SIA3) were identified in NAFLD patients HCC with cirrhosis. Here, PCDHB16 is linked to metabolic dysfunction-associated steatotic liver disease.