Moreover, our SCENIC analysis11 identified HNF4A as a transcription factor (TF) specifically enriched in hepatocytes of HCC and NAFLD but not in healthy tissues, with its target genes (e.g., IRS1 and FGFR3) exhibiting similar expression dynamics (Fig. 3C, Figure S2A, Table S3). Here, FGFR3 is linked to metabolic dysfunction-associated steatotic liver disease.