Interestingly, we found that compared with other clusters, many stemness-associated genes were more dysregulated in cluster 3 of the ZS-SEQ-HCC cohort, including ARPC5L [19], ASAP1 [20,21], CLDN4 [22], ELF3 [23,24], MAP2K2 [25], and PRKCD [26] (Fig. S12A and B). Here, CLDN4 is linked to hepatocellular carcinoma.