The Cellular and Immune Context of YTHDC1 in Hepatocellular Carcinoma: A Single-Cell and Multicohort Study.

BACKGROUND

YTHDC1 is a nuclear N6-methyladenosine reader involved in RNA processing. Its abundance, cellular distribution, and relationship with the immune microenvironment in hepatocellular carcinoma (HCC) remain incompletely characterized.

METHODS

We integrated paired tumor-adjacent transcriptomic and proteomic cohorts, three single-cell RNA-sequencing datasets containing 249,080 quality-controlled cells, four outcome cohorts, three immune checkpoint inhibitor (ICI) cohorts, paired clinical specimens, and cell-based YTHDC1-knockdown assays. Patient-level analyses covered hepatocyte programs, immune states, expression-supported ligand-receptor axes, survival, ICI response, and exploratory single-cell network perturbation.

RESULTS

YTHDC1 protein abundance was higher in 160 paired CPTAC samples (Hedges' g = 1.21, 95% confidence interval [CI] 1.01-1.42), whereas RNA effects varied across cohorts. Single-cell analysis localized YTHDC1 across hepatic and immune compartments and identified patient-level associations with hepatocyte, lymphoid, and myeloid programs. SPP1-CD44 received the strongest cross-cohort expression support among prespecified hepatocyte-to-myeloid axes. A transferred hepatocyte state showed a pooled tumor-adjacent effect of g = 0.42 (95% CI 0.04-0.80), and higher YTHDC1 abundance was associated with poorer overall survival in study-aware univariable models (hazard ratio 1.20, 95% CI 1.06-1.36). In 37 ICI-treated patients, the pooled responder-nonresponder effect for YTHDC1 was small (g = 0.05, 95% CI -0.60 to 0.71). Exploratory virtual knockout showed modest cross-cohort agreement in network perturbation ranks. Paired clinical tissues supported increased YTHDC1 mRNA and protein abundance, and YTHDC1 silencing reduced proliferation-related readouts and THP-1 migration in two HCC cell lines.

CONCLUSIONS

YTHDC1 is increased at the protein level in HCC and is situated within identifiable hepatocyte and immune programs. Functional assays support its contribution to HCC cell proliferation and tumor cell-dependent macrophage-like cell migration under the tested conditions.