Extended Data Fig. 2: CLEC12B is selectively upregulated in tumor-infiltrating NK cells and positively correlates with immune checkpoint receptor expression in HCC.

a-d, Single-cell RNA-seq analysis showing that CLEC12B expression in NK cells is significantly higher in HCC tumor-infiltrating (IT, n = 17) compared to peritumoral tissue (PT, n = 17) unpaired samples with CLEC12B⁺ NK cells (a). Gene Ontology (GO) enrichment of pathways down-regulated vs. up-regulated in CLEC12B⁺ NK cells (from IT NK cell subset), derived by comparison of CLEC12B⁺ vs. CLEC12B⁻ NK cells (b). Analysis of TCGA HCC tumors (n = 374) and peritumoral tissues (n = 50) showing CLEC12B/CD56 transcript ratio is significantly higher in tumors compared to peritumor tissues (c). Correlation in the same TCGA HCC tumor cohort (n = 374) between normalized CLEC12B/CD56 expression and various immune-checkpoint receptor/CD56 ratios (d): TIGIT, PDCD1, HAVCR2, LAG3. e-g, Mass cytometry analysis of HCC patients (n = 19). Gating strategy (e). Numbers in the drawn gates indicate the cell percentages. Representative flow cytometry plots (f) and quantification (g) of CELC12B expression in CD3+ cells. h, Correlation between CLEC12B and the expression of LAG-3 inhibitory receptors was analyzed in the PT and IT NK cells. i, Heat map represented correlation between the expression level of CLEC12B and the expression levels of HACVR2, TIGIT, PDCD1, and LAG3 in LIHC (n = 371); Data in a, c, g are presented as mean ± s.e.m. Data in (d, h) is shown with shaded areas representing 95% confidence intervals. Box-and-whisker plots show the median (centre line), the interquartile range (25th–75th percentiles), and whiskers extending from the minimum to the maximum values (a), all individual data points are shown. Statistical significance was determined by unpaired two-tailed Student’s t-test (a, c) or paired two-tailed Student’s t-test (g) two-sided correlation analysis (d, h).Exact P values are indicated in the figures.

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