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. 2025 Apr 9;24:110. doi: 10.1186/s12943-025-02314-w

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© The Author(s) 2025

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Fig. 3 — Characteristics of tumor cells. A t-SNE visualization of two tumor regions TR1 and TR2 colored by distribution and patient tumors. R, responder; NR, non-responders. B Stacked barplot of the proportion of regions in each of the tumors. C Bubble chart of gene ontology enrichment for the tumor region markers. D Violin plots of the humoral immune, inflammatory, cholesterol biosynthetic process and carboxylic acid biosynthetic process scores of tumor cells between R and NR groups. E Bar plot showing the top 10 enrichment scores of significantly enriched pathways for up-regulated genes in pre-treatment bulk-seq data. F Heatmap showing the genes associated with humoral immune response pathway in the pre-treatment bulk-seq (liver biopsies) and ST-seq data. G Violin plot depicting the proliferation and hepatic level for tumor region. H Violin plot depicting the stemness level for each patient (upper panel), accompanied by a heatmap displaying the expression levels of liver cancer stem cell markers (lower panel). I. Correlation analysis between necrosis rate and stemness score in HCC