Evidence map›Paper›PMID 41203724›Full record

ArticleScientific reports2025

Interrogating subclonal heterogeneity of liver cancer with single-cell multi-omics analysis.

Liwen Zhang, Dandan Hu, Xing Peng, Dan Su, Lei Chang, Yi Guo, Kai Tian, Qingpei Huang, Enze Deng, Zhuojie Su and 7 more

Abstract read
In one paragraph

Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors.

Liwen Zhang *School of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Dandan Hu *State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Esophageal Cancer Institute, Guangzhou, China.
Xing Peng *Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
Dan Su *Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
Lei Chang *Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
Yi GuoSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Kai TianSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Qingpei HuangGuangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
Enze DengGuangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
Zhuojie SuSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Longxi LiSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Xiong XiongSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Weiyuan MaSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Hongjian QiSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China.
Yaojun ZhangState Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Esophageal Cancer Institute, Guangzhou, China. zhangyuj@sysucc.org.cn.
Yanxiao ZhangSchool of Life Sciences, Westlake University, No. 600 Dunyu Road, Hangzhou, 310030, Zhejiang, China. zhangyanxiao@westlake.edu.cn.
Xiaoying FanGuangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China. fan_xiaoying@gzlab.ac.cn.

Funding

Major Project of Guangzhou National Laboratory GZNL2024A03001
6 · The paper itself

Abstract

Hepatocellular carcinomas (HCC) with multinodular morphology were typically polyclonal and exhibited extensive heterogeneity. We explored the multiple-layer heterogeneity of HCC utilizing single-cell multiomics sequencing together with multiregional sampling. We found that Confluent Multi-Nodular samples exhibit more heterogeneous immune landscapes characterized by increased transcriptome heterogeneity and more complex immune-related interactions compared to Single Nodular (SN) samples. We identified differential DNA methylation patterns among distinct tumor foci in a subset of liver cancer patients. Global DNA hypomethylation in cancer cells predominantly occurs in partially methylated domains. We predicted and validated two genes, GADD45A and SNHG6, as potential drivers of DNA hypomethylation. Lastly, we demonstrated that DNA methylation distance serves as a more robust metric than gene expression distance for reconstructing tumor evolutionary trajectories.

Indexed as

Carcinoma, HepatocellularGenetic HeterogeneityLiver NeoplasmsSingle-Cell AnalysisCell Cycle ProteinsDNA MethylationGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMaleMultiomicsTranscriptomeCell Cycle Proteins

Identifiers

PMID41203724
PMCPMC12594797

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.