Evidence map›Paper›PMID 40783590›Full record

ArticleNPJ precision oncology2025

A core driver gene set identified based on geMER reveals its potential driver mechanism in pan-cancer.

Jing Gan, Yuncong Wang, Zhuoran Shi, Haoyu Hu, Manyi Xu, Xinrong Li, Wenbo Dong, Jiaheng He, Yusen Zhao, Yakun Zhang and 6 more

Abstract read
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In one paragraph

Article in NPJ precision oncology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

16 authors.

Jing Gan *College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Yuncong Wang *College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Zhuoran ShiThe Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
Haoyu HuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Manyi XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Xinrong LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Wenbo DongCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Jiaheng HeCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Yusen ZhaoCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Yakun ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Yue SunCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Caiyu ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Qianyi LuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Shangwei NingCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. ningsw@ems.hrbmu.edu.cn.
Yan JinCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. jinyan@hrbmu.edu.cn.
Hui ZhiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China. zhihui@ems.hrbmu.edu.cn.

Funding

National Natural Science Foundation of China,China 32070672National Natural Science Foundation of China,China 32170674National Natural Science Foundation of China,China 82172353Outstanding Youth Foundation of Heilongjiang Province of China YQ2022C034Scientific Research Project of Heilongjiang Province of China CZKYF2021-2-B012
6 · The paper itself

Abstract

Increasing evidence underscores the driving role of coding and non-coding variants in cancer development. Analyzing gene sets in biological processes offers deeper insights into the molecular mechanisms of carcinogenesis. Here, we developed geMER to identify candidate driver genes genome-wide by detecting mutation enrichment regions within coding and non-coding elements. We subsequently designed a pipeline to identify a core driver gene set (CDGS) that broadly promotes carcinogenesis across multiple cancers. CDGS comprising 25 genes for 25 cancers displayed instability in DNA aberrations. Variants within the TTN enrichment region may influence the folding of the I-set domain by altering local polarity or side-chain chemistry properties of amino acids, potentially disrupting its antigen-binding capacity in LUAD. Multi-omics analysis revealed that APOB emerged as a candidate oncogene in LIHC, whose genetic alterations within the enrichment region may activate key TFs, upregulate DNA methylation levels, modulate critical histone modifications, and enhance transcriptional activity in the HepG2 and A549 cell lines compared to Panc1. Additionally, CDGS mutation status was an independent prognostic factor for the pan-cancer cohort. High-risk patients tended to develop an immunosuppressive microenvironment and demonstrated a higher likelihood of responding to ICI therapy. Finally, we provided a user-friendly web interface to explore candidate driver genes using geMER ( http://bio-bigdata.hrbmu.edu.cn/geMER/ ).

Identifiers

PMID40783590
PMCPMC12335558

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