Evidence map›Paper›PMID 39831920›Full record

ArticleCellular oncology (Dordrecht, Netherlands)2025

Three-dimensional genome architecture in intrahepatic cholangiocarcinoma.

Youfeng Liang, Cong Li, Renchao Zou, Lu Ying, Xiaoyang Chen, Zhaohai Wang, Wenjing Zhang, Mingxuan Hao, Hao Yang, Rui Guo and 13 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cellular oncology (Dordrecht, Netherlands), 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. Review
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

23 authors.

Youfeng Liang *College of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Cong Li *The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
Renchao Zou *Department of Urology, Second Affiliated Hospital of Kunming Medical University, Kunming, 650000, China.
Lu YingCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Xiaoyang ChenCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Zhaohai WangThe First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
Wenjing ZhangCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Mingxuan HaoCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Hao YangThe First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
Rui GuoCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Guanglin LeiThe Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China.
Fang SunThe Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China.
Kexu ZhaoCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Yu ZhangThe Fifth Medical Center, Chinese PLA General Hospital, Beijing, 100039, China.
Jia DaiCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Shangya FengCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Keyue ZhangCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Luyuan GuoCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Shuyue LiuCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China.
Chuanxing WanCollege of Life Science and Technology, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, Tarim University, Alar, Xinjiang, 843300, China.
Lin WangDepartment of Urology, Second Affiliated Hospital of Kunming Medical University, Kunming, 650000, China. wanglinfey@126.com.
Penghui YangThe First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China. ypenghuiamms@hotmail.com.
Zhao YangCollege of Life Science and Technology, Innovation Center of Molecular Diagnostics, Beijing University of Chemical Technology, Beijing, 100029, China. yangzhao@mail.buct.edu.cn.

Funding

National Natural Science Foundation of China 92359202Open Competition to Select the Best Candidates" Key Technology Program for Nucleic Acid Drugs of NCTIB NCTIB2022HS01016Scientific and Technological Research Project of Xinjiang Production and Construction Corps 2022AB022the Joint Project of Biomedical Translational Engineering Research Center of Beijing University of Chemical Technology-China-Japan Friendship Hospital XK2023-21
6 · The paper itself

Abstract

purposeIntrahepatic cholangiocarcinoma (ICC) is a common primary hepatic tumors with a 5-year survival rate of less than 20%. Therefore, it is crucial to elucidate the molecular mechanisms of ICC. Recently, the advance of high-throughput chromosome conformation capture (Hi-C) technology help us look insight into the three-dimensional (3D) genome structure variation during tumorigenesis. However, its function in ICC pathogenesis remained unclear.

methodsHi-C and RNA-sequencing were applied to analyze 3D genome structures and gene expression in ICC and adjacent noncancerous hepatic tissue (ANHT). Furthermore, the dysregulated genes due to 3D genome changes were validated via quantitative real-time PCR and immunohistochemistry.

resultsPrimarily, the intrachromosomal interactions of chr1, chr2, chr3, and chr11 and the interchromosomal interactions of chr1-chr10, chr13-chr21, chr16-chr19, and chr19-chr22 were also significantly distinct between ANHT and ICC, which may potentially contribute to the activation of cell migration and invasion via the upregulation of WNT10A, EpCAM, S100A3/A6, and MAPK12. Interestingly, 56 compartment regions from 23 chromosomes underwent A to B or B to A transitions during ICC oncogenesis, which attenuated the complement pathway through the downregulation of C8A/C8B, F7, F10, and F13B. Notably, topologically associated domain (TAD) rearrangements were identified in the region containing HOPX (chr4: 57,514,154-57,522,688) and ACVR1 (chr2:158,592,958-158,732,374) in ICC, which may contribute to the hijacking of remote enhancers that were previously outside the TAD and increased expression of HOPX and ACVR1.

conclusionsThis study reveals relationship between 3D genome structural variations and gene dysregulation during ICC tumorigenesis, indicating the molecular mechanisms and potential biomarkers.

Indexed as

Bile Duct NeoplasmsCholangiocarcinomaGenome, HumanFemaleGene Expression Regulation, NeoplasticHumansMaleMiddle AgedACVR1BiomarkerHOPXIntrahepatic cholangiocarcinomaThree-dimensional (3D) genome architecture

Identifiers

PMID39831920
PMCPMC12119775

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LicenceCC BY-NC-ND
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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.