Evidence map›Paper›PMID 39190284›Full record

ArticleBreast cancer (Tokyo, Japan)2024

Hub metastatic gene signature and risk score of breast cancer patients with small tumor sizes using WGCNA.

Yu-Tien Chang, Zhi-Jie Hong, Hsueh-Han Tsai, An-Chieh Feng, Tzu-Ya Huang, Jyh-Cherng Yu, Kuo-Feng Hsu, Chi-Cheng Huang, Wei-Zhi Lin, Chi-Ming Chu and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Breast cancer (Tokyo, Japan), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

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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

3 citing papers in PubMed.

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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

12 authors.

Yu-Tien ChangSchool of Public Health, National Defense Medical Center, Taipei City, Taiwan.
Zhi-Jie HongDivision of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu Dist., Taipei City, 114202, Taiwan.
Hsueh-Han TsaiDivision of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu Dist., Taipei City, 114202, Taiwan.
An-Chieh FengDivision of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu Dist., Taipei City, 114202, Taiwan.
Tzu-Ya HuangSchool of Public Health, National Defense Medical Center, Taipei City, Taiwan.
Jyh-Cherng YuDivision of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu Dist., Taipei City, 114202, Taiwan.
Kuo-Feng HsuDivision of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu Dist., Taipei City, 114202, Taiwan.
Chi-Cheng HuangDepartment of Surgery, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, 11217, Taiwan.
Wei-Zhi LinAIoT Center, Tri-Service General Hospital, Taipei City, Taiwan.
Chi-Ming ChuSchool of Public Health, National Defense Medical Center, Taipei City, Taiwan.
Chia-Ming LiangDivision of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu Dist., Taipei City, 114202, Taiwan.
Guo-Shiou LiaoDivision of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu Dist., Taipei City, 114202, Taiwan. liaogs20371@gmail.com.ORCID http://orcid.org/0000-0003-1082-679X

Funding

Tri-Service General Hospital 801GB112190
6 · The paper itself

Abstract

backgroundBreast cancer (BC) is the most common cancer in women and accounts for approximately 15% of all cancer deaths among women globally. The underlying mechanism of BC patients with small tumor size and developing distant metastasis (DM) remains elusive in clinical practices.

methodsWe integrated the gene expression of BCs from ten RNAseq datasets from Gene Expression Omnibus (GEO) database to create a genetic prediction model for distant metastasis-free survival (DMFS) in BC patients with small tumor sizes (≤ 2 cm) using weighted gene co-expression network (WGCNA) analysis and LASSO cox regression.

resultsABHD11, DDX39A, G3BP2, GOLM1, IL1R1, MMP11, PIK3R1, SNRPB2, and VAV3 were hub metastatic genes identified by WGCNA and used to create a risk score using multivariable Cox regression. At the cut-point value of the median risk score, the high-risk score (≥ median risk score) group had a higher risk of DM than the low-risk score group in the training cohort [hazard ratio (HR) 4.51, p < 0.0001] and in the validation cohort (HR 5.48, p = 0.003). The nomogram prediction model of 3-, 5-, and 7-year DMFS shows good prediction results with C-indices of 0.72-0.76. The enriched pathways were immune regulation and cell-cell signaling. EGFR serves as the hub gene for the protein-protein interaction network of PIK3R1, IL1R1, MMP11, GOLM1, and VAV3.

conclusionPrognostic gene signature was predictive of DMFS for BCs with small tumor sizes. The protein-protein interaction network of PIK3R1, IL1R1, MMP11, GOLM1, and VAV3 connected by EGFR merits further experiments for elucidating the underlying mechanisms.

Indexed as

Biomarkers, TumorBreast NeoplasmsClass Ia Phosphatidylinositol 3-KinaseFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticGene Regulatory NetworksHumansMatrix Metalloproteinase 11Membrane ProteinsMiddle AgedNeoplasm MetastasisPrognosisProportional Hazards ModelsProto-Oncogene Proteins c-vavReceptors, Interleukin-1 Type IBiomarkers, TumorClass Ia Phosphatidylinositol 3-KinaseIL1R1 protein, humanMatrix Metalloproteinase 11Membrane ProteinsMMP11 protein, humanPIK3R1 protein, humanProto-Oncogene Proteins c-vavReceptors, Interleukin-1 Type IVAV3 protein, humanBreast cancerDistant metastasis-free survivalLASSO cox regressionSmall tumor sizeWeighted gene co-expression network analysis

Identifiers

PMID39190284
PMCPMC11489208

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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.