Evidence map›Paper›PMID 39234248›Full record

ArticleFrontiers in immunology2024

Ding-Ming Song, Tong Shen, Kun Feng, Yi-Bo He, Shi-Liang Chen, Yang Zhang, Wen-Fei Luo, Lu Han, Ming Tong, Yanyang Jin

Abstract read
In one paragraph

Article in Frontiers in immunology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 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

10 authors.

Ding-Ming Song *Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
Tong Shen *Department of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
Kun FengDepartment of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
Yi-Bo HeDepartment of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
Shi-Liang ChenDepartment of Clinical Lab, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
Yang ZhangDepartment of Vascular Surgery, Fuwai Yunnan Cardiovascular Hospital, Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, Yunnan, China.
Wen-Fei LuoJinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
Lu HanDepartment of Infectious Diseases, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China.
Ming TongDepartment of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
Yanyang JinDepartment of Urology, Jinzhou Medical University, The First Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Background: Bladder cancer, a highly fatal disease, poses a significant threat to patients. Positioned at 19q13.2-13.3, LIG1, one of the four DNA ligases in mammalian cells, is frequently deleted in tumour cells of diverse origins. Despite this, the precise involvement of LIG1 in BLCA remains elusive. This pioneering investigation delves into the uncharted territory of LIG1's impact on BLCA. Our primary objective is to elucidate the intricate interplay between LIG1 and BLCA, alongside exploring its correlation with various clinicopathological factors. Methods: We retrieved gene expression data of para-carcinoma tissues and bladder cancer (BLCA) from the GEO repository. Single-cell sequencing data were processed using the "Seurat" package. Differential expression analysis was then performed with the "Limma" package. The construction of scale-free gene co-expression networks was achieved using the "WGCNA" package. Subsequently, a Venn diagram was utilized to extract genes from the positively correlated modules identified by WGCNA and intersect them with differentially expressed genes (DEGs), isolating the overlapping genes. The "STRINGdb" package was employed to establish the protein-protein interaction (PPI) network.Hub genes were identified through the PPI network using the Betweenness Centrality (BC) algorithm. We conducted KEGG and GO enrichment analyses to uncover the regulatory mechanisms and biological functions associated with the hub genes. A machine-learning diagnostic model was established using the R package "mlr3verse." Mutation profiles between the LIG1^high and LIG1^low groups were visualized using the BEST website. Survival analyses within the LIG1^high and LIG1^low groups were performed using the BEST website and the GENT2 website. Finally, a series of functional experiments were executed to validate the functional role of LIG1 in BLCA. Results: Our investigation revealed an upregulation of LIG1 in BLCA specimens, with heightened LIG1 levels correlating with unfavorable overall survival outcomes. Functional enrichment analysis of hub genes, as evidenced by GO and KEGG enrichment analyses, highlighted LIG1's involvement in critical function such as the DNA replication, cellular senescence, cell cycle and the p53 signalling pathway. Notably, the mutational landscape of BLCA varied significantly between LIG1 Conclusions: Our research demonstrates that LIG1 plays a crucial role in promoting bladder cancer malignant progression by heightening proliferation, invasion, EMT, and other key functions, thereby serving as a potential risk biomarker.

Indexed as

Biomarkers, TumorDNA Ligase ATPMachine LearningSingle-Cell AnalysisUrinary Bladder NeoplasmsAgedCell Line, TumorComputational BiologyFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticGene Regulatory NetworksHumansMaleMiddle AgedPrognosisBiomarkers, TumorDNA Ligase ATPLIG1 protein, humanbioinformaticsLIG1machine-learningsingle-celltumorinfiltrating immune cellurothelial bladder cancer

Identifiers

PMID39234248
PMCPMC11371609

What OpenQuestion holds

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LicenceCC BY
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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.