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. 2022 Oct 10:12:1001400.
doi: 10.3389/fonc.2022.1001400. eCollection 2022.

Screening potential biomarkers of cholangiocarcinoma based on gene chip meta-analysis and small-sample experimental research

Hengyan Shen  1   2 , Xinyu Bai  2 , Jie Liu  2 , Ping Liu  2 , Tao Zhang  1
Affiliations

Screening potential biomarkers of cholangiocarcinoma based on gene chip meta-analysis and small-sample experimental research

Hengyan Shen et al. Front Oncol. .

Abstract

Cholangiocarcinoma (CCA) is a rare malignant tumor associated with poor prognosis. This study aimed to identify CCA biomarkers by investigating differentially expressed genes (DEGs) between CCA patients and healthy subjects obtained from the Gene Expression Omnibus database. Bioinformatics tools, including the Illumina BaseSpace Correlation Engine (BSCE) and Gene Expression Profiling Interactive Analysis (GEPIA), were used. The initial DEGs from GSE26566, GSE31370, and GSE77984 were analyzed using GEO2R and Venn, and protein-protein interaction networks were constructed using STRING. The BSCE was applied to assess curated CCA studies to select additional DEGs and them DEGs across the 10 biosets, which was supported by findings in the literature. The final 18 DEGs with clinical significance for CCA were further verified using GEPIA. These included CEACAM6, EPCAM, LAMC2, MMP11, KRT7, KRT17, KRT19, SFN, and SOX9, which were upregulated, and ADH1A, ALDOB, AOX1, CTH, FGA, FGB, FGG, GSTA1, and OTC, which were downregulated in CCA patients. Among these 18 genes, 56 groups of genes (two in each group) were significantly related, and none were independently and differentially expressed. The hub genes FGA, OTC, CTH, and MMP11, which were most correlated with the 18 DEGs, were screened using STRING. The significantly low expression of FGA, OTC, and CTH and significantly high expression of MMP11 were verified by immunohistochemical analysis. Overall, four CCA biomarkers were identified that might regulate the occurrence and development of this disease and affect the patient survival rate, and they have the potential to become diagnostic and therapeutic targets for patients with CCA.

Keywords: bioinformatics; biomarkers; cholangiocarcinoma; differentially expressed genes; meta-analysis.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Genes that differed between normal subjects and CCA patients, including all intersecting genes in the three data sets. (A) 9 DEGs were upregulated (logFC>2). (B) 10 DEGs were downregulated (logFC<-2).
Figure 2
Figure 2
PPI network intersection of differential genes between the CCA patients and normal subjects was determined based on the STRING database.
Figure 3
Figure 3
Heatmap of 18 DEGs and 10 biosets. Genes that correspond to the same biosets have a value of zero. A higher −log (p-values) corresponds to a higher positive correlation. The format is Gene_GSE bioset_Bioset name.
Figure 4
Figure 4
GEPIA website-based verification of the expression of nine upregulated genes associated with poor prognosis (*P < 0.05).
Figure 5
Figure 5
GEPIA website-based verification of the expression of nine downregulated genes associated with poor prognosis (*P < 0.05).
Figure 6
Figure 6
Network and heat map display correlation analysis of 18 gene expression in CCA. (A) Heatmap of correlation between genes. (B) The PPI network relationships of the gene combinations.
Figure 7
Figure 7
(A) Representative images of IHC staining from eleven primary CCA specimens and eleven paracancer normal tissue specimens (200x magnification). (B) Statistical analysis of the mean optical density (MOD) of CTH, FGA, OTC and MMP11 staining in CCA specimens and normal tissues. The bar chart shows the mean ±SEM of more than three independent experiments (***P< 0.001).
Figure 8
Figure 8
Heatmap of the correlation of (FGA, OTC, CTH, and MMP11) with clinical CCA stage-specific and/or metastatic markers.
See this image and copyright information in PMC

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References

    1. Blechacz B. Cholangiocarcinoma: Current knowledge and new developments. Gut Liver (2017) 11(1):13–26. doi: 10.5009/gnl15568 - DOI - PMC - PubMed
    1. Khan AS, Dageforde LA. Cholangiocarcinoma. Surg Clin North Am (2019) 99(2):315–35. doi: 10.1016/j.suc.2018.12.004 - DOI - PubMed
    1. Rizvi S, Khan SA, Hallemeier CL, Kelley RK, Gores GJ. Cholangiocarcinoma - evolving concepts and therapeutic strategies. Nat Rev Clin Oncol (2018) 15(2):95–111. doi: 10.1038/nrclinonc.2017.157 - DOI - PMC - PubMed
    1. Brindley PJ, Bachini M, Ilyas SI, et al. . Cholangiocarcinoma. Nat Rev Dis Primers (2021) 7(1):65. doi: 10.1038/s41572-021-00300-2. - DOI - PMC - PubMed
    1. Chong DQ, Zhu AX. The landscape of targeted therapies for cholangiocarcinoma: current status and emerging targets. Oncotarget (2016) 7(29):46750–67. doi: 10.18632/oncotarget.8775 - DOI - PMC - PubMed