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Exploration of potential key pathways and genes in multiple ocular cancers through bioinformatics analysis

  • Oncology
  • Published:
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Abstract

Purpose

Primary cancers of the eye are common in ocular diseases. The objective of this study was to explore the underlying mechanisms and the potential target genes in multiple ocular cancers by bioinformatics approach.

Method

These gene expression profiles of GSE24673 (Retinoblastoma), GSE44295 (Uveal melanoma), and GSE103439 (Basal cell carcinoma of the eyelid) were downloaded from Gene Expression Omniniub (GEO) database. The differentially expressed genes (DEGs) in the three gene chips were identified by limma package in R software and gene integration was performed by using “RobustRankAggreg” package. Gene set enrichment analysis (GSEA) and the Gene Ontology (GO) were performed to the selected genes. Moreover, survival analysis was used to estimate uveal melanoma dataset.

Results

In total, 509 DEGs were identified in GSE24673 (retinoblastoma), 305 DEGs were identified in GSE44295 (uveal melanoma), and 753 DEGs were identified in GSE103439 (basal cell carcinoma of the eyelid). Among those genes, only IGF2BP3 was shared for the three cancer types. A total of 20 DEGs were identified through gene integration (score < 0.05) and IGF2BP3 was ranked the top. Moreover, GO analysis results showed that the 20 DEGs were significantly enriched in WNT signaling pathway, DNA damage, and apoptotic process. GSEA showed that pathways related with cellular respiratory chain are differentially enriched in IGF2BP3 low expression phenotype. Finally, two genes (ID3 and SLC6A15) can predict the overall survival in uveal melanoma patients.

Conclusions

This findings and results of study showed that the identification of DEGs and key pathways gives a promotion to understand the molecular mechanisms underlying the development of ocular cancers, which contribute to a more comprehensive understanding of cancers of the eye and provide new insights for these studies at gene level.

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Abbreviations

GEO:

Gene Expression Omniniub

DEGs:

differentially expressed gene

GSEA:

gene set enrichment analysis

GO:

Gene Ontology

CC:

cellular component

BP:

biological processes

MF:

molecular function

TCGA-UVM:

The Cancer Genome Atlas-uveal melanomas

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Authors and Affiliations

  1. Department of Ophthalmology, The People’s Hospital of Leshan, Leshan, 614000, China

    Qi Wan & Jing Tang

  2. State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510064, China

    Qi Wan

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  1. Qi Wan
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Correspondence to Jing Tang.

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Wan, Q., Tang, J. Exploration of potential key pathways and genes in multiple ocular cancers through bioinformatics analysis. Graefes Arch Clin Exp Ophthalmol 257, 2329–2341 (2019). https://doi.org/10.1007/s00417-019-04410-2

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  • DOI: https://doi.org/10.1007/s00417-019-04410-2

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