Retinoblastoma gene expression profiling based on bioinformatics analysis

BMC Medical Genomics

Research

Mingzhi Lu¹  Yiqiao Xing¹  Xuejiao Xu²  Wei Du²  Wei Zuo²  Jingwen Zhou²  Jun Mao²  Ying Chen²  Huirong Xu²  Siduo Lu³ 

[1] Aier Eye Hospital of Wuhan University, Wuhan, China;The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China;The First Affiliated Hospital of Kunming Medical University, Yunnan, China;

关键词: Retinoblastoma;    Bioinformatics analysis;    Biomarkers;    ceRNA;    Regulatory network;   

DOI  :  10.1186/s12920-023-01537-4

 received in 2023-02-21, accepted in 2023-05-09,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundRetinoblastoma (RB) is frequently occurring malignant tumors that originate in the retina, and their exact cause and development mechanisms are yet to be fully comprehended. In this study, we identified possible biomarkers for RB and delved into the molecular mechanics linked with such markers.MethodsIn this study GSE110811 and GSE24673 were analyzed. Weighted gene co-expression network analysis (WGCNA) was applied to screen modules and genes associated with RB. By overlapping RB-related module genes with differentially expressed genes (DEGs) between RB and control samples, differentially expressed retinoblastoma genes (DERBGs) were acquired. A gene ontology (GO) enrichment analysis and a kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis were conducted to explore the functions of these DERBGs. To study the protein interactions of DERBGs, a protein–protein interaction (PPI) network was constructed. Hub DERBGs were screened using the least absolute shrinkage and selection operator (LASSO) regression analysis, as well as the random forest (RF) algorithm. Additionally, the diagnostic performance of RF and LASSO methods was evaluated using receiver operating characteristic (ROC) curves and single-gene gene set enrichment analysis (GSEA) was conducted to explore the potential molecular mechanisms involved with these Hub DERBGs. In addition, the competing endogenous RNA (ceRNA) regulatory network of Hub DERBGs was constructed.ResultAbout 133 DERBGs were found to be associated with RB. GO and KEGG enrichment analyses revealed that the important pathways of these DERBGs. Furthermore, the PPI network revealed 82 DERBGs interacting with each other. By RF and LASSO methods, PDE8B, ESRRB, and SPRY2 were identified as Hub DERBGs in patients with RB. From the expression assessment of Hub DERBGs, it was found that the levels of expression of PDE8B, ESRRB, and SPRY2 were significantly decreased in the tissues of RB tumors. Secondly, single-gene GSEA revealed a connection between these 3 Hub DERBGs and oocyte meiosis, cell cycle, and spliceosome. Finally, the ceRNA regulatory network revealed that hsa-miR-342-3p, hsa-miR-146b-5p, hsa-miR-665, and hsa-miR-188-5p may play a central role in the disease.ConclusionHub DERBGs may provide new insight into RB diagnosis and treatment based on the understanding of disease pathogenesis.

【 授权许可】

CC BY   
© The Author(s) 2023

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