Original Article
Coexpression and expression quantitative trait loci analyses of the angiogenesis gene-gene interaction network in prostate cancer
Abstract
Background: Prostate cancer (PCa) shows a substantial clinical heterogeneity. The existing risk classification for PCa prognosis based on clinical factors is not sufficient. Although some biomarkers for PCa aggressiveness have been identified, their underlying functional mechanisms are still unclear. We previously reported a gene-gene interaction network associated with PCa aggressiveness based on single nucleotide polymorphism (SNP)-SNP interactions in the angiogenesis pathway. The goal of this study is to investigate potential functional evidence of the involvement of the genes in this gene-gene interaction network.
Methods: A total of 11 angiogenesis genes were evaluated. The crosstalks among genes were examined through coexpression and expression quantitative trait loci (eQTL) analyses. The study population is 352 Caucasian PCa patients in the Cancer Genome Atlas (TCGA) study. The pairwise coexpressions among the genes of interest were evaluated using the Spearman coefficient. The eQTL analyses were tested using the Kruskal-Wallis test.
Results: Among all within gene and 55 possible pairwise gene evaluations, 12 gene pairs and one gene (MMP16) showed strong coexpression or significant eQTL evidence. There are nine gene pairs with a strong correlation (Spearman correlation ≥0.6, P<1×10-13). The top coexpressed gene pairs are EGFR-SP1 (r=0.73), ITGB3- HSPG2 (r=0.71), ITGB3- CSF1 (r=0.70), MMP16-FBLN5 (r=0.68), ITGB3-MMP16 (r=0.65), ITGB3-ROBO1 (r=0.62), CSF1- HSPG2 (r=0.61), CSF1-FBLN5 (r=0.6), and CSF1-ROBO1 (r=0.60). One cis-eQTL in MMP16 and five trans-eQTLs (MMP16-ESR1, ESR1-ROBO1, CSF1-ROBO1, HSPG2-ROBO1, and FBLN5-CSF1) are significant with a false discovery rate q value less than 0.2.
Conclusions: These findings provide potential biological evidence for the gene-gene interactions in this angiogenesis network. These identified interactions between the angiogenesis genes not only provide information for PCa etiology mechanism but also may serve as integrated biomarkers for building a risk prediction model for PCa aggressiveness.
Methods: A total of 11 angiogenesis genes were evaluated. The crosstalks among genes were examined through coexpression and expression quantitative trait loci (eQTL) analyses. The study population is 352 Caucasian PCa patients in the Cancer Genome Atlas (TCGA) study. The pairwise coexpressions among the genes of interest were evaluated using the Spearman coefficient. The eQTL analyses were tested using the Kruskal-Wallis test.
Results: Among all within gene and 55 possible pairwise gene evaluations, 12 gene pairs and one gene (MMP16) showed strong coexpression or significant eQTL evidence. There are nine gene pairs with a strong correlation (Spearman correlation ≥0.6, P<1×10-13). The top coexpressed gene pairs are EGFR-SP1 (r=0.73), ITGB3- HSPG2 (r=0.71), ITGB3- CSF1 (r=0.70), MMP16-FBLN5 (r=0.68), ITGB3-MMP16 (r=0.65), ITGB3-ROBO1 (r=0.62), CSF1- HSPG2 (r=0.61), CSF1-FBLN5 (r=0.6), and CSF1-ROBO1 (r=0.60). One cis-eQTL in MMP16 and five trans-eQTLs (MMP16-ESR1, ESR1-ROBO1, CSF1-ROBO1, HSPG2-ROBO1, and FBLN5-CSF1) are significant with a false discovery rate q value less than 0.2.
Conclusions: These findings provide potential biological evidence for the gene-gene interactions in this angiogenesis network. These identified interactions between the angiogenesis genes not only provide information for PCa etiology mechanism but also may serve as integrated biomarkers for building a risk prediction model for PCa aggressiveness.
