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.