Microarray meta‐analysis defines global angiogenesis‐related gene expression signatures in human carcinomas

Abstract

Angiogenesis is a prerequisite for progression of cancers. The number of genes linked to angiogenesis suggests the existence of complex gene-networks, which remain to be elucidated. To identify angiogenesis genes deregulated in carcinomas, we performed a meta-profiling analysis of published gene expression microarray studies. Own microarray and quantitative RT-PCR data were obtained from a colorectal carcinoma cohort. Applying highly stringent inclusion criteria, 15 cancer array studies were suitable for our analysis. These studies provided 789 tumor specimens and 190 samples of healthy tissues yielding a total of approx. 1,000,000 gene expression measurements. Meta-analysis on the expression of 480 angiogenesis-related genes in 10 cancer types identified a characteristic, entity-independent "global" cancer expression signature of 25 angiogenesis-related genes showing high frequency down-regulation when compared to corresponding healthy tissues. Furthermore, we characterized 25 genes displaying frequent up-regulation, yet less often than the 25 down-regulated genes. Comparative inter-study cross-validation revealed that both signatures discriminate cancers from healthy tissues with high accuracy in independent test sets. Moreover, own microarray data of colorectal carcinomas confirmed the specific and sensitive discriminating potential of both signatures. These results were validated by quantitative RT-PCR for eight genes displaying the highest differences in the microarray analysis. Our study for the first time defines global gene expression signatures linked to angiogenesis in carcinomas. Our findings suggest that gene down-regulation may represent a central aspect of tumor angiogenesis.