Identification of the vascular lineage specific transcriptome using two platforms

Angiogenesis and lymphangiogenesis have important roles in cancer progression and inflammatory diseases, but it has been a challenge to evaluate theses processes quantitatively. Using two different microarray platforms, we first identified the comprehensive lineage specific transcriptomes of human lymphatic (LEC) and blood vascular (BVEC) endothelial cells. We identified 226 lymphatic signature genes and 342 signature genes for blood vascular endothelium. In silico analyses of the biologic pathways associated with these genes revealed lineage specific functions for each cell type. Using a selection of 85 identified lineage specific genes, we developed a TaqMan RT PCR based, microfluidic card formatted low density microvascular differentiation array (LD MDA) that can be used to reliably identify and quantify endothelial cells based on their lineage specific differentiation. Furthermore, using LD MDA, we were able to quantify levels of angiogenesis and lymphangiogenesis in tissue samples from patients with chronic inflammatory skin disease, indicating that this assay might be developed as a novel tool for the rapid and quantitative evaluation of pathological (lymph)angiogenesis in clinical and pre clinical studies. Keywords: cross-platform study For cross comparison of the results obtained with both microarray technologies, the probes were annotated with locus link IDs and genes that were present on both platforms were aligned using the Spotfire software (Spotfire; Somerville, MA). Present calls were set by a p value cutoff of 0.05 and identified by the Affymetrix Microarray Suite Software 5.0, or by a signal to noise ratio (S/N) > 3 and quality flag < 5,000 determined by the AB1700 microarray software tool.