Effect of CD5-2 on endothelial cells with or without VE-cadherin expression

Purpose: The goals of this study are to confirm whether CD5-2 works through VE-cadherin Methods: mRNA profiles of HUVEC and VE-cadherin-/- EC treated with either control or CD5-2 were generated by deep sequencing using Illumina Hiseq4000 platform and 150 bp paired-end reads were generated. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indices of the reference genome were built using Bowtie (v2.2.3) and paired-end clean reads were aligned to the reference genome using TopHat (v2.0.12). Differentially expressed genes were then determined using DESeq R package (v1.12.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P-value<0.05 and FDR<0.005 were assigned as differentially expressed. Results: 585 differentially expressed genes (DEGs) in CD5-2 treated ECs compared with control treated ECs (P < 0.05; false discovery rate [FDR] ≤ 0.005). In stark contrast to that seen in normal ECs, in VE-cadherin-/- ECs, no gene was significantly differently expressed between control and CD5-2 treated group when using the same cut-off criteria, Conclusions: Our study suggests VE-cadherin is essential for the CD5-2 mediated gene changes mRNA profiles of HUVEC and VE-cadherin-/- EC treated with either control or CD5-2 were generated by deep sequencing, a pool of 3-5 biological replicates, using Illumina Hiseq4000 platform