Supplementary MaterialsFigure S1: A. primers. B. Fluorescence intensity curves for qPCR

Supplementary MaterialsFigure S1: A. primers. B. Fluorescence intensity curves for qPCR for VEGF165b using isoform specific primers. C. Melt curve for VEGF165a. D. Melt curve for VEGF165b(DOCX) pone.0068399.s002.docx (188K) GUID:?8C10E8C2-7212-4020-9B5A-48DAEDF2FF30 Abstract Vascular Endothelial Growth Factor-A (VEGF-A) can be generated as multiple isoforms by alternative splicing. Two families of isoforms have been described in humans, pro-angiogenic isoforms typified by VEGF-A165a, and anti-angiogenic isoforms typified by VEGF-A165b. The practical determination of expression levels of alternative isoforms of the same gene may be complicated by experimental protocols that favour one isoform over another, Endoxifen cost and the use of specific positive and negative controls is essential for the interpretation of findings on expression of the isoforms. Here we address some of the difficulties in experimental design when investigating alternative splicing of VEGF isoforms, and discuss the use of appropriate control paradigms. We demonstrate why use of specific control experiments can prevent assumptions that VEGF-A165b is not present, when in fact it is. We reiterate, and confirm previously published experimental design protocols that demonstrate the importance of using positive controls. These include using known target sequences to show that this experimental conditions are suitable for PCR amplification of VEGF-A165b mRNA for both q-PCR and RT-PCR and to ensure Endoxifen cost that mispriming does not occur. We also provide evidence that demonstrates that detection of VEGF-A165b protein in mice needs to be tightly controlled to prevent detection of mouse IgG by a secondary antibody. We also show Endoxifen cost that human VEGF165b protein can be immunoprecipitated from cultured human cells and that immunoprecipitating VEGF-A results in protein that is detected by VEGF-A165b antibody. These findings support the conclusion that more information around the biology of VEGF-A165b isoforms is required, and confirm the importance of the experimental RHOA design in such investigations, including the use of specific positive and negative controls. Introduction Vascular Endothelial Growth Factor-A is generated as multiple splice isoforms using alternative splice sites within exons 6, 7 and 8 in normal and pathological tissues [1], [2]. Alternative splicing of the terminal exon, exon 8 gives rise to two families of isoforms, VEGF-Axxxa and VEGF-Axxxb, Endoxifen cost which have the same number of amino acids but different C terminal sequences [3]. The differences between these two families of isoforms lie in the deletion of 66 nucleotides from the beginning of exon 8 arising from a 3 alternative splice site. The VEGF-Axxxb family was serendipitously discovered in 2002, after the amplification of PCR products using primers in the 3 untranslated region of exon 8 of cDNA generated from multiple normal human kidney samples collected at the time of nephrectomy and frozen. It was notable that this product was less commonly found in the renal carcinomata from the same whole organ samples [3]. Since 2002, in addition to the VEGFxxxb isoform first identified, VEGF-A165b, studies have also exhibited the isoforms VEGF-A121b [4], VEGF-A189b [5] and VEGF-A145b [6]. Most of these studies have investigated expression in fresh human tissue, and most studies have found the VEGF-Axxxb mRNA to be downregulated in pathological conditions such as cancer [7], diabetic retinopathy [6], Denys Drash Syndrome (a condition caused by Endoxifen cost a mutation of the tumour suppressor gene WT1) [8], and retinal vein occlusion [9]. In contrast VEGF-A165b has been shown to be upregulated in systemic sclerosis [10] and in asthma [11]. The regulation of VEGF splicing has been investigated and it has been exhibited that in epithelial cells, growth factor stimulation (e.g. by IGF) induces phosphorylation of the Serine Arginine Rich Factor 1 (SRSF1) by the kinase SR protein Kinase 1, enabling nuclear localisation of SRSF1 and binding to the VEGF pre-mRNA, facilitating splicing to the proximal splice site, and VEGF165a expression [12]. SRPK1 over-expression, for instance by removal of transcriptional repression in WT1 mutant cells [13], results in.