In silico identification and characterization of transcription factor binding sites upstream of the human PDGF gene

Abstract

The platelet-derived growth factor (PDGF) and its receptors are vital for a wide range of physiological processes such as development, proliferation, and migration, as well as pathological processes like tumor growth and invasion. Our aim here was to characterize in silico novel cis-regulatory elements (CREs) in the promoter sequences of PDGF genes to identify the transcription factors (TFs) associated with these sites. To do so, we retrieved those promoter sequences close to the transcription start site (TSS) from the ExPASy eukaryotic promoter database (EPD) and performed an in silico search and prediction of novel CREs in the promoter sequences of PDGF genes; then, we evaluated possible enriched transcription factors for these CREs. Our work demonstrated the co-expression between PDGFB and the transcription factor predicted to bind to the PDGF and POU2F1 in glioblastoma with a moderate correlation between the two (R2=0.24). Similar positive associations were observed for PDGFB with ZNF680 (R2= 0.21) and PDGFB with FOXF1 (R2= 0.32). These findings suggest putative relationships between PDGFB and specific transcription factors in glioblastoma, although functional regulatory interactions remain to be experimentally validated. Overall, the data highlighted selective coexpression patterns involving PDGFB and candidate transcription factors. These observations provide a basis for further investigation of potential transcriptional relationships in glioblastoma biology.