Quantification of PDGFRA alternative transcripts improves the screening for X–PDGFRA fusions by reverse transcriptase-polymerase chain reaction

Abstract

Hematological malignancies with eosinophilia are often associated with fusions in PDGFRA, PDGFRB, or FGFR1 genes. RT-PCR has proved to be useful for finding new PDGFRA gene fusions, but some studies have shown overexpression of the TK domain which cannot be explained by the existence of such aberrations. This fact could be related to the expression of alternative PDGFRA transcripts. We show that quantification of the expression of three different PDGFRA fragments discriminates between PDGFRA alternative transcripts and fusion genes, and we have tested this novel methodological approach in a group of eosinophilia cases. Our data show that alternative PDGFRA transcripts should be taken into account when screening for PDGFRA aberrations, such as gene fusions, by RT-PCR. Expression from an internal PDGFRA promoter seems to be a frequent event, in both normal and leukemic samples, and is probably related to physiological conditions, but it could have a role in other tumors. Even so, we show that our RQ-PCR methodology can discriminate expression of alternative transcripts from the presence of X–PDGFRA fusion genes.

Keywords:

• Fusion genes
• PDGFRA
• alternative transcripts
• RQ-PCR

Declaration of interest: This work has been funded with the help of the Institute of Health Carlos III (FIS PI040037), Spanish Ministry of Science and Innovation (SAF 2007-62473), the PIUNA Program of the University of Navarra, and the Caja Navarra Foundation through the Program ‘You choose, you decide’ (Project 10.830). F.J.N is the recipient of a ‘Jerónimo de Ayanz’ award from the Government of Navarra.