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PDGFRB is a member of the tyrosine kinase family and PDGFRB gene rearrangements, already reported in myeloproliferative neoplasms (MPN), lead to its constitutive activation, ultimately affecting cell proliferation and migration. Patients with PDGFRB rearrangements respond to imatinib mesylate therapy. The t(2;5)(p16.2;q33.1) (PDGFRB/SPTBN1) has been reported only in one case of atypical MPN. SPTBN1 is a cytoskeletal protein with a role in mitotic spindle assembly.

The aim of the study was to fully characterize the partner fusion gene products formed as a result of the t(2;5)(p16.2;q33.1), encountered for the first time in a MDS patient.

A 78-years-old man presented for investigation of macrocytic anemia in 2012. Bone marrow smear showed mild dysplastic features in the granulocytic and megakaryocytic series. Bone marrow biopsy showed 60% cellularity and 4% CD34+ cells. The findings were consistent with MDS diagnosis. One year later, a new biopsy showed 23% CD34+ cells and dyserythropoiesis. The patient was administrated imatinib mesylate and since July 2014 has achieved hematological remission.
Following karyotypic analysis on bone marrow cells, interphase and metaphase FISH studies with specific BAC probes (UCSC Genome Bioinformatics, Source Bioscience) were performed in order to refine the chromosome breakpoints and detect the partner genes. RP11-100O5/RP11-368O19 BAC probes encompassing the PDGFRB gene at 5q33.1 and RP11-423Ν19/RP11-1022E1 BAC probes flanking the SPTBN1 gene at 2p16.2, were fluorescently labeled by nick-translation and used as dual-color break-apart probes. For the molecular characterization of the partner genes, 5’ rapid amplification of cDNA ends, followed by single step 5’RACE PCR was performed using a 5’Gene Racer primer (Life Technologies) and a reverse primer for PDGFRB exon 15. Second step PCR was carried out with a 5’Gene Racer nested primer and a reverse nested primer for PDGFRB exon 15. Following cloning, sequence analysis of the PCR products was conducted to fully characterize the fusion transcripts.

At diagnosis the karyotype was: 46,XY,t(2;5)(p16;q33)[20]/46,XY[5]. iFISH detected PDGFRB and SPTBN1 gene rearrangements in 56% of the cells. Based on those results, the patient was administrated imatinib mesylate and has favorably responded thus far. Metaphase FISH revealed translocation of 5’ PDGFRB at 2p16.2 and fusion with the 3’ SPTBN1 onto derivative chromosome 2. Accordingly, the 5’ of SPTBN1 was translocated at 5q33.1 and fused with the 3’ PDGFRB onto derivative 5. For the molecular characterization of the fusion gene transcripts, cloning and sequencing of the 5’RACE PCR products, showed that SPTBN1 exons 1-3 were fused to PDGFRB exon 12 onto derivative chromosome 5.

Cytogenetics identified the PDGFRB/SPTBN1 fusion gene generated from the rare translocation t(2;5)(p16.2;q33.1). Thorough molecular mapping analyses revealed that the genomic breakpoints were located at exon 3 of SPTBN1 gene and exon 12 of PDGFRB gene, leading to a PDGFRB/SPTBN1 fusion transcript comprising exons 1-3 of SPTBN1 gene and exon 12 of PDGFRB gene onto derivative chromosome 5. Importantly, the involvement of tyrosine kinase gene PDGFRB in t(2;5), encountered for the first time in a MDS case, prompted the administration of a successfully tailored-based signal transduction therapy (imatinib mesylate) to the patient.