In hematologic malignancies, deletion of 3p25-26 is a rare but recurrent cytogenetic aberration, indicating the presence of tumor suppressor gene (TSG) on this choromosome arm.
We revealed a t(3;5)(p25;q35) that was identified by conventional cytogenetics results in a novel fusion of KIAA0379 on 3p25 to NUP98 on 11p15 in a patient with refractory MDS/AML by the molecular analysis. Fluorescence in situ hybridization (FISH) analysis using whole chromosomal painting and telomeric probes unclosed a criptic three-way translocation t(3;5;11)(p25;q35;p15). FISH restriction using BAC contig revealed that the 3p25 breakpoint is involved in KIAA0379 which locates between BAC 792N12 and 259O19. Split signals of BAC 265K23 for 5q35 and 348A20 for 11p15 showed that NSD1 on 5q35 and NUP98 on 11p15 are the responsible genes of this translocation. As the results of this translocation, expression of three chimeric transcripts were identified by RT-PCR. In KIAA0379-NUP98, exon 18 of KIAA0379 was fused in-flame with exon 13 of NUP98. In NUP98-NSD1, exon 12 of NUP98 was fused in-flame with exon 7 of NSD1. NSD1-KIAA0379 resulted in out-flame fusion. To investigate the expression of KIAA0379 in leukemic cells, RT-PCR for full-length KIAA0379 transcript was performed on bone marrow cells from the patient and a healthy volunteer, and leukemic cell line K562, HL-60 and KG-1a cells. Full-lengh PCR product with expected size was found in all samples, however, short variant transcript was amplified significantly from KG-1a and HL-60 cells. Subsequent sequence analysis of the short PCR product from KG-1a cells revealed a direct fusion of a part of exon 10 to a part of exon 28 without any hidden splicing sites. Southern blot analysis using a cloned KIAA0379 cDNA fragment suggested an internal deletion of KIAA0379 in KG-1a cells. KIAA0379 locates at 3p25.1 about 5.5Mb centromeric to VHL and is predicted to have 28 ankyrin repeat motifs by computational analysis. It is thought to be involved in protein to protein interaction whereas its precise funtion remains unclear. Immunostaining for KIAA0379 protein in NIH3T3 cells transfected with the wild KIAA0379 and the short variant KIAA0379 revealed that the wild KIAA0379 protein localized in cytoplasm and nuclear membrane, on the other hand, the truncated KIAA0379 protein localized exclusively on nuclear membrane. KIAA0379-NUP98 fusion protein is expected to localize on nuclear membrane by sub-localization signal of C-terminal of NUP98. Therefore, dysfunction of KIAA0379 protein might lead to leukemogenesis and KIAA0379 may be potential candidate for a novel TSG. In addition, it has been reported that t(5;11)(q35;p15.5) results in NUP98-NSD1 fusion in childhood AML. To our knowledge, this is the first report in adult case.