Detection of the NUP214-ABL Rearrangement in T-ALL by High-Density Oligonucleotide Arrays: Evidence of the Value of This Approach in the Identification of Gene Amplifications.
Authors: Chiaretti Sabina , Tavolaro Simona , Ghia Emanuela , Ariola Cristina , Matteucci Caterina , Maggio Roberta , Vitale Antonella , Ritz Jerome , Mecucci Cristina , Guarini Anna , Foà Robert 
Published: April 2020

Abstract
The translocation t(9;22), hallmark of CML, is also detected in B-lineage acute lymphoblastic leukemia (ALL). This aberration leads to the BCR/ABL rearrangement that induces a constitutive activation of the tyrosine kinase ABL1. Although BCR/ABL rearrangements were previously considered a rare event in T-ALL, recent data showed the involvement of ABL1 also in this malignancy. Specifically, a new fusion gene involving ABL1 and NUP214, both located at the 9q34 region, has been reported. This abnormality was detected by FISH analysis and reconfirmed by array CGH and PCR analysis. We previously evaluated by microarrays a set of 128 adults with ALL: leukemic cells from 33 patients were of T-cell origin. In the present study, we analyzed the expression levels of ABL1, with the aim of identifying T-ALL cases who may have an involvement of ABL1. Overall, mean expression levels of ABL1 were: pre-B BCR/ABL+ ALL: 1202.71 ± 67.15; pre-B BCR/ABL- ALL: 629.06 ± 23.91; T-ALL: 758.56 ± 42.26, indicating that ABL1 is more highly expressed in T-lineage ALL than in BCR/ABL-B-lineage ALL. Detailed analysis of the T-ALL subset identified 3 cases who had very high levels of ABL1, comparable to those expressed in the BCR/ABL+ cases, and 1 further case with ABL1 expression levels higher than the mean values of BCR/ABL+ cases. Notably, 3/4 patients were refractory to induction chemotherapy. To understand the mechanisms underlying overexpression of ABL1, reverse transcriptase PCR (RT-PCR) was performed and showed the presence of the NUP214-ABL1 in the case having the highest levels of ABL1, whereas the remaining 3 cases were negative. FISH analysis confirmed the presence of NUP214-ABL1 in this case. Quantitative PCR (Q-PCR) of the ABL1 gene was also performed on the same set of T-ALL cases and showed a high degree of correlation between microarray analysis and Q-PCR. HOX11 expression was increased in 2/3 cases, but was not exclusive of these samples; HOX11L2 expression was not evaluated because this transcript was not represented in the platform used. However, FISH analysis excluded the presence of the t(5;14) in all 3 cases. Conventional cytogenetics revealed a normal karyotype in 1 patient, a 4p deletion and an additional marker chromosome in 1, a del(6q) in the case with the highest ABL expression, and was not evaluable in 1. Similarly, CGH analysis showed unbalances in all cases. None of these cases carried a deletion of CDKN2A. Following these findings, we evaluated by both Q-PCR and RT-PCR 15 newly diagnosed T-ALL patients: none of them showed high levels of ABL1. In summary, these results show the value of microarray analysis for the identification of cases carrying specific chromosomal amplifications, i.e. NUP214-ABL1. To our knowledge, this is the first report that identifies this DNA amplification by investigating RNA expression levels of the corresponding transcript. Moreover, our results indicate that this aberration is less frequent than previously reported, being detected in our overall series in 2% of cases. Further investigations are ongoing on the remaining 3 samples to explain the mechanisms underlying ABL overexpression.