Episomal amplification of NUP214-ABL1 fusion gene in B-cell acute lymphoblastic leukemia

To the editor:

The NUP214-ABL1 fusion gene is found amplified as multiple (5-50) episomal copies in 6% of T-cell acute lymphoblastic leukemia (T-ALL).^1,2  Alterations of the TLX1, TLX3, CDKN2A/B, and NOTCH1 genes are commonly associated with NUP214-ABL1 T-ALL. Recently, the NUP214-ABL1 fusion gene has been reported in 2 of 15 cases of B-cell acute lymphoblastic leukemia (B-ALL)³  identified by RNA-sequencing with no evidence of episomal amplification, suggesting an intrachromosomal rearrangement. In 1 of 2 cases, phosphoflow analysis demonstrated increased CRK-like protein phosphorylation, suggesting active ABL1 signaling, that was sensitive to tyrosine kinase inhibitors (TKIs). We now report the first case of B-ALL associated with extrachromosomal, episomal amplification of NUP214-ABL1. All methods can be found in supplemental Methods (available on the Blood Web site; see the Supplemental Materials link at the top of the online article).

A 22-year-old male presented with a hemoglobin 108 g/L, white cell count 12.72 × 10⁹/L, and platelet count 65 × 10⁹/L. Bone marrow aspirate and trephine revealed 99% blast cells expressing CD79a, CD19, CD10, CD20, surface IgM, HLA-DR, cytTdT, and CD7 (Figure 1A-B). The latter 2 markers are more suggestive of bi-lineage blasts, but there was no cytCD3 CD2, CD4, CD5, CD7, CD8, cytMPO, CD33, CD13, CD15, and CD117 expression. The karyotype was: 47,XY,+X.

Interphase fluorescence in situ hybridization (FISH) using a BCR-ABL1 probe demonstrated 50-80 extrachromosomal copies of ABL1; FISH probes targeting 3′ regions of ABL1 and NUP214 confirmed episomal NUP214-ABL1 amplification in ∼ 99% of cells (Figure 1C). Conversely, a probe targeting the 5′ region of ABL1 showed a normal signal pattern. This signal configuration is the same as previously shown in T-ALL.²  Multiplex ligation–dependent probe amplification (MLPA) confirmed amplification of both ABL1 and NUP214 (data not shown). Although FISH, MPLA, and SNP6.0 analysis showed no rearrangement of TLX1 and TLX3, aberrant TLX1/3 expression cannot be excluded. MLPA showed focal deletions of exons 2-7 of IKZF1 and exons 1-2 within the CDKN2A/B locus. SNP6.0 analysis confirmed NUP214 and 3′ ABL1 amplification (supplemental Figure 1). SNP data also confirmed IKZF1 and CDKN2A/B loss and showed other copy number aberrations including some previously implicated in B-ALL; FHIT,⁴ TBL1XR1,⁵  and the histone cluster at 6p22⁶  (supplemental Table 1).

The patient was treated with induction therapy (vincristine, daunorubicin, pegylated asparaginase, prednisolone, and CNS prophylaxis http://www.ctsu.ox.ac.uk/research/mega-trials/leukemia-trials/ukall-2003/). A day 29 marrow showed complete morphologic remission, but PCR-based IgVH MRD rearrangement studies revealed 1 in 10⁴ cells with clonal IgVH rearrangement. The patient successfully underwent cyclophosphamide/total body irradiation myeloabalative sibling donor allogenic stem cell transplantation and is in complete remission at 4 months.

NUP214-ABL1–positive patient primary cells were cultured with low and high concentrations of imatinib (0.5 and 5μM), dasatinib (10 and 150nM), nilotinib (0.5 and 5μM), and ponatinib (10 and 100nM; Figure 1D; concentrations based on IC₅₀ values and maximally achievable plasma concentrations in chronic myeloid leukemia patients). After a 72-hour culture, compared with no drug control, there was no significant reduction in viable cell numbers and no increase in apoptosis in any experimental arm. In contrast, BCR-ABL1 lymphoblastic cell line BV-173 demonstrated anticipated TKI sensitivities. Moreover, in T-ALL the mutant fusion kinase appeared more sensitive in vitro than BCR-ABL1 to TKIs.⁷  It is noteworthy, there are only case reports documenting mixed clinical responses to TKIs in NUP214-ABL T-ALL.^8,9 

It is unclear to what extent subtypes of NUP214-ABL1 seen in T-ALL, and now described in B-ALL, differ biologically. In part, these differences in drug sensitivity may arise kinase amplification in our case and differential kinase activation between NUP214-ABL1 and BCR-ABL1.⁷  Differences may arise not only from variable NUP214-ABL1 copy number, but also the nature of cooperating mutations. In our case, these likely include IKZF1 and the CDKN2A/B locus, important B-ALL aberrations. This variable genetic landscape may, in part, account for differential in vitro sensitivity to TKIs.