Concurrent BCR::ABL1 and SET::NUP214 Fusions in Blast-Phase Chronic Myeloid Leukemia

Abstract

Introduction:

Concurrent atypical BCR::ABL1 transcripts and SET::NUP214 fusions are rare in chronic myeloid leukemia (CML) and may complicate disease classification and treatment decisions.

Methods:

Clinical, morphologic, cytogenetic, fluorescence in situ hybridization, and next-generation sequencing findings were reviewed in a patient with de novo myeloid blast-phase CML.

Results:

A 68-year-old man presented with hyperleukocytosis and was diagnosed with myeloid blast-phase CML harboring an atypical e13a3 BCR::ABL1 transcript and concurrent SET::NUP214 fusion. Single-agent dasatinib induced rapid remission, clearance of both fusion transcripts, and sustained molecular remission beyond 15 months.

Conclusion:

Concurrent atypical BCR::ABL1 and SET::NUP214 fusions are rare in myeloid blast-phase CML. Despite this molecular complexity, durable molecular remission was achieved with single-agent dasatinib.

Background

Chronic myeloid Leukemia (CML) is a myeloproliferative neoplasm defined by the presence of the BCR::ABL1 fusion gene, which results from the t(9;22) translocation and drives constitutive tyrosine kinase activity. In addition to canonical BCR::ABL1 rearrangements, atypical fusion transcripts and co-occurring genomic alterations may complicate diagnosis, disease classification, and response assessment¹. Rare BCR::ABL1 breakpoints may evade detection by standard PCR-based assays. At the same time, additional fusion events, such as CBFB::MYH11, GATA2::MECOM, and SET::NUP214, have been reported in CML and may raise consideration of alternative diagnoses, including acute myeloid leukemia (AML) with t(9;22)^1–3. These features can create uncertainty regarding the dominant disease driver, clonal architecture, and optimal therapeutic approach. Here, we describe a case of myeloid blast-phase CML with an atypical BCR::ABL1 transcript and concurrent SET::NUP214 fusion, highlighting the diagnostic challenges, molecular complexity, and therapeutic implications of dual fusion events.

Case Presentation

A 68-year-old male with no significant past medical history presented with several weeks of progressive lethargy, abdominal distention, and watery diarrhea. Family members reported marked functional decline, with the patient becoming largely bedbound prior to presentation. He denied fever, chills, or bleeding. Initial evaluation at an outside hospital revealed profound leukocytosis with a white blood cell (WBC) count of 503 ×10⁹/L, prompting transfer for a higher level of care. Computed tomography (CT) scan of the abdomen and pelvis demonstrated marked splenomegaly, hepatomegaly with features of portal hypertension, and enlarged retroperitoneal and pelvic lymph nodes.

On arrival, laboratory studies confirmed persistent leukocytosis (WBC 411 ×10⁹/L) with 20–22% circulating blasts, hemoglobin of 6.1 g/dL, and platelet count of 103 × 10⁹/L. Metabolic evaluation was notable for elevated uric acid, hyperphosphatemia, and acute kidney injury (creatinine 1.61 mg/dL), consistent with spontaneous tumor lysis syndrome. The patient was admitted to the intensive care unit, where he underwent leukapheresis and a single session of hemodialysis with subsequent clinical stabilization. Cytoreduction was initiated with hydroxyurea, and supportive management included intravenous fluids, rasburicase, and allopurinol.

Bone marrow biopsy showed a markedly hypercellular marrow (approximately 100% cellularity) with 22% myeloblasts and marked basophilia, consistent with chronic myeloid leukemia, myeloid blast phase. The blast morphology, including nuclear irregularities and dark basophilic cytoplasmic granules, and immunophenotype (CD45-dim/CD117-dim, with expression of CD13, CD33, and strong CD123 by flow cytometry), together with marked basophilia, were suggestive of basophilic blast differentiation. Fluorescence in situ hybridization (FISH) confirmed a typical dual-fusion pattern of BCR::ABL1/ABL1::BCR in 97% of cells using the Vysis LSI BCR/ABL1 dual-color, dual-fusion probe (Abbott Laboratories, Abbott Park, IL, USA). Targeted next-generation sequencing (NGS) using the Rapid NGS Myeloid Panel (Oncomine Myeloid Assay GX v2, ThermoFisher Scientific) identified an atypical BCR::ABL1 b2a3 (e13a3) transcript, predicted to result in a rare p203 isoform that may not be detected by routine PCR testing. In addition, a concurrent SET::NUP214 fusion was identified. BCR::ABL1 p190 and p210 transcript variants were not detectable by RT-qPCR (NeoGenomics Laboratories Inc., Fort Myers, FL, USA).

The patient was initiated on dasatinib 100 mg daily, which was subsequently escalated to 140 mg daily. No systemic chemotherapy was administered, other than a transient course of hydroxyurea for cytoreduction. His hospital course was complicated by febrile neutropenia secondary to Clostridium difficile infection, acute urinary retention requiring catheter intervention, and significant physical deconditioning with sacral pressure injury. Despite these complications, the patient demonstrated rapid hematologic and morphologic improvement.

At one-month follow-up, repeat bone marrow evaluation showed a variably cellular marrow (30–50%) with trilineage hematopoiesis and no morphologic or immunophenotypic evidence of acute leukemia, consistent with morphologic remission of the blast-phase component. However, BCR::ABL1/ABL1::BCR dual-fusion remained detectable by FISH in 38.5% of cells. In addition, FISH analysis using the DEK/NUP214 dual-color, dual-fusion probe (MetaSystems Group, Inc., Medford, MA, USA) detected an extra NUP214 signal in 4.5% of cells. Notably, two of the three observed NUP214 signals were atypical in size (smaller). This atypical signal pattern indicated a NUP214 rearrangement independent of DEK, thereby corroborating the presence of the SET::NUP214 fusion detected by NGS. NGS analysis continued to detect both BCR::ABL1 and SET::NUP214 fusions.

Serial follow-up evaluations demonstrated an ongoing and deepening response to single agent TKI therapy. Four months after presentation, bone marrow examination showed no morphologic or immunophenotypic evidence of residual leukemia. Repeat FISH and karyotyping analyses revealed normalization with no evidence of persistent CML. Serial cerebrospinal fluid analyses obtained as part of central nervous system intrathecal prophylaxis were negative for leukemic involvement. Longitudinal molecular monitoring demonstrated progressive reduction in disease burden. Peripheral blood NGS detected low-level BCR::ABL1 transcripts (0.2% from baseline) five months after presentation (SET::NUP214 had cleared) but subsequently became undetectable. Both BCR::ABL1 and SET::NUP214 fusions were no longer detected on NGS from bone marrow evaluation performed six months after diagnosis, and these have remained undetectable by serial NGS monitoring from peripheral blood >15 months from initial diagnosis.

At most recent follow-up 18 months after presentation with blast-phase CML, the patient remains in complete remission on dasatinib 140 mg daily. NGS demonstrates no detectable minimal residual disease and peripheral blood counts have normalized. Given the depth and durability of the response, allogeneic hematopoietic stem cell transplantation has been deferred, and the patient continues on tyrosine kinase inhibitor therapy with molecular monitoring every three months.

Discussion

This case is notable for the presence of two distinct fusion events: an atypical BCR-ABL1 transcript (e13a3) and a concurrent SET::NUP214 fusion. While BCR::ABL1 is the defining lesion in CML, atypical breakpoints such as b2a3 (e13a3) are rare and may not be detected by standard PCR-based assays, complicating both diagnosis and longitudinal monitoring¹. The concurrent presence of a SET::NUP214 fusion highlights the unusual genomic complexity of this case. Although described in various acute leukemia subtypes^{4, 5}, only two cases of CML with concurrent BCR::ABL1 and SET::NUP214 fusions have been previously reported, both by Chen et al., making the present case the third reported instance. In the first reported case, treatment with decitabine and venetoclax plus ponatinib achieved a partial response, after which the patient underwent allogeneic hematopoietic stem cell transplantation and remained in complete hematologic and molecular remission at last follow-up. In the second case, idarubicin and cytarabine followed by dasatinib achieved morphologic remission; however, the patient relapsed four months after chemotherapy, discontinued treatment, and died three years after initial CML diagnosis². Given the association of SET::NUP214 with treatment resistance and adverse clinical outcomes, the deep and durable response observed in our patient is particularly notable^{5, 6}.

The structural basis of the SET::NUP214 fusion in this case remains uncertain. In the absence of ABL1 deletion by FISH analysis, the fusion is unlikely to have arisen through a simple interstitial deletion⁴. Conventional karyotype analysis was attempted; however, no metaphase cells were available for analysis, limiting our assessment of additional cytogenetic abnormalities. The close genomic proximity of SET (9q34.11), ABL1 (9q34.12), and NUP214 (9q34.13) suggests alternative mechanisms may be involved, including a translocation between homologous chromosomes 9, a paracentric inversion in the 9q34 region, or an insertional event involving NUP214 into SET or SET into NUP214^{4, 7}. Definitive characterization of the underlying clonal architecture could be enhanced by advanced genomic approaches such as optical genome mapping or long-read sequencing.

An additional challenge in this case was determining the dominant driver of disease and, consequently, the appropriate diagnostic classification. Initial molecular profiling demonstrated high-level BCR::ABL1 positivity by FISH (97%), supporting BCR::ABL1 as the primary driver. Repeat bone marrow evaluation one month after TKI initiation demonstrated persistent BCR::ABL1 positivity (38.5%) and NUP214 rearrangement (4.5%) by FISH, supporting clonal evolution from a stemline clone harboring BCR::ABL1 to a subclone harboring both BCR::ABL1 and SET::NUP214. NGS detected a relative increase in SET::NUP214 fusion transcript abundance compared to BCR::ABL1. This raised the question of whether this case may represent AML with t(9;22) rather than blast-phase CML. Additional features, including de novo presentation, basophilic differentiation, concurrent SET::NUP214 fusion, and atypical BCR::ABL1 breakpoint, further support this diagnostic consideration⁸. Several findings, however, favored a diagnosis of blast-phase CML, including the marked leukocytosis with left-shifted myelopoiesis at presentation, high level of BCR::ABL1 positivity, faster molecular clearance of the SET::NUP214 fusion, durable response to dasatinib with eventual BCR::ABL1 clearance, and early persistence of the BCR::ABL1 fusion in non-blast hematopoietic cells ^9,10.

This apparent increase in SET::NUP214 fusion transcript levels by NGS on post-treatment biopsy also raised the possibility of a shift in clonal dominance or the emergence of a therapy-resistant population. However, RNA-based fusion measurements may not reliably reflect clonal burden, as transcript levels are influenced by biological and technical factors. Using vendor bioinformatics software normalization parameters, no meaningful difference in relative abundance was observed between SET::NUP214 and BCR::ABL1.

Conclusion

Despite presenting with high-risk features, including blast-phase presentation and concurrent genomic alterations, the patient demonstrated a rapid and deep response to TKI therapy, achieved complete molecular remission, avoiding immediate allogeneic transplantation. This outcome suggests that genomic complexity, including additional fusion events, does not consistently predict resistance to ABL1 kinase-directed therapy. Instead, these findings highlight the continued central role of BCR::ABL1 signaling as the dominant driver of disease biology at de novo presentation in the absence of overt sub-clonal evolution and prior TKI exposure, even in blast phase disease. Clinically, this case underscores the importance of integrating molecular, cytogenetic, and clinical features when making treatment decisions, particularly in patients with atypical BCR::ABL1 transcripts and co-occurring genomic alterations, which may be interrelated and co-targetable, as they can still respond to single-agent TKI. This case also demonstrates the potential to avoid increased toxicity associated with chemotherapy plus TKI combinations and allogeneic transplantation, especially at older age, based on the molecular biology of the driver clone. Further prospective investigations are needed to systematically define the prognostic and therapeutic implications of concurrent fusion events in blast phase CML.

Figure 1.

Morphologic, immunohistochemical, and cytogenetic findings in a case of chronic myeloid leukemia in blast crisis.

(A) Bone marrow (BM) aspirate smear (Wright-Giemsa, ×1000) demonstrates increased blasts with cytoplasmic granules and nuclear irregularities, consistent with basophilic differentiation. (B) BM core biopsy (H&E, ×40) shows 100% cellular marrow with near-complete replacement of hematopoietic elements by blast infiltration. (C) Peripheral blood smear demonstrates leukocytosis with left-shifted granulocytes, increased blasts, and basophilia. (D) Immunohistochemistry for CD123 shows positivity in a subset of blasts; in conjunction with the overall immunophenotype, the findings support blasts with basophilic differentiation. (E) Fluorescence in situ hybridization (FISH) using the Vysis LSI BCR/ABL1 dual-color, dual-fusion translocation probe (ABL1: Spectrum Orange; BCR: Spectrum Green) demonstrates dual-fusion signals representing BCR::ABL1 and ABL1::BCR rearrangements, confirming the Philadelphia chromosome. Arrows indicate fusion signals. (F) FISH using the MetaSystems DEK/NUP214 dual-color, dual-fusion probe (DEK: Spectrum Green; NUP214: Spectrum Orange) reveals an extra NUP214 signal with two atypical smaller signals (arrows), indicating a NUP214 rearrangement occurring independently of DEK.

Figure 2.

Co-occurring BCR::ABL1 (e13a3) and SET::NUP214 (e7::e18) gene fusions identified by RNA-based next-generation sequencing in a case of chronic myeloid leukemia in blast crisis.

(A) Schematic overview of the two fusion events at the genomic level. The upper bar represents chromosome 22 and the lower bar represents chromosome 9, depicted with standard Giemsa banding (GRCh37/hg19). The BCR::ABL1 fusion (blue arc) arises from the t(9;22)(q34;q11) Philadelphia chromosome translocation, joining BCR at 22q11.23 to ABL1 at 9q34.12. The SET::NUP214 fusion (brown arc) juxtaposes SET at 9q34.11 and NUP214 at 9q34.13, two loci approximately 2.57 Mb apart on chromosome 9q34. Colored ticks indicate the position of each gene locus on the respective chromosome. (B) Structural characterization of the BCR::ABL1 e13a3 (b2a3) fusion transcript. Chromosome ideograms indicate the genomic origin of each fusion partner: BCR (NM_004327.4; 22q11.23; genomic breakpoint chr22:23,631,808, GRCh37/hg19) and ABL1 (NM_005157.6; 9q34.12; genomic breakpoint chr9:133,730,188, GRCh37/hg19). Notably, ABL1 exon 2 is absent from the fusion transcript, with BCR exon 13 joining directly to ABL1 exon 3 — an atypical isoform distinct from the canonical e13a2 (b2a2). The resulting fusion transcript (BCR exons 1–13 fused to ABL1 exons 3–11) is shown in the lower track; junction exons are highlighted in yellow. ABL1 exon 2, which would be present in the canonical transcript, is marked as skipped. (C) Structural characterization of the SET::NUP214 e7::e18 (S7N17) fusion transcript. SET (NM_003011.5; 9q34.11; genomic breakpoint chr9:131,456,321, GRCh37/hg19) is transcribed on NUP214 (NM_005085.4; 9q34.13; genomic breakpoint chr9:134,027,123, GRCh37/hg19). The fusion transcript joins SET exons 1–7 to NUP214 exons 18–36; junction exons are highlighted in yellow. Exon proportions are schematic; intron lengths are not drawn to scale.