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Objective: To investigate the transcript distribution, rare transcript sequence characteristics and clinical outcomes in patients with BCR::ABL1 fusion gene-positive leukemia. Methods: The patients with newly diagnosed and relapsed BCR::ABL1-positive leukemia who underwent leukemia fusion gene screening at Hebei Yanda Lu Daopei Hospital from April 2012 to December 2024 were retrospectively collected. The clinical data of the patients were collected. The distribution of BCR::ABL1 fusion gene transcripts and the sequences of rare transcripts were analyzed, and the clinical outcomes of patients with rare transcripts were observed. Results: A total of 990 patients were enrolled, including 592 males and 398 females, with a median age of 37 years (range 1-94 years). All patients were tested positive for only one type of BCR::ABL1 transcript, and no co-expression of different transcripts was observed in the same patient. Common transcripts accounted for 96.3% (953 patients), while rare transcripts accounted for 3.7% (37 patients). Among 325 patients in chronic phase chronic myeloid leukemia (CML) and 85 patients in acute phase CML, P210 was the predominant type, observed in 310 (95.4%) and 80 (94.1%) cases, respectively; rare transcripts were identified in 14 (4.3%) and 5 (5.9%) cases, respectively. Among 511 acute acute B-lymphocytic leukemia (B-ALL) patients, P190 was the predominant type (70.5%), followed by P210 (26.8%) and rare transcripts (2.8%). Two acute T-lymphocytic leukemia (T-ALL) patients exhibited P190 and e6a2 transcripts, respectively. Common transcripts were also predominant in patients with acute myeloid leukemia (AML) and acute leukemias of ambiguous lineage (ALAL), with rare transcripts accounting for 3.8% (1/26) and 4.8% (2/41), respectively. Sequence analysis of 37 rare transcripts revealed that splicing variants occurred in ABL1 exon 3 (e1a3, e14a3, e13a3) in 23 patients (62.2%), and in different exons of BCR (e6a2, e8a2, variant e13a2, e19a2) in 14 patients (37.8%). Both e8a2 and variant e13a2 were associated with intronic insertions of varying lengths. Five patients with the e13a3 transcript responded well to tyrosine kinase inhibitor (TKI) therapy and achieved complete remission; among the 10 patients with e1a3 transcript and 5 patients with e19a2 transcript, 4 and 3 patients died or failed to achieve remission, respectively. Conclusions: In patients with BCR::ABL1 fusion gene positive leukemia, the transcripts are mainly of the common type, and the rare type is rare. The rare type transcripts show high heterogeneity. The splicing variations mainly occur in ABL1 exon 3 or different exons of BCR, and some are accompanied by intron sequence insertions. Patients with e13a3 type of rare transcripts respond well to TKI treatment, while patients with the e1a3 and e19a2 have poor prognosis.