Persistent detection of alternatively spliced BCR-ABL variant results in a failure to achieve deep molecular response

Treatment with tyrosine kinase inhibitors (TKI) may sequentially induce TKI-resistant BCR-ABL mutants in chronic myeloid leukemia (CML). Conventional PCR monitoring of BCR-ABL is an important indicator to determine therapeutic intervention for preventing disease progression. However, PCR cannot separately quantify amounts of BCR-ABL and its mutants, including alternatively spliced BCR-ABL with an insertion of 35 intronic nucleotides (BCR-ABL^{I ns35bp}) between ABL exons 8 and 9, which introduces the premature termination and loss of kinase activity. To assess the clinical impact of BCR-ABL mutants, we performed deep sequencing analysis of BCR-ABL transcripts of 409 samples from 37 patients with suboptimal response to frontline imatinib who were switched to nilotinib. At baseline, TKI-resistant mutations were documented in 3 patients, whereas BCR-ABL^{I ns35bp} was detected in all patients. After switching to nilotinib, both BCR-ABL and BCR-ABL^{I ns35bp} became undetectable in 3 patients who attained complete molecular response (CMR), whereas in the remaining all 34 patients, BCR-ABL^{I ns35bp} was persistently detected, and minimal residual disease (MRD) fluctuated at low but detectable levels. PCR monitoring underestimated molecular response in 5 patients whose BCR-ABL^{I ns35bp} was persisted, although BCR-ABL^{I ns35bp} does not definitively mark TKI resistance. Therefore, quantification of BCR-ABL^{I ns35bp} is useful for evaluating “functional” MRD and determining the effectiveness of TKI with accuracy.