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

Abstract

Treatment with tyrosine kinase inhibitors (TKIs) may sequentially induce TKI-resistant BCR-ABL mutants in chronic myeloid leukemia (CML). Conventional polymerase chain reaction (PCR) monitoring of BCR-ABL is an important indicator to determine therapeutic intervention for preventing disease progression. However, PCR cannot quantify separately amounts of BCR-ABL and its mutants, including alternatively spliced BCR-ABL with an insertion of 35 intronic nucleotides (BCR-ABL^Ins35bp) 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 into nilotinib. At baseline, TKI-resistant mutations were documented in 3 patients, whereas BCR-ABL^Ins35bp was detected in all patients. After switching to nilotinib, both BCR-ABL and BCR-ABL^Ins35bp became undetectable in 3 patients who attained complete molecular response (CMR), whereas in remaining all 34 patients, BCR-ABL^Ins35bp was persistently detected, and minimal residual disease (MRD) fluctuated at low but detectable levels. PCR monitoring underestimated MR in 5 patients whose BCR-ABL^Ins35bp was persisted, although BCR-ABL^Ins35bp does not inevitably mark TKI-resistance. Therefore, quantification of BCR-ABL^Ins35bp is useful for evaluating "functional" MRD and determining effectiveness of TKIs with accuracy.

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