Deep sequencing of BCR-ABL1 kinase domain mutations in chronic myeloid leukemia patients with resistance to tyrosine kinase inhibitors

Abstract

Tyrosine kinase inhibitor (TKI) therapy is the current treatment of choice for patients with chronic phase chronic myeloid leukemia (CML) leading to rapid and durable hematological as well as molecular responses. However, emergence of resistance to TKIs has been the major obstacle to treatment success on long term. In this regard kinase domain mutations are the most common mechanism of therapy failure. In this study, we analyzed peripheral blood samples from 17 CML patients who had developed resistance to various TKIs by using next-generation sequencing parallel to Sanger sequencing. BCR-ABL1 kinase domain mutations have been found in 59% of the cohort. Our results demonstrate that next-generation sequencing results in a higher mutational detection rate than reported with conventional sequencing methodology. Furthermore, it showed the clonal diversity more accurately.

Next-generation sequencing for BCR-ABL1 kinase domain mutation testing in patients with chronic myeloid leukemia: a position paper

“…The so-called “myeloid panels” include the ABL1 exons coding for the KD, but DNA-based mutation screening would mainly have untranslocated ABL1 as a substrate, thus dangerously “diluting” mutations down to a level that might be undetectable even by NGS. Some studies have reported the setup and application of in-house-developed protocols for BCR-ABL1 KD mutations screening implemented on different NGS platforms [29–31, 34, 35, 38, 60–62].…”

Novel Illumina‐based next generation sequencing approach with one‐round amplification provides early and reliable detection of BCR‐ABL1 kinase domain mutations in chronic myeloid leukemia

“…This is especially important for BCR‐ABL1 KD mutation monitoring, regardless of sequencing platform, due to transcript amplification (Potapov & Ong, ). For this reason, previous studies, which used the Roche NGS platform, suggested setting the VAF limit between 1% and 5% (Machova Polakova et al ., ; Soverini et al ., ; Erbilgin et al ., ). In our study, we adopted Q5 polymerase (New England Biolabs, Ipswich, MA, USA) for amplification of BCR‐ABL1 KD, which is currently the most accurate PCR polymerase (280 times more accurate than “reference” Taq polymerase) (Potapov & Ong, ).…”

“…Next‐generation sequencing (NGS) as an alternative method can provide enhanced sensitivity and earlier mutation detection. The NGS platform used most frequently for BCR‐ABL1 KD sequencing is 454 from Roche (Basel, Switzerland) (Machova Polakova et al ., ; Baer et al ., ; Soverini et al ., ; Erbilgin et al ., ). The use of Ion Torrent (Thermo Fisher Scientific, Waltham, MA, USA) technology and the widely implemented Illumina (San Diego, CA, USA) platform has been reported by fewer authors to date (Eyal et al ., ; Deininger et al ., ; Kizilors et al ., ).…”

Current Outlook on Autophagy in Human Leukemia: Foe in Cancer Stem Cells and Drug Resistance, Friend in New Therapeutic Interventions

“…The identification of BCR-ABL1 as the major driver in the pathogenesis of CML led to the development of targeted therapies with ABL1 tyrosine kinase inhibitors (TKIs) such as Imatinib, Dasatinib, and Ponatinib [58,59]. Treatments with TKIs in the initial chronic phase of CML have been shown to induce remarkable haematological and cytogenetic responses, however, treatments of advanced stage patients or individuals with ABL1 kinase domain mutations are much more challenging and most importantly, none of these monotherapies are curative [60,61,62]. Strong evidence indicates that LSCs, including quiescent LSCs, are insensitive to TKIs and constitute a critical source of leukemia recurrence and a significant reservoir for the emergence of TKI-resistant sub-clones, necessitating lifelong treatment for most patients [57,63,64,65,66,67,68,69,70].…”