Dynamic evolution of ponatinib‐resistant mutations in BCR–ABL1‐positive leukaemias revealed by next‐generation sequencing
Year: 2020
Type: article
Abstract: Tyrosine kinase inhibitors (TKIs) targeting BCR–ABL1 oncoprotein revolutionized the therapy of leukaemias carrying this fusion. However, there are still chronic myeloid leukaemia (CML) patients who are sequentially resistant to different TKIs and even worse therapies in BCR–ABL1-positive B cell acute lymphoblastic leukaemia (B-ALL).1 Ponatinib is the only registered third-generation TKI effective against almost all single BCR–ABL1 kinase domain (KD) mutations, including the gatekeeper T315I. Unfortunately, clinical and in vitro studies have shown that certain compound mutations (CMs, two or more nucleotide substitutions that change one or multiple codons) confer resistance to ponatinib,2-4 but with inconsistent reports.5 The results may be affected by the sensitivity of the detection methodology and the ability to discriminate polyclonal mutations and CMs. As compared to Sanger sequencing (SS), next-generation sequencing (NGS) provides a powerful tool for mutation screening with higher sensitivity, quantitative subclone analysis, and determination of CMs. Recently, a multicentre study reported that NGS-based screening provides a more accurate picture of BCR–ABL1 KD mutations in CML and suggest incorporating it in clinical decision algorithms.1 Nevertheless, the dynamic kinetics of ponatinib-resistant mutations have been scarcely investigated. Here we report the dynamic evolution of ponatinib-resistant mutations observed in heavily TKI-treated patients monitored by NGS-based mutation screening. An NGS-based protocol was designed for screening BCR–ABL1 KD mutations within the region of ABL1 NM_005157:c.697_1533/p.D233_G511 (Data S1). The minimum read depth is 2000×, and the variant allele frequency (VAF) detection limitation is 2%. Ethical approval was provided by the Ethics Committee of Hebei Yanda Lu Daopei Hospital, signed informed consent was obtained, and research was conducted in accordance with the Declaration of Helsinki. Case 1 (Fig 1A) was a 29-year-old male who was diagnosed with CML in 2009. He progressed to the blast phase after imatinib and dasatinib maintenance for seven years with T315I mutation (VAF 47%) and 35·16% BCR–ABL1 transcripts in bone marrow (BM). Ponatinib-based TKIs plus chemotherapy were administrated, but T315I mutation remained although blast in BM had decreased. A comprehensive relapse occurred following five months of ponatinib and imatinib combination therapy, with 56·51% BCR–ABL1 transcripts and T315I (97%) in BM. Ponatinib plus dasatinib combined with high-intensity chemotherapy were then implemented. Unfortunately, NGS investigation of KD mutations revealed mutations in compound Y253H/T315I (5%), E255K/T315I (19%), Q252H/T315I (9%), T315M (9%), as well as T315I (8%), with 39·96% BCR–ABL1 transcripts six months later. The patient then underwent salvage allogeneic haematopoietic stem cell transplantation, and ponatinib-based targeted therapy proceeded. However, the blast was not well controlled, and VAF of the above mutations changed dynamically. The patient died from a comprehensive relapse with Q252H/T315I (c.756G>C/c.944C>T, Figure S1A) as the dominant clone. Case 2 (Fig 1B) was a seven-year-old boy with a diagnosis of BCR–ABL1-positive B-ALL. NGS investigation of KD mutations showed polyclonal D276G (7%), F311I (27%), and F317L (31%) in BM after 18 months of chemotherapy plus imatinib administration. He was then treated with ponatinib, and the BCR–ABL1 transcripts in BM rapidly decreased with clearance of the above mutations. However, G250E (5%) and D276G/T315L (4%) appeared after a month and then rapidly progressed to D276G/T315L (32%), G250W/E255V/F311I (4%), and F311I/T315I (58%) polyclonal CMs within three months. The patient died from a rapidly comprehensive relapse under sustained ponatinib therapy, with D276G/T315L (c.827A>G/c.943_945delinsCTC, Figure S1B) as the only clone. Case 3 (Fig 1C) was a 46-year-old female with a diagnosis of BCR–ABL1-positive B-ALL. Q252H (20%) and T315I (44%) appeared rapidly after two months of chemotherapy and imatinib administration. TKI was then replaced with ponatinib, and remission was achieved once with a decrease in both mutations and BCR–ABL1 went negative. However, relapse occurred five months later with dynamically polyclonal CMs. T315I diminished under ponatinib administration, but the derived T315I/F359V (c.944C>T/1075T>C) and T315L (c.943_944delinsCT) (Figure S1C) arose and accumulated. The patient abandoned treatment when relapse became uncontrollable. Case 4 was a 62-year-old female with a 98% blast in the BM after diagnosis of BCR–ABL1-positive B-ALL. Chemotherapy combined with dasatinib was administrated, and blast cells rapidly decreased to 0·1% by flow cytometry after 40 days. Nevertheless, T315I was identified by SS. Treatment was then changed to more intensive chemotherapy combined with ponatinib, but the blast increase was sustained. She came to our hospital with 68% blast in BM seven months after T315I identification and sustained ponatinib maintenance. NGS screening for KD mutations showed Q252H/Y253H (c.756G>T/c.758A>T, 82%) and T315L/T319S (c.943_944delinsCT/c.955A>T, 10%) mutations (Figure S1D), and serum ponatinib concentration was 22 ng/ml as determined by mass spectrometry. The patient gave up treatment because of granulocytopenia and severe infection. With the increase of CML patients who underwent long-term TKI therapy and the increasing application of TKIs in BCR–ABL1-positive B-ALL, as well as the extensive use of sequential TKIs, the dynamics of resistant clones has become more complicated. Ponatinib is now the last hope for patients who were heavily treated and went through resistance to multiple TKIs due to its efficacy against nearly all single-nucleotide mutations.6 Given the unique efficacy against the intractable T315I but with noteworthy severe side effects, a considerable proportion of patients treated with ponatinib will harbour baseline T315I.4 However, there were CMs highly resistant to TKIs, including ponatinib, especially in heavily treated CML and BCR–ABL1-positive B-ALL.2 Twelve key KD positions comprise the majority of TKI-resistant CMs.4 Reported ponatinib-resistant CMs could be clustered into two forms: T315I combined with mutations of other key positions, or other T315 amino acid substitutions.3, 4, 7, 8 Both forms of ponatinib-resistant CMs were evolved from the baseline T315I in evolutionary analysis. In addition to CMs that included T315, some other CMs also confer varying resistance to various TKIs.4 CMs become an emerging problem for patients receiving sequential TKI therapy and necessitate investigation of the resistance mutation spectrum for various TKIs to optimize therapy selection. There are new hopes for ponatinib-resistant patients. Asciminib, an allosteric inhibitor that targets the myristoyl site, has been reported effective in TKI-resistant CML patients, including those who failed ponatinib treatment.9, 10 One study also reported that asciminib and ponatinib combination therapy restores efficacy against CMs.11 Besides, ponatinib-resistant T315L and T315Y were reported sensitive to the approved vascular endothelial growth factor receptor TKI axitinib in vitro.3, 12 Here we depict the dynamic evolution of ponatinib-resistant mutations in four cases. There were three CMs involving T315 that became dominant at the end of ponatinib treatment. The CMs Q252H/T315I, T315I/F359V, and T315L, which we observed in cases 1 and 3, were evolved from the baseline T315I. The D276G/T315L in case 2 might have evolved from D276G, F311I/T315L, or other pre-existing undetected clones involving D276 or T315. In case 4, there were 82% Q252H/Y253H and 10% T315L/T319S CMs after seven months of ponatinib maintenance. We could not determine whether the patient previously harboured a low level of Q252H/Y253H or other mutations besides T315I due to lack of specimen availability. Nevertheless, our observation also indicates active mutation accumulation in heavily TKI-treated patients who transfer to ponatinib therapy, and further highlights the necessity to monitor the dynamic clonal evolution. We thank our patients for participating in this study. JC followed up the patients, collected the clinical information and samples, analysed the NGS data, and wrote the manuscript. FW and XM determined the BCR–ABL1 transcript level and analysed the data. JF, PC, HL, YZ, XC, YL, DN, YT, YG and ML performed the deep penal sequencing and Sanger sequencing, and analysed the data. JC and HL designed the study. HL supervised the study. The authors declare no competing financial interests. The study was approved by the Ethics Committee of Hebei Yanda Lu Daopei Hospital. Written informed consents were obtained in accordance with the Declaration of Helsinki. There was no funding specifically for the current work. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Source: British Journal of Haematology
DOI: 10.1111/bjh.17068
Authors: Jiaqi Chen, Fang Wang, Jiancheng Fang, Daijing Nie, Yang Zhang, Xue Chen, Yu Li, Yincheng Tan, Xiaoli Ma, Yongxin Guo, Panxiang Cao, Ming Liu, Hongxing Liu
Institutions: Beijing Dao Pei Hospital, Hebei Yanda Ludaopei Hospital
Language: English
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
Open Access status: bronze
OpenAlex ID: W3087570586