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Chronic myelogenous leukemia

BCR-ABL1 compound mutants: prevalence, spectrum and correlation with tyrosine kinase inhibitor resistance in a consecutive series of Philadelphia chromosome-positive leukemia patients analyzed by NGS

Leukemia volume 35, pages 2102–2107 (2021)Cite this article

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First- and second-generation tyrosine kinase inhibitors (TKIs) used for the treatment of chronic myeloid leukemia (CML) and Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL) have precise spectra of resistant BCR-ABL1 kinase domain (KD) mutations. Their sequential use may select for complex patterns resulting from the acquisition of multiple mutations either by the same or by distinct BCR-ABL1 alleles (compound mutants [CM] or polyclonal mutants [PM], respectively) [1, 2]. In silico molecular modeling [3] and in vitro drug sensitivity studies in cell lines [4, 5] have suggested that CMs might confer oncogenic properties and a degree of resistance substantially different (greater) than each individual mutation in separate clones would exhibit. In particular, when the IC50 of imatinib [3, 4], dasatinib [3, 4], nilotinib [4], bosutinib [4] and ponatinib [3,4,5] were assessed in BaF3 cells engineered to express a panel of CMs, the fold-increase over unmutated BCR-ABL1 led to hypothesize that several CMs would be challenging for all TKIs including ponatinib. The prevalence of CMs at baseline and at relapse has been investigated in 267 TKI-resistant chronic phase (CP)-CML patients enrolled in the Ponatinib Ph+ ALL and CML Evaluation (PACE) study [6]. Besides this, no further attempts have been made to compile a catalog of the most frequent CMs detectable in large series of Ph+ leukemia patients, nor to correlate in vitro predictions about TKI insensitivity with in vivo observations. We thus reviewed the results of routine BCR-ABL1 KD mutation screening performed by targeted next generation sequencing (NGS) over the past 4 years, in order to: (i) determine the prevalence and spectrum of CMs in a large series of patients; (ii) attempt a correlation between TKI resistance and the presence or acquisition of given CMs in vivo.

Between 2015 and 2019 we used NGS to analyze a consecutive series of 875 Ph+ leukemia patients on TKI therapy who were eligible for BCR-ABL1 mutation screening according to European LeukemiaNet (ELN) [7, 8] or European Society for Medical Oncology (ESMO) [9] recommendations. They included 734 CML patients with failure/warning response (disease phase at the time of testing: CP, n = 653; accelerated or blastic phase [AP/BP], n = 81) and 141 Ph+ ALL patients with resistant disease at the molecular or hematological level. Patient disposition is shown in Supplementary Table 1. NGS of amplicons of ~400 bp length generated by nested reverse transcription-polymerase chain reaction (PCR) was performed on a Roche GS Junior (until April 2017) or on an Illumina MiSeq (from May 2017 on) using custom protocols whose accuracy, sensitivity and reproducibility was checked within national [10] and international (EUTOS) control rounds. Read alignment and variant calling were done using the AmpSuite software (SmartSeq); lower detection limit was set to 3% [10]. Whenever mutation pairs mapped on the same reads, cis or trans configuration indicating CMs or PMs, respectively, was determined correcting for the likelihood of PCR recombination [11] as described in [6].

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Fig. 1: Frequency and type of CMs in Ph+ leukemia patients.

References

  1. Shah NP, Skaggs BJ, Branford S, Hughes TP, Nicoll JM, Paquette RL, et al. Sequential ABL kinase inhibitor therapy selects for compound drug-resistant BCR-ABL mutations with altered oncogenic potency. J Clin Invest. 2007;117:2562–9.

    Article  CAS  Google Scholar 

  2. Khorashad JS, Kelley TW, Szankasi P, Mason CC, Soverini S, Adrian LT, et al. BCR-ABL1 compound mutations in tyrosine kinase inhibitor-resistant CML: frequency and clonal relationships. Blood 2013;121:489–98.

    Article  CAS  Google Scholar 

  3. Gibbons DL, Pricl S, Posocco P, Laurini E, Fermeglia M, Sun H, et al. Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy. Proc Natl Acad Sci USA. 2014;111:3550–5.

    Article  CAS  Google Scholar 

  4. Zabriskie MS, Eide CA, Tantravahi SK, Vellore NA, Estrada J, Nicolini FE, et al. BCR-ABL1 compound mutations combining key kinase domain positions confer clinical resistance to ponatinib in Ph chromosome-positive leukemia. Cancer Cell. 2014;26:428–42.

    Article  CAS  Google Scholar 

  5. Byrgazov K, Lucini CB, Valent P, Hantschel O, Lion T. BCR-ABL1 compound mutants display differential and dose-dependent responses to ponatinib. Haematologica. 2018;103:e10–2.

    Article  CAS  Google Scholar 

  6. Deininger MW, Hodgson JG, Shah NP, Cortes JE, Kim DW, Nicolini FE, et al. Compound mutations in BCR-ABL1 are not major drivers of primary or secondary resistance to ponatinib in CP-CML patients. Blood. 2016;127:703–12.

    Article  CAS  Google Scholar 

  7. Soverini S, Hochhaus A, Nicolini FE, Gruber F, Lange T, Saglio G, et al. BCR-ABL kinase domain mutation analysis in chronic myeloid leukemia patients treated with tyrosine kinase inhibitors: recommendations from an expert panel on behalf of European LeukemiaNet. Blood. 2011;118:1208–15.

    Article  CAS  Google Scholar 

  8. Baccarani M, Deininger MW, Rosti G, Hochhaus A, Soverini S, Apperley JF, et al. European LeukemiaNet recommendations for the management of chronic myeloid leukemia: 2013. Blood. 2013;122:872–84.

    Article  CAS  Google Scholar 

  9. Hoelzer D, Bassan R, Dombret H, Fielding A, Ribera JM, Buske C, et al. Acute lymphoblastic leukaemia in adult patients: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol. 2016;27:v69–82.

    Article  CAS  Google Scholar 

  10. Soverini S, Bavaro L, De Benedittis C, Martelli M, Iurlo A, Orofino N, et al. Prospective assessment of NGS-detectable mutations in CML patients with nonoptimal response: the NEXT-in-CML study. Blood. 2020;135:534–41.

    Article  Google Scholar 

  11. Parker WT, Phillis SR, Yeung DT, Hughes TP, Scott HS, Branford S. Many BCR-ABL1 compound mutations reported in chronic myeloid leukemia patients may actually be artifacts due to PCR-mediated recombination. Blood. 2014;124:153–5.

    Article  CAS  Google Scholar 

  12. Schmitt MW, Pritchard JR, Leighow SM, Aminov BI, Beppu L, Kim DS, et al. Single-molecule sequencing reveals patterns of preexisting drug resistance that suggest treatment strategies in philadelphia-positive leukemias. Clin Cancer Res. 2018;24:5321–34.

    Article  CAS  Google Scholar 

  13. Soverini S, Rosti G, Iacobucci I, Baccarani M, Martinelli G. Choosing the best second-line tyrosine kinase inhibitor in imatinib-resistant chronic myeloid leukemia patients harboring Bcr-Abl kinase domain mutations: how reliable is the IC(5)(0)? Oncologist. 2011;16:868–76.

    Article  CAS  Google Scholar 

  14. Byrgazov K, Lucini CB, Berkowitsch B, Koenig M, Haas OA, Hoermann G, et al. Transposon-mediated generation of BCR-ABL1-expressing transgenic cell lines for unbiased sensitivity testing of tyrosine kinase inhibitors. Oncotarget. 2016;7:78083–94.

    Article  Google Scholar 

  15. Hochhaus A, Baccarani M, Silver RT, Schiffer C, Apperley JF, Cervantes F, et al. European LeukemiaNet 2020 recommendations for treating chronic myeloid leukemia. Leukemia. 2020;34:966–84.

    Article  CAS  Google Scholar 

  16. Eide CA, Zabriskie MS, Savage Stevens SL, Antelope O, Vellore NA, Than H, et al. Combining the allosteric inhibitor asciminib with ponatinib suppresses emergence of and restores efficacy against highly resistant BCR-ABL1 mutants. Cancer Cell. 2019;36:431–43 e5.

    Article  CAS  Google Scholar 

Download references

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Author notes

  1. Giovanni Martinelli

    Present address: Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy

Authors and Affiliations

  1. Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology “L. e A. Seràgnoli”, University of Bologna, Bologna, Italy

    Simona Soverini, Margherita Martelli, Luana Bavaro, Caterina De Benedittis, Michele Baccarani & Giovanni Martinelli

  2. Fondazione Policlinico Universitario A Gemelli-IRCCS, Istituto di Ematologia e Università Cattolica del Sacro Cuore, Rome, Italy

    Simona Sica & Federica Sorà

  3. Hematology Division, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy

    Alessandra Iurlo

  4. Department of Medicine, Section of Hematology, University of Verona, Verona, Italy

    Massimiliano Bonifacio

  5. Hematology Unit, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, Turin, Italy

    Patrizia Pregno

  6. Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy

    Sara Galimberti

  7. Hematology and BMT Unit, San Raffaele Scientific Institute IRCCS, Milan, Italy

    Francesca Lunghi

  8. Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari, Italy

    Francesco Albano

  9. Hematology Unit, Spedali Civili Azienda Ospedaliera, Brescia, Italy

    Mariella D’Adda

  10. Division of Hematology, Azienda Ospedialiero-Universitaria, Parma, Italy

    Monica Crugnola

  11. Hematology Unit, Azienda Unità Sanitaria Locale-IRCCS, Reggio Emilia, Italy

    Isabella Capodanno

  12. Azienda Ospedaliero-Universitaria di Bologna, via Albertoni 15, Bologna, Italia

    Fausto Castagnetti, Gabriele Gugliotta, Cristina Papayannidis, Gianantonio Rosti & Michele Cavo

  13. Istituto di Ematologia “Seràgnoli”, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università degli Studi, Bologna, Italia

    Fausto Castagnetti, Gabriele Gugliotta, Cristina Papayannidis, Gianantonio Rosti & Michele Cavo

  14. Unit of Medical Genetics, University of Parma, Parma, Italy

    Antonio Percesepe

  15. Department of Science and Innovation Technology (DISIT), University of Piemonte Orientale, Alessandria, Italy

    Flavio Mignone

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  1. Simona Soverini
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Correspondence to Simona Soverini.

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Conflict of interest

SS has received speaker fees from Incyte Biosciences. SSi has received honoraria for advisory boards from Incyte Biosciences. AI has received honoraria from Novartis, Pfizer and Incyte Biosciences. MB has received honoraria from Novartis, Incyte Biosciences, Pfizer. PP has received honoraria from Novartis, Incyte Biosciences, Bristol-Myers Squibb, Pfizer. SG has received speaker fees from Pfizer, Novartis, Incyte Biosciences. FA has received honoraria for advisory boards from Incyte Biosciences. FC has received honoraria from Novartis, Bristol‐Myers Squibb, Pfizer, Incyte Biosciences. GG has received honoraria from Novartis and Bristol‐Myers Squibb. GR has received honoraria from Novartis, Bristol-Myers Squibb, Pfizer, Incyte Biosciences. GM has been a consultant and has received speaker fees from Incyte Biosciences, Pfizer. The remaining authors declare that they have no competing interests.

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Soverini, S., Martelli, M., Bavaro, L. et al. BCR-ABL1 compound mutants: prevalence, spectrum and correlation with tyrosine kinase inhibitor resistance in a consecutive series of Philadelphia chromosome-positive leukemia patients analyzed by NGS. Leukemia 35, 2102–2107 (2021). https://doi.org/10.1038/s41375-020-01098-w

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