Next-Generation Sequencing in Non-BCR-ABLMechanisms Resistance in Patients with Chronic Myeloid Leukemia: Results of a Pilot Study
Authors: Buldakov Ilya , Voloshin Sergey , Fominykh Mikhail , Shuvaev Vasily , Petrov Sergey , Chechetkin Alexander , Martynkevich Irina 
Published: November 2020

Introduction.In recent times, more and more data are available on the mechanisms of development of primary and secondary resistance to therapy with tyrosine kinase inhibitors (TKIs) in patients with CML. The use of next-generation sequencing (NGS) allows detecting mutations in theBCR-ABLkinase domain (KD) in some patients with resistance to TKI therapy. However, the reasons for resistance in patients without mutations in theBCR-ABLKD are still unclear.
Aim.To determineBCR-ABL-independent molecular genetic markers of resistance to TKI therapy in patients with CML using NGS.
Materials and methods.We examined blood samples from 15 patients with resistant CP CML (8 men and 7 women) aged 32 to 59 years (Me = 44 years). Resistance to TKI therapy was determined according to the ELN 2013 criteria. In this group: 2 patients received therapy with 2 TKIs, 8 patients with 3 TKIs, 3 patients - 4 TKIs, and 2 patients received 5 TKIs (Me = 3 TKIs).
Cytogenetic test revealed trisomy 8 in 3 patients. One patient was diagnosed with the T315I mutation at once. The patients underwent NGS examination of the myeloid panel, which included 55 genes, with an average reading depth of 1000x using a MiSeq device (Illumina). The 2% threshold of variant allele frequency (VAF) was used. The clinical significance of mutations was evaluated using the COSMIC, ClinVar and OMIM databases.
Results.By NGS we identified genetic aberrations in all patients: an average of 5 mutations (from 1 to 10 in one patient). A total of 77 mutations with unclear clinical significance were identified: 54 of them were missense mutations, 22 were synonymous mutations, and 1 frameshift mutation. The most common abnormalities were found in theNF1(10),TET2(8),ATRX(7), andSTAG2(6) genes. In 2 patients, the simultaneous presence of mutations in theATRXandNF1genes was found, they had a primary-resistant course of the disease, MMR was not achieved even on the 3rd and 4th lines of targeted therapy. Three patients were found to have simultaneous mutations in theNF1andSTAG2genes, including two patients who also had a primary-resistant course of the disease, and one of them showed resistance to all 5 TKIs. In 2 patients with the simultaneous presence of mutations in theATRXandTET2genes, resistance to 2 TKIs was registered; CCyR without MMR was achieved only with ponatinib. In 3 patients with singleSTAG2mutations, MMR was achieved on the third line of TKI. One patient with 3 mutations inTET2also achieved MMR only on the third line TKI.
Mutations inTET2are more common in Ph-negative MPNs. In our study, mutations were most often detected in theNF1,ATRXandSTAG2genes. Although mutations in theNF1andATRXgenes have been described previously, they were found in responding patients with CP CML (Kim et. al. Blood 2017). In our study, mutations in these genes were found in therapy-resistant patients with an unfavorable course of the disease. TheNF1gene encodes a GTPase activating protein (GAP), which is involved in inhibiting the RAS/MAPK signal transduction pathway and is a tumor suppressor. Mutations in this gene are often associated with the development of CMML and JMML, resistance to therapy and decreased overall survival. TheATRXgene encodes a protein involved in chromatin remodeling, regulation of transcription, replication, and maintenance of telomere structure. TheSTAG2gene encodes a protein that is part of the cohesin complex.
Possibly, abnormalities in these genes may belong to a clone of leukemic stem cells (Vetrie et. al. Nature 2020), cause their resistance to TKI,BCR-ABL-independent proliferative potential and their genetic instability. In addition, some of these mutations, possibly, are preleukemic - they could precede the emergence of the Ph-clone in such patients by the mechanism of clonal hematopoiesis of indeterminate potential and may cause an unfavorable prognosis. This allowed us to suggest the prognostic and therapeutic value of mutations in theNF1,ATRXandSTAG2genes in CP CML patients with resistance to TKI therapy.
Conclusion.The obtained results of a pilot study of NGS use for predictingBCR-ABL-independent resistance to TKI therapy in patients with CML can serve as a basis for further research aimed at developing prognostic models and choosing a treatment method for resistance to targeted therapy.

Disclosures
Voloshin: Novartis:Honoraria, Speakers Bureau.Fominykh:Novartis:Honoraria, Speakers Bureau;Pfizer:Honoraria, Speakers Bureau;BMS:Honoraria, Speakers Bureau.Shuvaev:Novartis:Honoraria, Speakers Bureau;BMS:Honoraria, Speakers Bureau;Pfizer:Honoraria, Speakers Bureau.Martynkevich:Pfizer:Honoraria, Speakers Bureau;BMS:Honoraria, Speakers Bureau;Novartis:Honoraria, Speakers Bureau.