title: Unraveling the complexity of tyrosine kinase inhibitor-resistant populations by ultra-deep sequencing of the BCR-ABL kinase domain.
abstract: In chronic myeloid leukemia and Philadelphia chromosome-positive acute lymphoblastic leukemia, tyrosine kinase inhibitor (TKI) therapy may select for drug-resistant BCR-ABL mutants. We used an ultra-deep sequencing (UDS) approach to resolve qualitatively and quantitatively the complexity of mutated populations surviving TKIs and to investigate their clonal structure and evolution over time in relation to therapeutic intervention. To this purpose, we performed a longitudinal analysis of 106 samples from 33 patients who had received sequential treatment with multiple TKIs and had experienced sequential relapses accompanied by selection of 1 or more TKI-resistant mutations. We found that conventional Sanger sequencing had misclassified or underestimated BCR-ABL mutation status in 55% of the samples, where mutations with 1% to 15% abundance were detected. A complex clonal texture was uncovered by clonal analysis of samples harboring multiple mutations and up to 13 different mutated populations were identified. The landscape of these mutated populations was found to be highly dynamic. The high degree of complexity uncovered by UDS indicates that conventional Sanger sequencing might be an inadequate tool to assess BCR-ABL kinase domain mutation status, which currently represents an important component of the therapeutic decision algorithms. Further evaluation of the clinical usefulness of UDS-based approaches is warranted.
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy. simona.soverini@unibo.it
authors.forename: Simona
authors.initials: S
authors.lastname: Soverini
authors.forename: Caterina
authors.initials: C
authors.lastname: De Benedittis
authors.forename: K
authors.initials: K
authors.lastname: Machova Polakova
authors.forename: Adela
authors.initials: A
authors.lastname: Brouckova
authors.forename: David
authors.initials: D
authors.lastname: Horner
authors.forename: Michele
authors.initials: M
authors.lastname: Iacono
authors.forename: Fausto
authors.initials: F
authors.lastname: Castagnetti
authors.forename: Gabriele
authors.initials: G
authors.lastname: Gugliotta
authors.forename: Francesca
authors.initials: F
authors.lastname: Palandri
authors.forename: Cristina
authors.initials: C
authors.lastname: Papayannidis
authors.forename: Ilaria
authors.initials: I
authors.lastname: Iacobucci
authors.forename: Claudia
authors.initials: C
authors.lastname: Venturi
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Bochicchio
authors.forename: Hana
authors.initials: H
authors.lastname: Klamova
authors.forename: Federica
authors.initials: F
authors.lastname: Cattina
authors.forename: Domenico
authors.initials: D
authors.lastname: Russo
authors.forename: Paola
authors.initials: P
authors.lastname: Bresciani
authors.forename: Gianni
authors.initials: G
authors.lastname: Binotto
authors.forename: Barbara
authors.initials: B
authors.lastname: Giannini
authors.forename: Alexander
authors.initials: A
authors.lastname: Kohlmann
authors.forename: Torsten
authors.initials: T
authors.lastname: Haferlach
authors.forename: Andreas
authors.initials: A
authors.lastname: Roller
authors.forename: Gianantonio
authors.initials: G
authors.lastname: Rosti
authors.forename: Michele
authors.initials: M
authors.lastname: Cavo
authors.forename: Michele
authors.initials: M
authors.lastname: Baccarani
authors.forename: Giovanni
authors.initials: G
authors.lastname: Martinelli
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D020134:Catalytic Domain / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D005260:Female; D016044:Fusion Proteins, bcr-abl / Q000737:chemistry / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D047428:Protein Kinase Inhibitors / Q000627:therapeutic use*; D011505:Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D012189:Retrospective Studies; D055815:Young Adult
chemical_list: D047428:Protein Kinase Inhibitors; D011505:Protein-Tyrosine Kinases; D016044:Fusion Proteins, bcr-abl