Three novel alternative splicing mutations in BCR-ABL1 detected in CML patients with resistance to kinase inhibitors.
BACKGROUND
Multiple types of mutations in the BCR-ABL1 kinase domain have been reported. We previously reported a common alternatively spliced BCR-ABL mRNA with a 35-nucleotide insertion (35INS). We report three novel alternative splicing mutants expressed as the dominant transcripts in patient with chronic myelogenous leukemia and resistance to kinase inhibitors.


METHODS
We screened RNA from more than 200 patients with resistance to more than one of the three kinase inhibitors for ABL1 kinase domain mutations by direct sequencing.


RESULTS
We found three not previously described splice mutants. All three showed >90% mutant transcript. The first resulted from the insertion of 79 nucleotides into the ABL1 exon 8-9 junction. The inserted sequence contained a sequence from regions of intron 8, located 120 bp apart: the 35-nucleotide sequence previously described, and an additional 44-nucleotide segment downstream from 35INS. The combined 79-nucleotide insertion splice mutant showed the same protein change as 35INS (p C475YfsX11). The second splice mutation comprised an 84-nucleotide sequence from intron 7 inserted into the ABL1 exon7-8 junction, also causing a frameshift and protein truncation (p A424EfsX18). The third splice derived from a 231-nucleotide sequence from intron 4 retained in the ABL1 exon 4-5 junction adding 40 intron-encoded amino acids and leading to a frameshift and early termination (p E275LfsX41).


CONCLUSIONS
These findings, when combined with the data on 35INS, support the concept that loss of the C-terminus of BCR-ABL1 is associated with significant resistance to kinase inhibitors; this mechanism appears to be a major source of resistance to kinase inhibitors.
Department of Hematology/Oncology, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 92675, USA.
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W
Ma
F
F
Giles
X
X
Zhang
X
X
Wang
Z
Z
Zhang
T-S
TS
Lee
C-H
CH
Yeh
M
M
Albitar
D017398:Alternative Splicing / Q000235:genetics*; D000595:Amino Acid Sequence; D001483:Base Sequence; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D005091:Exons; D016044:Fusion Proteins, bcr-abl / Q000235:genetics*; D006801:Humans; D007438:Introns; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000188:drug therapy* / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D047428:Protein Kinase Inhibitors / Q000627:therapeutic use*; D016415:Sequence Alignment
D047428:Protein Kinase Inhibitors; D016044:Fusion Proteins, bcr-abl