Cytogenetic Aberration Profile of Chronic Myeloid Leukemia and Its Dynamic Changes During Imatinib Therapy,

Abstract 3755

Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder characterized by excessive production of myeloid cells and the presence of the BCR-ABL fusion oncogene resulting from the t(9;22) reciprocal translocation. The leukemic clone in CML often accumulates other somatic lesions that may collaborate with BCR-ABL oncogenicity or confer resistance to tyrosine kinase inhibitors. The chromosomal instability in CML is believed to be caused by the BCR-ABL oncogene. We hypothesized that the accumulation of cytogenetic lesions in CML are acquired after the t(9;22). Thus, imatinib therapy should not only cause the molecular remission of BCR-ABL positivity but also the remission of most cytogenetic lesions. If cytogenetic lesions preceded t(9;22) acquisition, a residual clone should be detectable after remission of BCR-ABL positivity. In order to test these predictions, we determined high-resolution karyotypes of CML patients at diagnosis and at time points with variable durations of imatinib therapy. At the same time, we aimed to characterize the overall cytogenetic aberration profile of CML at different disease stages.

The copy number abnormalities and loss of heterozygosity coupled with acquired uniparental disomy (UPD) were determined using Affymetrix SNP 6.0 arrays. Overall 62 patients were included in the study.

For 13 patients paired DNA samples were available, the first one taken at diagnosis and the second after treatment with imatinib. These samples were used to evaluate the cytogenetic remission after treatment. In 7 out of 13 patients we could detect an additional chromosomal aberration at diagnosis. Interestingly, the clone size assessment based on copy number signal intensity data was concordant with BCR-ABL burden. Analysis of the follow-up samples revealed that 6 patients with additional cytogenetic aberrations at diagnosis showed complete cytogenetic remission. In one patient imatinib therapy led to significant reduction of the BCR-ABL burden but a residual BCR-ABL negative clone persisted. This residual clone exhibiting del6p, del10q and del13q was detectable as a minor clone at diagnosis and it fully replaced the BCR-ABL positive clone after 8 months of imatinib therapy. This data indicates that the BCR-ABL fusion was either acquired through the clonal progression of the initial clone carrying described cytogenetic aberrations, or two distinct clones were present at diagnosis.

In order to define the cytogenetic profile of CML samples we analyzed an additional number of 12 patient samples taken at diagnosis, as well as 37 samples taken after treatment with tyrosine kinase inhibitors. In 35.5% of the patients we could detect cytogenetic lesions, consisting of 28 deletions, 9 gains and 1 UPD. The most recurrent deletions were in the breakpoint region of the BCR (n=3) and ABL (n=5). Deletions of 13q (4 events) defined two common deleted regions (CDR) overlapping with previously defined CDR in other myeloproliferative neoplasms and chronic lymphoid leukemia. Other set of deletions clustered on chromosome 7p targeting 5 genes, among which was ABCB5, a member of ATP-binding cassette transporter family. One of the patients was also found to be a carrier of 11pUPD. In order to characterize the target gene within the UPD region we performed whole exome next generation sequencing of this sample and found 9 candidate mutations which are currently evaluated.

Compared to other myeloproliferative neoplasms, CML exhibits low cytogenetic complexity. This is demonstrated by the fact that only 35.5% of patients have chromosomal aberrations in addition to t(9;22). Our data indicates that the majority of aberrations in CML occur after t(9;22) during the clonal evolution of the leukemic cells. Most of these aberrations disappear after treatment with tyrosine kinase inhibitors. However in a proportion of patients clonal hematopoiesis persists, even after successful targeting of BCR-ABL positive cells. In these patients imatinib therapy does not restore polyclonal hematopoiesis despite the BCR-ABL remission. The persistence of a clone prone to accumulation of other mutations can potentially lead to induction of other hematological phenotypes.