Molecular-defined clonal evolution in patients with chronic myeloid leukemia independent of the BCR-ABL status

Abstract

To study clonal evolution in chronic myeloid leukemia (CML), we searched for BCR-ABL-independent gene mutations in both Philadelphia chromosome (Ph)-negative and Ph-positive clones in 29 chronic-phase CML patients by targeted deep sequencing of 25 genes frequently mutated in myeloid disorders. Ph-negative clones were analyzed in 14 patients who developed clonal cytogenetic abnormalities in Ph-negative cells during treatment with tyrosine kinase inhibitors (TKI). Mutations were detected in 6/14 patients (43%) affecting the genes DNMT3A, EZH2, RUNX1, TET2, TP53, U2AF1 and ZRSR2. In two patients, the mutations were also found in corresponding Ph-positive diagnostic samples. To further investigate Ph-positive clones, 15 randomly selected CML patients at diagnosis were analyzed. Somatic mutations additional to BCR-ABL were found in 5/15 patients (33%) affecting ASXL1, DNMT3A, RUNX1 and TET2. Analysis of individual hematopoietic colonies at diagnosis revealed that most mutations were part of the Ph-positive clone. In contrast, deep sequencing of subsequent samples during TKI treatment revealed one DNMT3A mutation in Ph-negative cells that was also present in Ph-positive cells at diagnosis, implying that the mutation preceded the BCR-ABL rearrangement. In summary, BCR-ABL-independent gene mutations were frequently found in Ph-negative and Ph-positive clones of CML patients and may be considered as important cofactors in the clonal evolution of CML.

Spectrum of somatic mutation dynamics in chronic myeloid leukemia following tyrosine kinase inhibitor therapy

“…38,39 Other mutations were within genes known to be commonly mutated in myeloid disorders including CML such as TP53, KMT2D (MLL2), and TET2. [27][28][29]32,40 Our results clearly indicate that the acquisition of new mutations during TKI therapy was strongly correlated with treatment failure. to TKI therapy (BCR-ABL measured at 0.12% at follow-up), suggesting its presence in a Ph 2 clone as well.…”

“…[42][43][44] Such preleukemic mutations have been reported in other hematologic malignancies but have not been explored in CML extensively. 32,[42][43][44][45][46][47] The present study showed the presence of such mutations in CML patients (16%, 16 of 100 cases) which needs to be confirmed in a larger number of patients and investigated for its clinical relevance. Pattern 1 mutations can be considered indirect evidence of a preleukemic Ph 2 clone from which the leukemic Ph 1 clone evolved (illustrated in Figure 5).…”

“…[27][28][29][30][31] In particular, somatic mutations in genes associated with chromatin modification and DNA methylation are often enriched; in contrast, the other 6 pathways are not enriched in CML. [27][28][29]32 The origins, clinical implications, and associations with BCR-ABL transcript changes of relevant somatic mutations remain mostly unknown.…”

“…32 Preleukemia is a stage of the evolution of cancer in many patients, characterized by the growth of cells carrying a subset of genetic or epigenetic mutations necessary for leukemogenesis. 33 Leukemic transformation occurs upon the acquisition of additional genetic lesions.…”

Rapid conversion of chronic myeloid leukemia to chronic myelomonocytic leukemia in a patient on imatinib therapy

“…Tyrosine kinase inhibitors (TKIs) suppress the Ph + cell clone, restoring polyclonal hematopoiesis 2 . However, clonal cytogenetic abnormalities in Ph − cells become detectable in some patients achieving a cytogenetic response to TKIs, and slow evolution to myelodysplasia or acute myeloid leukemia (AML) has been observed 2, 3 . In rare cases, identical abnormalities were demonstrated both in Ph + and Ph − cells, but most cases are consistent with independently acquired abnormalities, although an undetected common ancestral event cannot be excluded (reviewed in 4 ).…”