Clonal Heterogeneity in Patients with Myelodysplastic Syndromes (MDS) and Complex Karyotypes

Introduction: Complex chromosomal aberrations (CCAs) are seen in approximately 20% of patients with newly-diagnosed MDS and are associated with poor prognosis. Bone marrow cells of MDS patients with CCAs are characterized by a high degree of genomic instability, which is connected with an increased risk of formation of different subclones with additional aberrations. The phenomenon of clonal evolution can be observed either at diagnosis or during the disease progression. At diagnosis it is manifested by the presence of two or more related subclones derived from one founder clone. These subclones can obtain a proliferative advantage leading to the clonal expansion. The aim of the study was to perform detailed genome-wide analyses of bone marrow cells of previously untreated MDS patients with CCAs, to investigate the clonal heterogeneity and to assess the frequency and clinical significance of related cytogenetic subclones with complex karyotypes.

Methods: A comprehensive molecular cytogenetic analysis of fixed bone-marrow cells from 182 adults with CCAs (³3 aberrations) identified with conventional G-banding in the diagnosis of MDS was performed. The CCAs were studied through FISH with Vysis DNA probes (Abbott, Des Plaines, IL) and mFISH/mBAND methods (MetaSystems, Altlussheim, Germany). Genomic imbalances were identified with CytoChip Cancer SNP 180K (BlueGnome, Cambridge, UK) or with Illumina Human CytoSNP-12 arrays (Illumina, San Diego, CA).

Results: Cytogenetic subclones were detected in 143 of 183 patients with complex karyotypes (78.6%). Among them, 98/183 cases (53.8%) displayed a defined number of subclones, whereas in 45/183 patients (24.7%) a precise definition of the individual subclones was not possible due to the high number of heterogeneous findings. Therefore these patients were subsumed as having composite karyotype. In 138/143 cases with clonal heterogeneity (94.9%) subclones showed related karyotypes. Twelve patients had one clone with an interstitial 5q deletion as the sole abnormality and other subclones with additional changes. One of these 12 cases displayed a subclone with complex karyotype in which deleted chromosome 5 was involved in an unbalanced translocation. Five patients (5.1%) had a combination of related clones with del(5q) and additional changes and unrelated subclones without this aberration. Complex aberrations were often associated with the loss of heterozygosity (LOH) of 17p (44%), however a difference in the frequency of LOH 17p in groups with and without clonal heterogeneity was not ascertained (p = 0.782). Moreover, the overall survival (OS) of patients with clonal heterogeneity did not differ from that of patients with one homogeneous complex aberrant clone (p = 0.391). Median OS in both groups was three months only.

Conclusions: The results of this study confirmed clonal heterogeneity at the cytogenetic level as a frequent finding in patients with MDS and complex karyotypes. Although clonal diversity has been implicated as a driving mechanism of tumor development and progression and is usually associated with more aggressive disease, in this cohort of MDS cases with complex karyotypes, the presence of different subclones did not affect patients’ overall survival. It seems that the dismal prognosis of patients with CCAs is generally correlated with overall genomic instability and the complexity of aberrations. This may be manifested at different genetic levels by various phenomena such as increasing number of aberrations, accumulation of gene mutations and/or losses of heterozygosity of tumor-suppressor genes (including LOH TP53), involvement of deleted chromosome 5 in unbalanced rearrangements, extensive chromosome shattering, and clonal heterogeneity as well.

Supported by RVO-VFN64165, GACR P302/12/G157/1, PRVOUK-P27/LF1/1, and MHCR 00023736.