Over the past decade, numerous studies utilizing comparative genomic hybridization techniques, single-nucleotide polymorphism (SNP) arrays, and, most recently, whole-genome and whole-exome sequencing have elucidated new findings that bear relevance to the biology and natural history of chronic lymphocytic leukemia (CLL). What is critical to any such study is the quality of the test material, meaning that samples should be collected at a uniform time from a cohort being managed uniformly and that test samples should be paired with germline material.
The above criteria were met in a study by Edelmann et al. who recently reported one of the most comprehensive assessments of genomic copy number variation in symptomatic, but as yet untreated, CLL patients (patients were enrolled in a clinical trial, the German CLL8 study, of first-line therapy but had not begun treatment at the time the peripheral blood samples used in the current study were collected). The experimental design was based on SNP-array analysis that was used to assess copy number alterations (CNAs) using DNA prepared from CD19+ mononuclear cells from 353 patients. Unlike many other previously published analyses, the current study included a strategy for identifying tumor-specific abnormalities. In this case, paired samples were analyzed in 144 patients, with DNA from CD19- mononuclear cells serving as the non-tumor control. To validate accuracy, Edelmann and colleagues compared the SNP-array results with those obtained from interphase cytogenetic analyses using four standard florescence in situ hydridization (FISH) probes. Those comparisons demonstrated that all of the genomic deletions and additions observed by FISH were reproduced by the SNP-array. Further, the frequency of non-FISH-defined CNAs was low (0.55) and appeared independent of IgVH mutational status and FISHdefined genomic abnormalities other than del(17p13.1), mutant TP53, and del(11q22.3) where the frequency was 1.06. In total, two-thirds of the cases carried no CNAs other than those detected by standard FISH. Collectively, these findings suggest that genomic instability is not a common component of the pathophysiology of CLL.
From the SNP array analysis came characterization of both minimally deleted regions in the common karyotype abnormalities and identification of less frequent genomic aberrations previously undocumented. High-resolution analysis of the common 13q14 deletion suggested that in addition to deletion of microRNAs miR-16-1 and miR-15a, deletion of two long non-coding RNA genes, DLEU1 and DLEU2, likely contribute to disease pathogenesis. Most frequent among the previously unidentified genomic alterations was del(15q15.1), which was present in 4 percent of patients, with the smallest deleted region found within the MGA gene locus. Subsequent nucleotide sequencing revealed somatic mutation of MGA in one of 59 patients. MGA is part of the network of MAX and MAX-interacting proteins that are involved in regulatory mechanisms involved in cell proliferation, differentiation, and apoptosis, suggesting that deletion of MGA may contribute to CLL pathogenesis in a small percentage of patients. However, del(15q15.1) had no prognostic significance relative to overall survival. Evidence of chromothripsis (extreme chromosome reorganization thought to occur in a one-step catastrophic event and defined in this study as the presence of at least 10 switches between 2 or 3 copy number states on an individual chromosome) was identified in a small subset of patients and negatively impacted on both progression-free survival and overall survival. However, the majority of the patients with evidence of chromothripsis had unmutated IgVH and high-risk genomic aberrations, including one-third with a concomitant TP53 mutation. The current study did not include analysis of samples at the time of relapse to assess of the contribution of clonal evolution to treatment failure. Such studies will likely be a focus of future research as the treatment phase of the CLL8 study matures and more samples from patients who have relapsed become available.
In Brief
The importance of this study centers around both analysis of DNA samples from a clinically uniform cohort of symptomatic CLL patients who were treatment-naïve and the use of paired, non-tumor DNA that allowed confirmation of the tumor specificity of the observed CNAs. Outside of those that were also detected by standard FISH, relatively few CNAs were independently identified by SNP-array analysis, suggesting a minor role for genomic instability in the pathogenesis of even symptomatic patients who are treatment-naïve. CNAs were modestly more frequent among patients with high-risk genetic features, and this group was also more likely to have evidence of chromothripsis. However, chromothripsis was found in only a small portion of the study group (7/353), suggesting that catastrophic DNA rearrangement is uncommon in CLL. Rigorous studies such as those of Edelmann and colleagues, when coupled with next-generation sequence analysis, will further elucidate the pathobiology of CLL and identify genetic abnormalities that can be targeted for therapy.
Competing Interests
Dr. Byrd indicated no relevant conflicts of interest.
