Molecular Characterization of Chronic Lymphocytic Leukemia Patients with a High Number of Losses in 13q14.

Abstract 2871

Deletion at 13q14 (13q) is the most common genomic aberration in CLL. It is present in more than 50% of cases, and is the sole documented cytogenetic abnormality in 36% of the patients. These latter cases are known to have a more favorable clinical course. However, recent data from our group and others, suggest that patients with CLL and 13q deletion as the only FISH abnormality could have a different outcome depending on the number of cells displaying this aberration. Thus CLL patients with a high number of 13q cells usually had both shorter overall survival and shorter time to first therapy. However, to the best of our knowledge the molecular characteristics of these patients have not been so far analyzed in detail.

A total of 102 samples were selected for the study, 32 of which served as a validation cohort. A complete immunophenotypic analysis by flow cytometry and FISH studies were carried out in all cases. The median age was 68 years (range, 35 to 90 years). For the purpose of the study, only samples with one cytogenetic abnormality were included. For the gene expression profile analysis, according to our previous results, two groups of patients with 13q were compared: those in whom 80% or more of cells showed 13q (13qH) and those in whom fewer than 80% of cells showed 13q losses (13qL). The distribution of cases in the study cohort was: 13qH (n=25; 36%), 13qL (n=27; 39%), normal FISH (nCLL, n=8; 11%) and 17p/11q (n= 10; 14%); and in the validation cohort: 13qH (n=7; 22%), 13qL (n=11; 34%) and nCLL (n=9; 28%).

Peripheral blood mononuclear cells (PBMCs) were isolated from fresh peripheral blood samples using Ficoll gradient, snapfrozen and stored at 80°C. For the validation cohort, CD19positive B cells were purified by magnetically activated cell sorting (MACS) CD19 MicroBeads resulting in a >98% purity, as analyzed by flow cytometry. CD19positive normal B cells from peripheral blood of five healthy donors served as controls. All samples were hybridized with the Affymetrix Human Exon arrays 1.0 ST.

A total of 3 450 genes significantly distinguished 13qH from 13qL patients, defining the 13qH signature. To determine the biological significance of the deregulated genes, a further analysis was carried out, revealing that apoptosis, BCR and NFkB signaling were the most significant affected pathways in 13qH CLL patients. Moreover, 13qH CLL patients were also characterized by a striking overrepresentation of deregulated miRNAs. A total of 15 miRNAs were deregulated in 13qH relative to 13qL patients. HsamiR155 was the most highly upregulated miRNA (Rfold=3.70), while hsamiR223 was the most significantly downregulated (Rfold=0.10). The posttranscriptional regulatory network of miRNA and genes in CLL patients with more than 80% of 13q cells was carried out by analyzing the miRNAmRNA relationships and the pathway analysis demonstrated that B cell receptor signaling, PI3K signaling and NFkB signaling were among the most strongly affected pathways in 13qH patients, highlighting the importance of miRNA regulation in CLL. The influence of other factors with prognostic relevance in CLL, such as IGVH mutational status, was discarded. We also analyzed the gene signature of CLL high risk cytogenetic subgroups in comparison with 13q patients. Surprisingly, our results suggest that some of the biological characteristics of 13qH CLL patients were similar to those of highrisk cytogenetic subgroups, since they share the deregulation of several key signaling pathways. To validate the differences observed between the subgroups of 13q CLL patients and get a visualization of these, we applied the Principal Component Analysis (PCA) in an independent series of patients. The expression pattern of CD19+ cells from CLL patients was notably different from the gene expression profile of CD19+ cells from healthy donors. Thus, CLL patients with a high number of 13q cells can be differentiated based on their expression profile. By contrast, the gene expression of B lymphocytes from 13qL and normal FISH subgroups was similar.

Therefore, this study provides new evidences regarding the heterogeneity of 13q deletion in CLL patients. Thus an overexpression of BCR and NFKB patways and as well as a deregulation of the balance between the proliferative and apoptotic signals and miRNA expression are involved in cases with higher percentages of 13q- cells.