GENOMIC AND EPIGENETIC APPROACHES IN THE CLINICAL AND PROGNOSTIC STRATIFICATION OF CHRONIC LYMPHOCYTIC LEUKEMIA

Chronic lymphocytic leukemia (CLL) is characterized by highly clinical heterogeneity; the identification of factors that could predict the clinical course of early-stage CLL represents a crucial objective in this malignancy. The aim of the study is to identify novel biological markers that may be clinically relevant to envisage specific risk subgroups of CLL patients using both genomic (integrated FISH and microarray technology) and an epigenetic approach in highly purified B-cell populations obtained from early-stage CLLs (Binet stage A). The availability of information concerning the follow-up of the analyzed patients allowed the investigation of a potential prognostic significance associated with the biological markers identified. Genome-wide DNA profiling and FISH were used to perform a deletion-mapping analysis of 17p in a subset of 18 CLLs with TP53 deletion and in all the investigated cases, the breakpoints were scattered along the 17p10–p11.2 region. Additionally, gene expression profile (GEP) analysis revealed specific transcriptional patterns and altered molecular pathways associated with 17p aberrations. SNP-array technology and gene expression profiling data were also applied to investigate the 13q14 deletion occurring in a panel of 100 CLLs representative of the major genetics, molecular and biological features of the disease. Based on SNP-array, our study shows the presence of two different molecular groups of patients with del(13)(q14) based on the deletion size and the presence of biallelic deletions. Notably, global gene expression profiling identified a significant transcriptional deregulation specifically associated with the two groups. The genomic complexity detected by SNP-array approach indicates that a relatively high degree of genomic alterations is associated with early-stage CLLs. As regards the genomic changes, the most important and novel finding is the occurrence of 2p gain in a recurrent fraction of early-stage CLLs, which appears to represent an independent prognostic factor for treatment occurrence. An epigenetic approach was used to investigate global DNA hypomethylation affecting repeated sequences, such as long interspersed nuclear elements-1 (LINE-1), Alu and satellite α DNA (SAT-α DNA), reported to be associated with chromosomal instability. Our analysis was performed in a panel of 77 CLLs and 7 healthy donors using robust quantitative Pyrosequencing methodology to detect the methylation status of the three repetitive elements. For the first time, we reported a significant association between Alu, LINE-1 and SAT-α hypomethylation and the occurrence of the 17p13 deletion; our data also indicate that SAT-α hypomethylation may represent an independent negative prognostic marker significantly correlated with the need of starting treatment. Overall, our data further support: i) the use of microarray technology to characterize well-known lesions for a better prognostic stratification of the disease as well as to investigate genomic changes in CLL, allowing the definition of novel aberrations with pathogenetic and prognostic implications; ii) the use of an epigenetic approach to identify the potential clinical relevance of specific repetitive elements hypomethylation, which may be used as a novel prognostic indicator of unfavorable disease progression.