ATM gene alterations in chronic lymphocytic leukemia patients induce a distinct gene expression profile and predict disease progression

Abstract

Background: The genetic characterization of chronic lymphocytic leukemia cells correlates with the behavior, progression and response to treatment of the disease.

Design and methods: Our aim was to investigate the role of ATM gene alterations, their biological consequences and their value in predicting disease progression. The ATM gene was analyzed by denaturing high performance liquid chromatography and multiplex ligation probe amplification in a series of patients at diagnosis. The results were correlated with immunoglobulin gene mutations, cytogenetic abnormalities, ZAP-70 and CD38 expression, TP53 mutations, gene expression profile and treatment-free interval.

Results: Mutational screening of the ATM gene identified point mutations in 8/57 cases (14%). Multiplex ligation probe amplification analysis identified six patients with 11q deletion: all of them had at least 20% of deleted cells, analyzed by fluorescent in situ hybridization. Overall, ATM point mutations and deletions were detected in 14/57 (24.6%) cases at presentation, representing the most common unfavorable genetic anomalies in chronic lymphocytic leukemia, also in stage A patients. Patients with deleted or mutated ATM had a significantly shorter treatment-free interval compared to patients without ATM alterations. ATM-mutated cases had a peculiar gene expression profile characterized by the deregulation of genes involved in apoptosis and DNA repair. Finally, definition of the structure of the ATM-mutated protein led to a hypothesis that functional abnormalities are responsible for the unfavorable clinical course of patients carrying these point mutations.

Conclusions: ATM alterations are present at diagnosis in about 25% of individuals with chronic lymphocytic leukemia; these alterations are associated with a peculiar gene expression pattern and a shorter treatment-free interval.

Figure 1.

Statistical analysis of treatment-free survival. Evaluation of treatment-free interval in ATM-mutated and deleted CLL patients compared to patients without ATM alterations.

Figure 2.

Comparison between ATM-mutated and non-mutated CLL patients. Differentially expressed genes between ATM-mutated and ATM wild-type (WT) cases in all the CLL patients analyzed (A) and in IGHV unmutated subjects (B). Upper legend: green represents ATM-mutated cases, yellow ATM WT cases. Relative levels of gene expression are depicted with a color scale: red represents the highest level of expression and blue represents the lowest level.

Figure 3.

Comparison between MLPA+ and MLPA− CLL patients. Identification of 98 differentially expressed genes between MLPA+ cases and the remaining CLL samples. Upper legend: purple represents MLPA+ cases, light green MLPA− cases (A). Correlation between percentage of 11q22-23 deleted cells and expression levels of 6/13 transcripts localized on this chromosome region (B).

Figure 4.

Model of the ATM protein. Ribbon representation of the model of the ATM kinase domain (A). The amino acid residues involved by mutations (Arg2691 and Pro2699) and the ATP co-factor are represented by balls and stick. Details of the ATP binding region and the site of mutations are shown in (B).