Oligonucleotide microarrays demonstrate the highest frequency of ATM mutations in the mantle cell subtype of lymphoma

Abstract

Mutations have been described in the ataxia telangiectasia mutated (ATM) gene in small numbers of cases of lymphoid neoplasia. However, surveys of the ATM mutation status in lymphoma have been limited due to the large size (62 exons) and complex mutational spectrum of this gene. We have used microarray-based assays with 250,000 oligonucleotides to screen lymphomas from 120 patients for all possible ATM coding and splice junction mutations. The subtypes included were diffuse large B cell, mantle cell, immunoblastic large B cell, follicular, posttransplant lymphoproliferative disorder, and peripheral T cell lymphoma. We found the highest percentage of ATM mutations within the mantle cell (MCL) subtype (43%, 12 of 28 cases), followed by a lower level (10% of cases) in the other subtypes. A frame-shift ATM mutation was found in one peripheral T cell lymphoma patient. In six MCL cases examined, four ATM variants were due to somatic mutation in the tumor cells whereas two others seemed to be germ-line in origin. There was no difference in p53 mutation status in the ATM mutant and wild-type groups of MCL. There was no statistically significant difference in the median overall survival of patients with wild-type vs. mutated ATM in MCL. Additional mutational and functional analyses are needed to determine whether ATM mutations contribute to the development and progression of MCL or are just the consequence of genomic instability in MCL.

Figure 1

Distribution of 38 ATM sequence variants in lymphoma samples. Vertical lines show the boundaries of the 62 coding exons within the ATM transcript. The spacing between these lines is proportional to the size of each exon. Black, gray, and white circles above each exon indicate the presence of deleterious mutations, unclassified missense changes, and polymorphisms, respectively. The location of the PI3-kinase homology domain is listed under the appropriate exons.

Figure 2

Frequency of deleterious and missense ATM mutations in 124 lymphomas. The number of cases investigated is listed below each subtype.

Figure 3

Detection of mutations in a MCL sample by using the two-color loss of signal assay. Fluorescein-labeled wild-type reference and biotinylated test MCL sample N targets were cohybridized to the ATM microarray. To correct for reproducible differences in the hybridization efficiencies of reference and test targets, the ratio of reference-to-test target signal at each wild-type PM probe was normalized against ratios derived from 10 separate chip cohybridization experiments. Averaged sense and antisense strand ratios are plotted on the y axis against the nucleotide position of the corresponding PM probe on the x axis. The identity of each exon is listed between the vertical lines depicting their boundaries in the ATM transcript. Peaks at the mutated 6227 T/G, 8663 T/C, and 9023 G/A positions (giving rise to I2076S, I2888T, and R3008H missense changes, respectively) are labeled.

Figure 4

Overall survival by ATM mutational status. The median overall survival of mutant ATM cases (solid line) of 53.3 mo was not significantly different from the median survival of 25.1 mo in the wild-type ATM cases (dashed line).