Although mantle cell lymphoma (MCL) frequently harbors inactivated ataxia telangiectasia mutated (ATM) and p53 alleles, little is known about the molecular phenotypes caused by these genetic changes. We identified point mutations and genomic deletions in these genes in a series of cyclin D1-positive MCL cases and correlated genotype with gene expression profiles and overall survival. Mutated and͞or deleted ATM and p53 alleles were found in 56% (40͞72) and 26% (21͞82) of the cases examined, respectively. Although MCL patients with inactive p53 alleles showed a significant reduction in median overall survival, aberrant ATM status did not predict for survival. Nevertheless, specific gene expression signatures indicative of the mutation and genomic deletion status of each gene were identified that were different from wild-type cases. These signatures were comprised of a select group of genes related to apoptosis, stress responses, and cell cycle regulation that are relevant to ATM or p53 function. Importantly, we found the molecular signatures are different between cases with mutations and deletions, because the latter are characterized by loss of genes colocalized in the same chromosome region of ATM or p53. This information on molecular phenotypes may provide new areas of investigation for ATM function or may be exploited by designing specific therapies for MCL cases with p53 aberrations.cancer ͉ cell cycle ͉ genetics ͉ microarray ͉ signature M antle cell lymphoma (MCL) is an aggressive tumor that accounts for Ϸ6% of all non-Hodgkin lymphoma cases in the U.S., with higher rates in North America (1, 2). Although the median survival of MCL patients is only 3 years, some individuals survive Ͼ10 years from the time of diagnosis (2, 3). There is considerable interest in defining the molecular basis for this clinical heterogeneity to develop better prognostic markers and more effective therapies.MCL corresponds to B cells of the mantle zone of the lymphoid follicles that have acquired distinctive alterations in genes related to cell cycle control and apoptosis (4). The hallmark of these genetic alterations is the t(11;14)(q13;q32) translocation that juxtaposes the IGH locus near the CCND1 gene, resulting in the overexpression of cyclin D1 (5). A subset of MCL cases acquire p53 mutations, and these patients have a significantly shortened median survival relative to cases with wild-type p53 (6-8). Interestingly, the ataxia telangiectasia mutated (ATM) gene, whose product regulates some p53-dependent apoptosis pathways, is mutated or deleted in 25-40% of MCL cases (reviewed in refs. 9 and 10). Although preliminary studies suggest that ATM mutation status does not have a significant impact on patient survival (7, 11), they may have lacked the statistical power to identify more subtle effects on survival, such as the effect of functional subsets of mutations.We determined the ATM and p53 genotypes in a large cohort of MCL cases with previous gene expression profiles to further elucidate the relationship between molecular phe...