Primary malignant lymphoma of the brain: frequent abnormalities and inactivation of p14 tumor suppressor gene

Array-based DNA methylation profiling of primary lymphomas of the central nervous system

Background

Although primary lymphomas of the central nervous system (PCNSL) and extracerebral diffuse large B-cell lymphoma (DLBCL) cannot be distinguished histologically, it is still a matter of debate whether PCNSL differ from systemic DLBCL with respect to their molecular features and pathogenesis. Analysis of the DNA methylation pattern might provide further data distinguishing these entities at a molecular level.

Methods

Using an array-based technology we have assessed the DNA methylation status of 1,505 individual CpG loci in five PCNSL and compared the results to DNA methylation profiles of 49 DLBCL and ten hematopoietic controls.

Results

We identified 194 genes differentially methylated between PCNSL and normal controls. Interestingly, Polycomb target genes and genes with promoters showing a high CpG content were significantly enriched in the group of genes hypermethylated in PCNSL. However, PCNSL and systemic DLBCL did not differ in their methylation pattern.

Conclusions

Based on the data presented here, PCNSL and DLBCL do not differ in their DNA methylation pattern. Thus, DNA methylation analysis does not support a separation of PCNSL and DLBCL into individual entities. However, PCNSL and DLBCL differ in their DNA methylation pattern from non- malignant controls.

Frequent and variable abnormalities in p14 tumor suppressor gene in glioma cell lines

Ten glioma cell lines were examined for abnormalities of exon 1beta of the p14 gene and then for abnormalities of the entire p14 gene with the use of previous findings of other exons. Abnormalities of exon 1beta and the entire p14 gene were detected in eight of ten cases: homozygous deletion of the entire gene in six cases, hemizygous deletion of exon 1beta with homozygous deletion of downstream exons in one case, and hemizygous deletion of the entire coding region with a missense mutation (A97V) at the C-terminal nucleolar localization domain in one case. The remaining two cases revealed no such abnormalities. p14 gene expression was observed in the latter two cases and one case with A97V mutation in the hemizygously deleted coding region, but not in the others, including one case with only exon 1beta. In the three cases with p14 gene expression, immunocytochemistry revealed p14 nucleolar staining, suggesting the retention of the functional activity of p14 protein and, in the case with the A97V mutation, an insufficient mutational effect as well. The present findings of the frequent and variable p14 gene abnormalities, including rare-type ones with or without sufficient mutational effect in glioma cell lines, might be of value for better understanding of the p14 gene and its related pathways in glioma carcinogenesis.

Genetic and epigenetic biomarkers in cancer : improving diagnosis, risk assessment, and disease stratification

Gene expression patterns change during the initiation, progression, and development of cancer, as a result of both genetic and epigenetic mechanisms. Genetic changes arise due to irreversible changes in the nucleotide sequence, whereas epigenetic changes occur due to changes in chromatin conformation, histone acetylation, and methylation of the CpG islands located primarily in the promoter region of a gene. Both genetic and epigenetic markers can potentially be utilized to identify different stages of tumor development. Several such markers exhibit high sensitivity and specificity for different tumor types and can be assayed in biofluids and other specimens collected by noninvasive technologies. In spite of the availability of large numbers of diagnostic markers, only a few have been clinically validated so far. The current status and the challenges in the field of genetic and epigenetic markers in cancer diagnosis, risk assessment, and disease stratification are discussed.

CDKN2A germline mutations in individuals with cutaneous malignant melanoma

Cyclin-dependent kinase inhibitor type 2A (CDKN2A) has been identified as a major melanoma susceptibility gene based on the presence of germline mutations in high-risk melanoma families. In this study, we sought to identify and characterize the spectrum of CDKN2A mutations affecting p16 inhibitor of cyclin-dependent kinase type 4 (INK4a) in individuals with melanoma using a population-based study design. DNA samples from 1189 individuals with incident multiple primary melanoma (MPM) and 2424 with incident single primary melanoma unselected for family history of melanoma were available for screening of CDKN2A (p16INK4a) mutations. Variants were classified for functional impact based on intragenic position, existing functional data, sequence, and structural analysis. The impact of individual mutations and functional groupings was assessed by comparing frequencies in cases of MPM versus cases with a single first primary melanoma, and by comparing the reported incidence rates in first-degree relatives. Our results show that mutations occur infrequently in these high-risk groups, and that they occur mainly in exons 1alpha and 2. Rare coding variants with putative functional impact are observed to increase substantially the risk of melanoma. With the exception of the variant in position -34 of CDKN2A of known functional consequence, the remaining rare variants in the non-coding region have no apparent impact on risk.

Update on primary central nervous system lymphoma

PURPOSE OF REVIEW

Primary central nervous system lymphoma is a rare form of extranodal non-Hodgkin's lymphoma that is confined to the central nervous system and eye. Numerous studies examining this disorder have been published in the past 2 years. This review will discuss recent advances in the understanding of the pathology, radiographic appearance, and treatment of this disorder.

RECENT FINDINGS

Novel treatment regimens continue to be studied for newly diagnosed and recurrent primary central nervous system lymphoma. As overall survival improves, the burden of late neurotoxicity has become more apparent. Neuropsychological testing of patients treated with chemoradiation shows significant cognitive deficits that can be attributed to whole brain irradiation. Standardization of phase II clinical trials across individual institutions remains an important goal within the oncology community. The International Primary Central Nervous System Lymphoma Collaborative Group (IPCG) has proposed guidelines for the baseline evaluation and response criteria for clinical trials of the disorder. In addition, series of patients with uncommon histological variants of primary central nervous system lymphoma have been published.

SUMMARY

In 2005, the optimal treatment for primary central nervous system lymphoma remains undefined. Treatment of newly diagnosed disease should include methotrexate-based chemotherapy but the role of irradiation and intrathecal chemotherapy remain unclear. Salvage therapy for progressive or recurrent primary central nervous system lymphoma is an area of active interest but no standard recommendations exist at the present time. Future studies on the biology of recurrent primary central nervous system lymphoma should help to clarify treatment options for these patients.