Expressions of the CIP/KIP family of CDK inhibitor proteins in primary intestinal large B-cell lymphomas: correlation with clinical outcomes

Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes

Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive form of non-Hodgkin lymphoma with variable biology and clinical behavior. The current classification does not fully explain the biological and clinical heterogeneity of DLBCLs. In this study, we carried out genomewide DNA methylation profiling of 140 DLBCL samples and 10 normal germinal center B cells using the HpaII tiny fragment enrichment by ligation-mediated polymerase chain reaction assay and hybridization to a custom Roche NimbleGen promoter array. We defined methylation disruption as a main epigenetic event in DLBCLs and designed a method for measuring the methylation variability of individual cases. We then used a novel approach for unsupervised hierarchical clustering based on the extent of DNA methylation variability. This approach identified 6 clusters (A-F). The extent of methylation variability was associated with survival outcomes, with significant differences in overall and progression-free survival. The novel clusters are characterized by disruption of specific biological pathways such as cytokine-mediated signaling, ephrin signaling, and pathways associated with apoptosis and cell-cycle regulation. In a subset of patients, we profiled gene expression and genomic variation to investigate their interplay with methylation changes. This study is the first to identify novel epigenetic clusters of DLBCLs and their aberrantly methylated genes, molecular associations, and survival.

Altered expression of Smad proteins in T or NK-cell lymphomas

PURPOSE

Smad proteins mediate cellular signaling through the transforming growth factor-beta family (TGF-betas). Smads 2 and 3 transmit signals from TGF-beta, and Smad4 is a common mediator, as well. However, little is known concerning the expression patterns of Smads in lymphoid tissue.

MATERIALS AND METHODS

Immunohistochemistry for Smad3 and Smad4 was performed on paraffin-embedded tissue sections collected from 26 T- or NK-cell lymphomas.

RESULTS

Nearly all cells in germinal centers were positive for Smad3, and more than 50% of paracortical cells were positive for Smad3 in reactive lymphoid tissue. When Smad4 immunostaining was conducted, nearly all the cells in the germinal centers showed diffuse cytoplasmic staining, and most of them exhibited nuclear positivity, as well. In addition, more than 50% of the cells in the paracortex were positive for Smad4. Furthermore, the Smad3 staining pattern was preserved in all malignant lymphomas, but four of these cases (15%) exhibited decreased expression of Smad4. All lymphoblastic lymphomas showed strong positivity in most of tumor cells, but one unspecified peripheral lymphoma, two nasal NK/T cell lymphomas, and one anaplastic large cell lymphoma were negative for Smad4.

CONCLUSIONS

These results suggest that TGF-beta-specific Smads may be actively involved in signal transduction in lymphoid organs and that Smad-mediated TGF-beta signaling pathways are operative in malignant lymphoma. In addition, loss of Smad4 expression might be associated with development of some T-cell lymphomas.

Methylation analysis of cyclin-dependent kinase inhibitor genes in primary gastrointestinal lymphomas

The CIP/KIP family of cyclin-dependent kinase inhibitors may act as tumor suppressors. To assess promoter hypermethylation as a potential underlying mechanism for loss of expression, methylation-specific polymerase chain reaction for p21 and p27 genes was performed in 13 gastric low-grade mucosa-associated lymphoid tissue (MALT) lymphomas, 13 gastric high-grade B-cell lymphomas, and 14 intestinal diffuse large B-cell lymphomas. p21 and p27 genes were unmethylated in normal Peyer's patch and tonsillar tissues. Promoter hypermethylation of p21 gene was detected only in some gastric low-grade MALT lymphomas (4/13, 31%). All gastric and intestinal high-grade lymphomas revealed unmethylated status of p21 gene. p27 gene was unmethylated in all cases of low- and high-grade gastrointestinal lymphomas. These results suggest that p21 promoter methylation is involved in some low-grade MALT lymphomagenesis in stomach and seems to be an early event in the gastric lymphomagenesis. And promoter methylation is not the underlying mechanism for loss of p27 protein expression in the malignant lymphomas of the stomach and intestine.