Genomic loss is our gain

Identification of biallelic chromosomal deletions in non-Hodgkin lymphoma cell lines coupled with gene expression profiling identifies novel tumor suppressor genes and potential therapeutic targets.

Chromosome imbalances occur frequently in B-cell non-Hodgkin lymphomas (B-NHLs), and likely contribute to pathogenesis via amplification of proto-oncogenes and deletion of tumor suppressor genes. Array-based comparative genomic hybridization (CGH) and high-density single-nucleotide polymorphism (SNP) arrays are sensitive genome-wide techniques to detect net gains and losses of genetic material. While application of these technologies has identified select imbalances with biologic and prognostic relevence,¹  the role of most of these imbalances remains poorly elucidated. Use of array-based CGH or high-density SNP array in concert with gene expression profiling allows focused investigation of genes within the imbalanced locus.

In this issue of Blood, Mestre-Escorihuela and colleagues report on the integrative use of array-based CGH and transcriptional profiling to identify novel tumor suppressor genes in a diverse set of B-NHL cell lines. Candidate genes are identified based on biallelic deletion coupled with decreased gene expression. Their analysis is then expanded to the broader set of B-NHLs to identify alternate mechanisms of tumor suppressor silencing.

Homozygous deletion of 16p13.13 is identified in a primary mediastinal B-cell lymphoma (PMBCL) line, with associated null expression of the gene LITAF. LITAF has not been well validated as a tumor suppressor, though it is a p53-inducible gene that may play a role in p53-mediated apoptosis.²  In evaluating other cell lines, the authors find decreased LITAF expression in multiple diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL) resulting from promoter methylation. Given the germinal center derivation of these lymphomas, LITAF silencing is notable because it is repressed by BCL6,³  a gene critical to the germinal center reaction, and the target of the most common recurring chromosome translocation in DLBCL. Though BCL6 directly suppresses expression of p53,⁴ BCL6-mediated repression of LITAF appears to occur independently of TP53.³  The authors accordingly demonstrate that BCL6 and LITAF are inversely expressed at the protein level, and that treatment with the hypomethylating agent, 5-azacytidine, restores LITAF expression. They do not report, however, whether re-expression affects cell viability. Such information would help tease out the significance of this particular gene in context of the protean downstream effects of BCL6.

The proapoptotic BCL2 family member, BIM, is identified at a locus of homozygous deletion in mantle cell lymphoma (MCL), while decreased expression in BL and PMBCL cell lines is found secondary to promoter methylation. As with the epigenetic silencingof LITAF in DLBCL, 5-azacytidine restores BIM expression, though whether this results in apoptosis is again unclear. Another proapoptotic BCL2 family member, NOXA, is silenced via homozygous deletion in a BL cell line, but also manifests decreased protein expression in additional cell lines due to a combination of heterozygous deletions with inactivating mutations of the remaining allele or promoter.

In sum, Mestre-Escorihuela and colleagues elegantly demonstrate the power of integrating gene copy number assessment with gene expression profiling to identify candidate tumor suppressor genes. They highlight the numerous mechanisms whereby gene expression may be silenced, including deletion, inactivating mutations, epigenetic modification, and others. The finding that a candidate tumor suppressor gene may be silenced via different mechanisms depending on the underlying tumor histology provides further insight into the biological differences across NHL subtypes. This report adds nicely to the existing literature, including the recent identification of BLIMP1 as a tumor suppressor gene in subsets of DLBCL.⁵  Both reports highlight the heterogeneity of pathogenic mechanisms between and within subtypes of B-NHL. We trust that understanding of the diverse and distinct mechanisms of lymphomagenesis will ultimately provide targets for the development of subset-directed therapies.