July-August 2012, Volume 9, Issue 4
Genetic Horizon Scanning in Large B-Cell Lymphoma
Published on: July 01, 2012
Dr. Johnson indicated no relevant conflicts of interest.
Lohr JG, Stojanov P, Lawrence MS, et al. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci USA. 2012;109:3879-3884.
Broad genomic analysis is providing fascinating insights into the pathobiology of diffuse large B-cell lymphoma (DLBCL), identifying both key driver mutations and potential therapeutic targets. This paper from Boston, that includes investigators from the Broad Institute, Massachusetts Institute of Technology, and the Dana-Farber Cancer Institute, is one of three recent studies that used whole-exome sequence analysis to map the mutational landscape in DLBCL. The other two analyses were conducted independently by the British Columbia Cancer Agency group in Vancouver1 and the Institute for Cancer Genetics, Columbia University, in New York.2 There are notable areas of overlap among the studies, pointing to mutational events that are fundamental to this type of lymphoma.
In the current study, tissue from 49 biopsy samples of DLBCL was subjected to whole-exome sequencing. To eliminate the dilutional effect of contamination by non-lymphoma cells contained in the biopsy specimens, the sequencing protocol mandated an average depth of exome coverage of 150-fold. A relatively high mutational rate (mean of 3.2 mutations per megabase with a range of 0.6-8.7) was observed. This rate was notably higher than that seen in chronic lymphocytic leukemia where the figure is usually below one mutation per megabase.
Among the 58 genes with rates of mutation significantly higher than would be expected by chance, there were a number previously identified as functionally important in DLBCL by other experimental methods, such as shRNA library screens and by the two papers cited above.1,2 These commonly mutated genes included CD79B, TP53, CARD11, MYD88, and EZH2. The latter is an epigenetic regulator, a class of genes also found to be mutated in a high proportion of germinal center lymphomas. Interestingly, this study also revealed frequent mutations in other epigenetic modifiers, such as MLL2 and MEF2B. That these genes have been shown to be mutated in other malignancies, including medulloblastoma and multiple myeloma, suggest that their protein products function as a tumor suppressors. Further, observed mutations in members of the Histone 1 family of genes lend additional weight to the hypothesis that epigenetic dysregulation is an important component of the pathobiology of DLBCL. Other genes found to be frequently mutated included the TNF receptor molecule, TNFRSF14, and a cell-cycle regulator, BTG1.
Mutations in the apoptosis suppressor BCL-2 are a well-described finding in lymphoma, and this study confirmed a relatively high mutational frequency, but with some distinctive features. Many of the mutations involved the WRCY motif, known to be an AID (activation-induced cytidine deaminase) target, and they largely occurred in the presence of a t(14;18) translocation that effects a balanced translocation between BCL-2 and the IgH locus. This observation supports the idea that mutations in BCL-2 arise through the same process as somatic hypermutation in immunoglobulin genes when t(14;18) is present. Notably, most of the mutations observed were synonymous, thereby not altering the normal function of the BCL-2 protein. The majority of mutations that were non-synonymous were clustered outside the BH domain of BCL-2, the region of the protein that determines key binding interactions with proapoptotic proteins. These observations suggest a selection pressure against nonfunctional mutations in the BH domain and are in keeping with the idea that suppression of apoptosis by BCL-2 is an important step in malignant transformation.
Mutant KRAS, NOTCH1, BRAF, SYK, and SGK1 are well recognized as drivers in some malignancies, but they have not been thought to contribute to the pathobiology of DLBCL. In the studies of Lohr and colleagues, mutations in these genes were identified but at a frequency that was insufficient to reach statistical significance. Nonetheless, identifying such mutations may be clinically relevant for an individual patient as targeted therapy aimed specifically at these driver mutations has already reached the clinic (e.g., the BRAF inhibitor vemurafenib) or is under development.
Although DLBCL is frequently cured with combination chemo/immunotherapy, the rapid increase in incidence during the latter part of the last century, particularly among older adults, has resulted in a large number of DLBCLs occurring among those who have difficulty tolerating intensive cytotoxic treatment. This group of patients is less likely to be cured, making identification of new approaches to therapy an imperative. Large-scale sequencing is one means of approaching the problem. The current study has confirmed some of the core pathological events in lymphoma development, highlighted new concepts in disease pathobiology of DLBCL such as epigenetic dysregulation, and shown that broad sequence analysis is a powerful tool for identifying new therapeutic objectives. There is little doubt that this technology will be an important part of our diagnostic and therapeutic armamentarium as we transition toward our twin goals of targeted therapy and personalized medicine.
1. Morin RD, Mendez-Lago M, Mungall AJ, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011;476:298-303.
2. Pasqualucci L, Trifonov V, Fabbri G, et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011;43:830-837.
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