NIH study shows Burkitt lymphoma is molecularly distinct from other lymphomas

Scientists have uncovered a number of molecular signatures in Burkitt lymphoma, including unique genetic alterations that promote cell survival, that are not found in other lymphomas. These findings provide the first genetic evidence that Burkitt lymphoma is a cancer fundamentally distinct from other types of lymphoma. The researchers, from the National Cancer Institute (NCI), part of the National Institutes of Health, and their collaborators, identified mutated genes and altered pathways that might be used as targets for the development of new pharmaceuticals or the application of existing drugs for people with Burkitt lymphoma. The study was published online Aug. 12, 2012, in the journal Nature. 

Burkitt lymphoma is a type of non-Hodgkin lymphoma, and three clinical subtypes of this disease have been recognized. In the United States, a sporadic subtype affects all ages but is most frequent in children. The EBV-associated endemic subtype (associated with the Epstein-Barr virus) is most common among children in Africa.  The human immunodeficiency virus (HIV) predisposes to a third Burkitt lymphoma subtype.

Past studies by the research team, led by Louis Staudt, M.D., Ph.D., of NCI’s Center for Cancer Research, established that Burkitt lymphoma can be readily distinguished from another type of non-Hodgkin lymphoma, diffuse large-B-cell lymphoma (DLBCL), based on signatures of gene activity. While it was known that the MYC tumor promoting gene is always active in Burkitt lymphoma, other genetic changes that cause this lymphoma were largely unknown.

In this study, the scientists employed methods known as RNA resequencing and RNA interference (RNAi) to identify new genes and pathways that might cooperate with MYC in the early stages of Burkitt lymphoma. RNA resequencing enabled the researchers to find additional mutated genes in Burkitt lymphoma cells, and RNAi -- in which the expression of individual genes can be silenced (knocked down or made inoperative) -- helped them identify genes and pathways that are critical for cell proliferation and survival.

The researchers performed RNA resequencing in biopsy samples from 28 patients with Burkitt lymphoma and from 13 different Burkitt lymphoma cell lines and re-analyzed previously published RNA sequencing data from 80 DLBCL biopsies.  To confirm their genetic findings, they used an additional 111 biopsies and cell lines from sporadic, endemic and HIV-associated Burkitt lymphoma as well as 186 DLBCL biopsies.

In addition to finding that, as expected, MYC was highly mutated in Burkitt lymphoma, the researchers identified mutations in many other genes not previously implicated in this cancer, many of which were rarely, if ever, mutated in DLBCL. Conversely, they found genes that are frequently mutated in DLBCL but not in Burkitt lymphoma, showing that these lymphomas use fundamentally different mechanisms to become cancerous.

Among the most commonly mutated genes in Burkitt lymphoma was TCF3, encoding a crucial regulator of normal B-cell function.  B-cells are white blood cells that produce antibodies and are important to immunity. They are also the cells of origin of Burkitt lymphoma and DLBCL.  Even more prevalent than TCF3 were mutations found in the ID3 gene which encodes a protein that blocks TCF3 action.  Together, these genes were mutated in almost 70 percent of the Burkitt lymphoma samples.  Most of these mutations interfered with the ability of ID3 to inhibit TCF3, allowing TCF3 to alter the activity of hundreds of genes in Burkitt lymphoma cells.  In fact, the researchers found that Burkitt lymphoma cell lines, but not DLBCL cell lines, died when TCF3 was turned off by RNAi.

The discovery of TCF3 and ID3 mutations in Burkitt led the researchers to identify a potent cell survival pathway that might be attacked therapeutically.  They showed that TCF3 promotes the survival of malignant lymphoma cells by amplifying signals from the B-cell receptor, a protein complex that spans the outer membrane of B-cells. 

The B-cell receptor allows normal B cells to sense foreign molecules in their vicinity, triggering their proliferation and survival as they mount an immune response. One of the signaling pathways that is activated by the B-cell receptor is called the PI(3) kinase pathway. A kinase is an enzyme that transmits signals and helps control complex processes in cells. The PI(3) kinase pathway is perhaps the most frequently activated signaling pathway in human cancer and activation of this pathway promotes cancer cell survival. Consequently, a considerable drug development effort is underway to identify PI(3) kinase pathway inhibitors, said Staudt, but no such inhibitor has yet been clinically tested in patients with Burkitt lymphoma.

Another gene, CCND3, was mutated in 38 percent of the Burkitt lymphoma cell samples. CCND3 is activated by TCF3 and encodes a protein (cyclin D3) that interacts with a kinase called CDK6 in Burkitt lymphoma cells to promote cell cycle progression. The authors found that drugs that inhibit CDK6 caused Burkitt lymphoma cells to arrest and die, indicating that CDK6 may be another important target for the development of therapies for this cancer.

“Our research suggests a number of targeted therapies that might be less toxic than the high-dose chemotherapy that is typically given to patients with Burkitt lymphoma in the U.S., even though they have cure rates approaching 90 percent,” said Staudt.  “Such targeted therapies might also help children in Africa with Burkitt lymphoma, who only have cure rates of about 50 percent because intensive chemotherapy cannot be delivered safely in that setting.”

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Reference:  Staudt L, et. Al. Burkitt Lymphoma Pathogenesis and Therapeutic Targets from Structural and Functional Genomics. Nature. August 12, 2012. DOI: 10.1038/nature11378.