by ecancer reporter Clare Sansom
Burkitt’s lymphoma (BL) is an uncommon, aggressive type of non-Hodgkin’s lymphoma that can, nevertheless, often be cured with intensive chemotherapy.
It most often affects children, and it is endemic in equatorial Africa where it is associated with Epstein-Barr virus (EBV) infection in about 95% of cases.
The disease that occurs sporadically in other parts of the world, which is only associated with EBV infection in about 20% of cases, is recognised as a separate subtype, and there is also a variant that is associated with HIV infection.
Both this disease and diffuse large B-cell lymphoma (DLBCL) develop from normal germinal centre B-cells, although their mechanisms of oncogenesis are different.
It is not yet clear whether there are also differences in oncogenic mechanisms between the various subtypes of BL.
A large group of researchers led by Louis Staudt of the National Cancer Institute, Bethesda, Maryland, USA has now used high throughput RNA sequencing and RNA interference screening to explore the genetic changes that occur during Burkitt’s lymphoma and the pathways that these disrupt.
Stadt and his colleagues first performed RNA re-sequencing (RNA-seq) on 13 Burkitt’s lymphoma cell lines and on biopsies taken from 28 patients with the sporadic form of the disease.
This data was compared with re-analyses of published data from 80 cases of DLBCL, 52 of which were germinal centre-like and the other 28 activated B-cell like. All putative single-nucleotide variants in the BL samples were re-confirmed using Sanger sequencing.
The researchers found that the patterns of mutated genes differed significantly between the two types of lymphoma. Some genes were frequently mutated in BL, others in DLBCL, and still others, including the tumour suppressor TP53, in both.
This initial analysis confirmed that the genetic profiles of the two diseases are distinctly different. Genes found to be frequently mutated in BL included MYC, which has previously been implicated in this disease, and TCF3 and its negative regulator ID3.
The protein product of TCF3 regulates the transcription of immunoglobulins and other B-cell restricted genes.
Mutations in both genes were found to be common in all Burkitt’s lymphoma subtypes but rare in other lymphomas, but there were differences between Burkitt’s subtypes in the proportion of mutations in TCF3 compared to ID3.
All observed TCF3 mutations affected the DNA-binding domain of one of the two splice isoforms of this protein, E47, suggesting that this isoform plays an important role in lymphoma pathogenesis.
Mutations in TCF3 are commonly found in only one allele and the expression of the E47 isoform is increased in mutated samples, suggesting that this gene functions as an oncogene.
Conversely, ID3 mutations, which are frequently found in both alleles, inactivate the protein, implying that this is a tumour suppressor gene.
Analysis of the location of these mutations suggested that they occur at the interface between the proteins, preventing a protein-protein interaction that can be assumed to inhibit the function of TCF3. The researchers used chromatin immunoprecipitation and genetic knockdown to identify the biochemical pathways that are controlled by TCF3 in BL.
They found many similarities between these pathways and those controlled by the gene in normal germinal B cells.
Increased expression of the E47 isoform of TCF3 in lymphoma cells activated the phosphatidylinositol-3-OH kinase (PI-3) pathway, which is known to promote cell survival, and inhibitors of this kinase were toxic to most of the lymphoma cell lines.
One other gene that was frequently mutated in BL was CCND3, which encodes cyclin D3. This protein is known to be a direct target of TCF3 and to regulate the progress of germinal centre B cells through the cell cycle.
Mutations in this gene were found in 38% of cases of sporadic Burkitt’s lymphoma and 67% of cases of HIV-associated disease but, interestingly, only in 1.8% of cases of the endemic subtype.
These mutations seemed to produce a stable isoform of the protein that promoted progression through the cell cycle. Although Burkitt’s lymphoma is curable, its treatment is toxic and regimens are difficult to follow in the regions where the disease is endemic.
These results suggest further drug targets that should provide more options for the treatment of this disease.
Reference: Schmitz, R., Young, R.M., Ceribelli, M. and 39 others (2012). Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature, published online ahead of print 12 August 2012. doi:10.1038/nature11378
(16 May 2013)
(13 May 2013)