Leukaemia and lymphoma are both heterogeneous cancers. Mutations in many oncogenes and tumour suppressor genes have been associated with specific types of these blood cancers, but even pathologically and histologically similar cases may be genetically diverse. Two studies published in the 10 March issue of Nature have now identified mutations in genes encoding enzymes that catalyse the addition of acetyl groups to amino acid residues (acetyltransferases), including the histone acetyltransferase CREBBP (also known as CREB-binding protein, or CBP) in non-Hodgkin's lymphoma and in relapsed acute lymphoblastic leukaemia. This suggests that drugs that inhibit histone deacetylation – the reverse process to that catalysed by this enzyme – may be appropriate treatments in these cancers.

The first study, led by Riccardo Dalla-Favera from Columbia University in New York, USA, with colleagues and co-workers from Memphis, TN, USA; Chicago, IL, USA; and Novara, Italy, concerned genetic analysis of diffuse large B-cell lymphoma (DLBCL). This is the most common form of B-cell non-Hodgkins lymphoma, and it also often evolves from follicular lymphoma. Dalla-Favera and his co-workers sequenced the complete coding genome (exome) of lymphoma cells and paired normal DNA from seven DLCBL patients, and analysed single nucleotide polymorphisms in a further 72 cases using microarrays. They identified point mutations or copy number variants at a total of 450 different genetic loci in the genomes of the DLBCL patients. Some of the most common mutations identified in these genomes were in two genes that encode acetyltransferases, CREBBP and, less often, EP300. These closely related genes are transcriptional co-activators: that is, they influence gene transcription indirectly by activating DNA-binding transcription factors. Their mechanism of action is the addition of acetyl groups to specific lysine residues on nuclear proteins including histones.

Following the whole-exome sequencing, the researchers re-sequenced the coding sequence of the CREBBP gene in a further 134 heterogeneous DLBCL samples. Thirty-four different sequence variants were discovered in these genes. Exactly half these, including nonsense mutations, insertions, deletions and splice site alterations, resulted in the deletion or truncation of the catalytic histone acetyltransferase (HAT) domain in the resulting protein; the remaining 50% were primarily missense mutations affecting the same domain. Further mutations, again often affecting the HAT domain, were discovered using microarray and fluorescence in situ hybridisation (FISH) analysis. Interestingly, most of samples carried mutations in only one allele, indicating that a reduction in the concentration of this protein was sufficient for lymphoma development.

The researchers then sequenced samples of other types of mature B-cell non Hodgkin's lymphoma, and found that similar CREBBP mutations occurred often in follicular lymphoma but not in other lymphoma types including Burkitt and marginal-zone lymphoma. These mutations were not found in the normal (germline) DNA of any of the DLBCL or follicular lymphoma patients. Also, mutations in the related EP300 gene were found in a significant number of cases of both diseases. Very few cases had mutations in both genes, indicating that the genes could be considered as at least partly functionally equivalent.

Dalla-Favera and his co-workers compared expression levels of the CREBBP and EP300 proteins in normal and transformed B-cells from patients with both lymphoma types. Some limited expression of both proteins was observed in most of the transformed B-cells, indicating that mutation in one allele did not prevent expression of the normal allele. A few cell lines, including, interestingly, some with no mutations in these genes, expressed no protein, indicating that other mechanisms of inactivating these genes must be involved. B-cells in which these proteins were inactivated or expressed at low levels showed defects in nucleoprotein acetylation; in particular, they were unable to inactivate by acetylation a known onco-protein, BCL6, or to activate the tumour suppressor p53 by the same mechanism.

The second study, by Charles Mullighan and colleagues at St. Jude Children's Research Hospital, Memphis, TN, USA, with co-workers at the National Cancer Institute, Bethesda, MD, USA, investigated the genetics of relapsed acute lymphoblastic leukaemia (ALL). This disease occurs most often in children and young people, and although it is curable, it often relapses after treatment and the prognosis for patients with relapsed ALL is poor. Mullighan and his co-workers re-sequenced 300 genes in matched samples of leukaemia cells obtained at diagnosis and at relapse from 23 children with different types of B-cell progenitor ALL. The sequenced genes were ones with a known or putative connection with leukaemia or cancer in general, and included CREBBP. A total of 52 somatic non-synonymous mutations, many of which were novel, were recorded in 32 different genes. Four of the 23 cases had somatic mutations in CREBBP; three of these were present at both diagnosis and relapse, and one at relapse only.

The researchers then sequenced the CREBPP gene and its homolog from a further 318 children with leukaemia. In all 48 of the cases of relapsed ALL samples were available at both diagnosis and relapse; the other, non-relapsed cases included 170 of ALL and 100 of AML. Mutations in CREBBP were common in relapsed ALL but very much rarer in leukaemia of either type that did not relapse. These were most commonly truncation mutations or missense mutations in the catalytic HAT domain. Furthermore, mouse embryonic fibroblasts expressing similarly mutated CREBBP had defects in histone acetylation, in cell proliferation and in the expression of genes that respond to glucocorticoids. This last finding is particularly interesting because it may implicate CREBBP mutations in resistance to the glucocorticoid dexamethasone, which is often used in ALL therapy.

Many of the mutations observed in these studies have not been found in solid tumours. Both these studies, however, suggest that inhibition of histone acetylation is an important step in the development of several types of lymphoma and leukaemia, and that drugs that restore normal levels of acetylation in these proteins, such as histone deacetylase inhibitors, may provide useful treatment options for these diseases.

References

[1] Pasqualucci, L., Dominguez-Sola, D., Chiarenza, A. and 15 others (2011). Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature 471, 189-195

[2] Mullighan, C.G., Zhang, J., Kasper, L.H. and 12 others (2011). CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471, 235-239