The current New England Journal of Medicine has an in-depth article on DNMT3A Mutations in Acute Myeloid Leukemia (AML).   Many of you will remember the discussion on this topic last month based on the two case studies that the same authors covered in the journal, where the DNMT3A mutation was shown to be associated with a poorer prognosis.  They now offer an update to the story:

“We did not find new recurring mutations in the first study but did observe a recurrent mutation in IDH1, encoding isocitrate dehydrogenase 1, in the second study. Subsequent work has confirmed and extended this finding, showing that mutations in IDH1 and related gene IDH2 are highly recurrent in patients with an intermediate-risk cytogenetic profile (20 to 30% frequency) and are associated with a poor prognosis in some subgroups of patients.

Improvements in sequencing techniques prompted us to reevaluate the first case with deeper sequence coverage, during which we discovered a frameshift mutation in the DNA methyltransferase gene DNMT3A.”

DNMT1, DNMT3A, and DNMT3B are genes that encode DNA methyltransferases.   These are enzymes that catalyse the addition of a methyl group to the cytosine residue of CpG dinucleotides.  Clusters of CpG dinucleotides are concentrated in regions upstream of genes.   It is known that increased methylation of these CpG islands is often associated with reduced expression of the downstream gene.

Aberrant DNA methylation has long been hypothesized to contribute to the pathogenesis of cancer.  However, cancer genomes tend to be hypomethylated, but hypermethylation of CpG islands in the promoters of tumor-suppressor genes (TSG) is also common in many tumours.  DNA methyltransferase inhibitors are currently one available option for the treatment AML, and includes drugs such as decitabine and azacitidine.  The response rates are generally fairly low and unpredictable, however, because there is no biomarker available to determine which patients will most likely respond to therapy.

Given the differences in the two case studies, the next step was clear:

“After discovering a frameshift mutation in DNMT3A with whole-genome sequencing, we conducted a study to determine whether DNMT3A is recurrently mutated in AML samples and whether DNMT3A mutations are associated with poor survival.”

To give an idea of the sheer scale of the datasets that these kind of GWAS studies generate in one patient, I was fascinated to read the following:

“We previously sequenced the AML genome of a sample obtained from Patient 933124 and obtained short single-end reads, yielding 98 billion base pairs of sequence and 91.2% diploid coverage of the genome. In this study, we obtained 116.4 billion base pairs with paired-end reads from the genome of the relapsed tumor, yielding 99.6% diploid coverage of the genome.”

What did they find?

The survival results based on the Kaplan-Meier curves clearly showed that those AML patients with no DNMT3A mutation clearly had better survival than those who did have the mutation, regardless of age and FLT3 mutation status.  You can check out the curves in the reference below.

The authors concluded that:

“DNMT3A mutations are highly recurrent in patients with de novo AML with an intermediate-risk cytogenetic profile and are independently associated with a poor outcome.”

What these results mean in practice (for now), is that the DNMT3A mutation offers a way to classify intermediate risk AML and thus an indication for earlier, more intensive treatment such as allogeneic stem cell transplant. Whether the mutation is druggable or not for future therapeutic intervention isn’t clear yet.

References:

ResearchBlogging.org Ley, T., Ding, L., Walter, M., McLellan, M., Lamprecht, T., Larson, D., Kandoth, C., Payton, J., Baty, J., Welch, J., Harris, C., Lichti, C., Townsend, R., Fulton, R., Dooling, D., Koboldt, D., Schmidt, H., Zhang, Q., Osborne, J., Lin, L., O’Laughlin, M., McMichael, J., Delehaunty, K., McGrath, S., Fulton, L., Magrini, V., Vickery, T., Hundal, J., Cook, L., Conyers, J., Swift, G., Reed, J., Alldredge, P., Wylie, T., Walker, J., Kalicki, J., Watson, M., Heath, S., Shannon, W., Varghese, N., Nagarajan, R., Westervelt, P., Tomasson, M., Link, D., Graubert, T., DiPersio, J., Mardis, E., & Wilson, R. (2010).  Mutations in Acute Myeloid Leukemia.  New England Journal of Medicine, 363 (25), 2424-2433 DOI: 10.1056/NEJMoa1005143

Ley, T., Ding, L., Walter, M., McLellan, M., Lamprecht, T., Larson, D., Kandoth, C., Payton, J., Baty, J., Welch, J., Harris, C., Lichti, C., Townsend, R., Fulton, R., Dooling, D., Koboldt, D., Schmidt, H., Zhang, Q., Osborne, J., Lin, L., O’Laughlin, M., McMichael, J., Delehaunty, K., McGrath, S., Fulton, L., Magrini, V., Vickery, T., Hundal, J., Cook, L., Conyers, J., Swift, G., Reed, J., Alldredge, P., Wylie, T., Walker, J., Kalicki, J., Watson, M., Heath, S., Shannon, W., Varghese, N., Nagarajan, R., Westervelt, P., Tomasson, M., Link, D., Graubert, T., DiPersio, J., Mardis, E., & Wilson, R. (2010).
Mutations in Acute Myeloid Leukemia New England Journal of Medicine DOI: 10.1056/NEJMoa1005143