Monday, May 12, 2014

DNMT3a mutations as predictors of poor outcome in AML

In my previous post, I introduced how the mutation of DNMT3a is frequent in differentiated hematopoietic stem cells in Acute Myeloid Leukemia. Before focusing on treatment, I wanted to first look further into why the DNMT3a mutation was a driver of AML progression.  Once a DNMT3a mutation is found in a patient, it signifies that the leukemia has progressed enough that the cancer will have a poor outcome.

Acute myeloid leukemia is already an aggressive cancer, but with a DNMT3a mutation, the cancer progression occurs at a much faster rate.  The Kaplan-Meier curves below show that in overall AML cases, as well as various groups of patients, mutation of DNMT3a is a predictor of lower survival rates. DNMT3a mutations were found in 0 of the 215 AML cases categorized with favorable outcome (1).

Figure 1. Overall Survival in AML patients with DNMT3a mutations. (Ley, Timothy J., et al, 2010)

The sample sizes are low, especially for comparison with FLT3 mutation, which makes the Kaplan-Meier estimations in blocks between monthly intervals. Finding the survival probability for a specific month after diagnosis would not be reliable, but the overall trend is consistent across across the estimations. The data shows that DNMT3a mutation presence is a more significant predictor of cancer fatality than any other mutation, and persists despite age, which is the largest factor in survival. It would be beneficial to include another graph categorizing patients by their response to treatment, because it is possible that the reasons for dramatically low survival in DNMT3a mutations may be partly due to those patients not yet having an effective targeted treatment for their type of leukemia.

The researchers also sequenced the 24 exons of DNMT3a from 188 AML bone marrow samples, shown in Figure 2 (1). The purple section represents the methyltransferase domain. The most common mutation is a missense mutation of R882H, followed by a missense mutation at R882C.

Figure 2. DNMT3A Mutations in 188 Patients with Acute Myeloid Leukemia. (Ley, Timothy J., et al, 2010)

The R882H mutation would be expected to disrupt normal functioning of DNMT3a in affecting transcriptional regulation of genes.  The Kaplan-Meier estimates back in Figure 1 show a separate curve for patients specifically with a R882 DNMT3a mutation. Based on this data, the R882 mutation only has a very slight, if any, difference in survival when compared to other DNMT3a mutations. 

Other studies on the R882 mutations disagree on whether the mutation type causes gain-of-function or loss-of-function for the methyltransferase, but it is likely that both occur at different densities of CpG sites (2). Holz-Schietinger provided evidence behind this idea by finding that there is a loss of methylation at clustered CpG islands, and hypermethylation at isolated CpG locations (3). The variation in mutant DNMT3a activity at different locations would make therapy more complicated than responding with a hypomethylating or hypermethylating agent because the mechanistic patterns of methylation locations are what changes, rather than the amount of methyl groups added. The small genetic mutations create larger epigenetic effects.

As for the clonal evolution pattern in AML, a high frequency of a common amino acid mutation would suggest that the reason behind the R882 mutation gives selective advantage to the cancerous cells' proliferation, rather than being a random error that happens to replicate undetected from a founder hematopoeitic stem cell. I think it is worth doing more analysis of the DNTM3a methylation patterns in future studies about AML, since there is conflicting information and even studies published within the past few months conclude that they don’t have enough evidence to make definitive statements. Concentrating specifically on R882 in DNMT3a could be the first step since it's the only recurrent mutation for AML.  By understanding the mechanisms behind aberrant DNA methylation, the therapies would be more effectively targeted for patients known to have DNMT3a mutations.

1) Ley, Timothy J., et al. "DNMT3A Mutations in Acute Myeloid Leukemia." The New 
     England Journal of Medicine (2010): 2424-33. Web. 12 May 2014. 
2) Schoofs, T., W. E. Berdel, and C. Müller-Tidow. "Origins of aberrant DNA 
     methylation in acute myeloid leukemia." Leukemia 28.1 (2014): 1-14. 
     Nature. Web. 12 May 2014. 

3) Holz-Shietinger, Celeste, Doug M. Matje, and Norbert O. Reich. "Mutations in DNA 
     Methyltransferase (DNMT3A) Observed in Acute Myeloid Leukemia Patients 
     Disrupt Processive Methylation." The Journal of Biological Chemistry 287.37 
     (2012): 30941-51. Web. 12 May 2014.