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Exome Sequencing Study IDs Recurrent DNMT3A Mutations in AML

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A new exome sequencing study is highlighting the importance of changes to a DNA methylation-related enzyme in a subset of acute myeloid leukemia cases.

Using a combination of exome sequencing and targeted resequencing, along with gene expression and methylation analyses, a Chinese research team has identified recurrent mutations in the DNA methyltransferase gene DNMT3A within a subtype of AML known as M5. The mutations, which turned up in about one-fifth of the AML-M5 cases tested, coincided with changes in the enzyme's activity and interactions with histone complexes, as well as alterations to gene expression patterns in affected samples.

The work is described in a paper appearing online in Nature Genetics yesterday.

Given their findings so far, those involved in the study argue that DNMT3A abnormalities may be crucial for the pathogenesis of some types of AML. Moreover, they noted, because mutations in the gene seem to correspond with worse outcomes in some AML patients, the finding may also have prognostic implications.

"Our work suggests a contribution of aberrant DNA methyltransferase activity to the pathogenesis of acute myeloid leukemia and provides a useful new biomarker for relevant cases," senior author Sai-Juan Chen, a medical genomics and systems biomedicine researcher at Shanghai Jiao Tong University, and co-authors wrote.

A whole-genome sequencing study of AML primary and relapse tumor and matched normal genomes published by Washington University researchers in the New England Journal of Medicine late last year also suggested that DNMT3A mutations tend to crop up in AML cases with poor outcomes and shorter survival times. That team found DNMT3A alterations in more than one-fifth of the AML tumors they screened.

For the current study, Chen and colleagues first used NimbleGen 2.1M human exome capture arrays in combination with Illumina GAIIx massively parallel sequencing to sequence protein-coding regions of the genome for matched tumor-normal samples from nine individuals with AML-M5 to an average of 100 times coverage each.

From the 220 SNPs and 46 small insertions and deletions detected in that phase of the study, the team homed in on 10 small insertions or deletions and 59 non-synonymous substitutions that were predicted to upset the affected gene's protein product.

Of these, PCR assays and Sanger sequencing experiments verified 58 substitutions and eight indels affecting 63 genes.

Along with genotyping experiments assessing these genes in a validation group of 98 more AML cases, the researchers also sequenced another five AML exomes without matched normal samples and sifted through published data to narrow in on six genes for targeted resequencing in the validation group.

DNMT3A was among the commonly affected genes, the researchers reported, harboring mutations in 20.5 percent of AML-M5 tumors tested. From their subsequent experiments, they found that these DNMT3A mutations coincide with changes to DNA methylation, gene expression patterns, and more.

In particular, the team tracked down three different substitutions that tend to occur at a particular DNMT3A codon. One of these changes showed up in nearly 14 percent of AML-M4 cases screened, hinting that epigenetic patterns may be upended in some cases of this AML subtype as well.

The team's analyses also pointed to ties between mutations in the DNMT3A gene and outcome measures such as overall survival and time to treatment failure, consistent with past research suggesting DNMT3A mutation status could yield prognostic insights.

"Although these findings need to be further studied in a larger sample size, the information obtained in this study based on analysis of clinical relevance could help improve the clinical management of AML-M5," the researchers concluded.

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