DNMT3A,   TET2,  TP53

MBD4 deficiency may lead to clonal hematopoiesis and early onset of acute myeloid leukemia

DNA methylation on cytosine residues is a major source of mutagenic stimulus, as 5-methylcytosine (5mC) has a tendency to undergo spontaneous deamination to thymine. This methylation is one of the most common ways for somatic mutations to occur and it is a prominent feature of age-related DNA damage. DNA glycosylates including methyl-binding domain 4 (MBD4) or thymine DNA glycosylase is responsible for the removal of mispaired thymine after deamination of 5mC. However, it is not known whether MBD4 provides protection against cancer development. A group of international researchers investigated the mechanisms and function of MBD4 in acute myeloid leukemia (AML). The results of their study were published in Blood by Sanders et al.

In this study, the researchers first performed genomic profiling on samples from three patients (EMCAML-1, WEHI-AML-1, and WEHI-AML-2, all younger than 35 years at diagnosis). Germline DNA sequencing demonstrated that all three patients had a loss-of-function in the gene encoding MBD4. Moreover, it was observed that MBD4-deficient AMLs display a 33-fold higher mutation burden above what is characteristic for AML and a unique mutational signature associated with 5mc deamination with greater than 95% mutations in CG>TG.

Furthermore, it was demonstrated that all three cases of AML with germline MBD4-deficiency had biallelic DNMT3A mutations and IDH1 or IDH2 hotspot mutations. To understand the order of somatic mutation acquisition, single cell genotyping performed on sequential bone marrow biopsies taken during treatment obtained from two cases of AML (EMC-AML-1, WEHI-AML-1) showed that mutations in DNMT3A, a key driver gene for both clonal hematopoiesis and AML, were acquired first before IDH mutations. Additionally, it was observed that a marked expansion of clones carrying DNMT3A mutations occurred in the remission phase following treatment.

To further investigate the role of DNMT3A mutations in the MBD4-deficient bone marrow, single-cell-derived colonies (SCDCs) obtained from EMC-AML-1 at different time points of treatment were genotyped. At diagnosis and relapse, leukemic clones were dominant, however, at remission, 20 of 30 SCDCs carried distinct mono- or biallelic CG-TG mutations in DNMT3A. Deep variant analysis across all samples showed CG>TG mutations in age-related clonal hematopoiesis (ARCH); 28 in DNMT3A, 10 in TP53, 5 in ASXL1 and 7 in TET2. The researchers stated that “these results emphasize the importance of 5mC damage as a source of mutations that drive clonal expansion in the blood, representing a key contributor to ARCH”.

In summary, the results from this study demonstrate the importance of 5mC damage as a source of mutations that drive clonal expansion in the blood, thus representing a key contributor to age-related clonal hematopoiesis. Additionally, germline MBD4- deficiency is associated with the development of early-onset AML, through the acquisition of recurrent mutations in DNMT3A. The researchers concluded that their study “highlight a crucial role for MBD4 in safeguarding against the damage wrought by 5mC deamination”.

References
  1. Sanders M. A. et al. MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML. Blood. 2018 Jul 26. DOI: 10.1182/blood-2018-05-852566. [Epub ahead of print].
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