Functional and epigenetic phenotypes of humans and mice with DNMT3A Overgrowth Syndrome

Abstract

Germline pathogenic variants in DNMT3A were recently described in patients with overgrowth, obesity, behavioral, and learning difficulties (DNMT3AOvergrowth Syndrome/DOS). Somatic mutations in the DNMT3A gene are also the most common cause of clonal hematopoiesis, and can initiate acute myeloid leukemia (AML). Using whole genome bisulfite sequencing, we studied DNA methylation in peripheral blood cells of 11 DOS patients and found a focal, canonical hypomethylation phenotype, which is most severe with the dominant negative DNMT3AR882H mutation. A germline mouse model expressing the homologous Dnmt3aR878H mutation phenocopies most aspects of the human DOS syndrome, including the methylation phenotype and an increased incidence of spontaneous hematopoietic malignancies, suggesting that all aspects of this syndrome are caused by this mutation.

DNMT3Aovergrowth syndrome is associated with the development of hematopoietic malignancies in children and young adults

“…Given the data presented here, and the finding of spontaneous leukemias developing in germline mouse models of DOS, 3,19 we suggest that DOS should be classified as a hematologic malignancy predisposition syndrome.…”

“…1 Mutations were found in all three functional domains of DNMT3A, and likely caused loss-offunction of the mutant allele. [1][2][3][4] Affected individuals shared distinctive facial features, intellectual disability, obesity, and tall stature. Although somatic mutations in DNMT3A are among the most common initiating events for normal karyotype AML patients and clonal hematopoiesis, [5][6][7][8][9] mutations of DNMT3A are rarely found in pediatric AML patients.…”

“…4 We recently described the DNA methylation landscape for 11 DOS patients (including one with a history of AML) compared to unaffected controls, which showed focal hypomethylation in nonleukemic peripheral blood cells that was more pronounced in patients with DNMT3A R882H than other DNMT3A mutations. 3 Although reports of AML have been described in two DOS patients, 2,11 and a single Tlymphoblastic lymphoma/leukemia, 12 the incidence of hematopoietic malignancies in DOS patients is not yet clear.…”

“…We were able to obtain samples to perform exome or whole genome sequencing (WGS) on diagnostic and remission samples (and a buccal swab sample) from Case 1 (germline mutation DNMT3A R882C ; of note, this is Case 3 in Smith, et. al 3 ) to identify cooperating mutations in the AML sample (Figure 1B, Supplemental Table 1). The founding clone at presentation contained AML-associated mutations in NPM1 (Variant allele frequency/VAF 37.6%), NF1 2505fs (VAF 37.9%), and MYC P72PT (VAF 35.9%); all the somatic founding clone mutations were completely cleared in a peripheral blood sample obtained 4.4 years later, when the patient was in morphologic remission (Figure 1C).…”

Somatic Dnmt3a inactivation leads to slow, canonical DNA methylation loss in murine hematopoietic cells

“…This inhibits formation of active homodimers, reducing its enzymatic activity by approximately 80% ( Russler-Germain et al., 2014 ). Reduction of enzymatic activity leads to a focal, canonical hypomethylation phenotype both in non-leukemic blood cells ( Smith et al., 2021 ) and in AML cells expressing the R882H mutation ( Spencer et al., 2017 ). However, many aspects of this process are not yet understood, including the rate of methylation loss in HSPCs (and their progeny) over time.…”