Landscape of biallelic DNMT3A mutant myeloid neoplasms

Abstract

DNA methyltransferase 3 A mutations (DNMT3A^MT) are frequent in myeloid neoplasia (MN) and mostly heterozygous. However, cases with multiple DNMT3A^MT can be also encountered but their clinical and genetic landscape remains unexplored. We retrospectively analyzed 533 cases with DNMT3A^MT identified out of 5,603 consecutive MNs, of whom 8.4% had multiple DNMT3A^MT hits. They were most frequent in acute myeloid leukemia (AML) with R882 variant accounting for 13.3% of the multi-hits. Multiple DNMT3A^MT more likely coincided with IDH2 (P = 0.005) and ETV6 (P = 0.044) mutations compared to patients with single DNMT3A^MT. When the sum of variant allele frequencies (VAFs) for multiple DNMT3A^MT exceeded 60%, we found a significant positive clonal burden correlation of the two DNMT3A variants (P < 0.0001) suggesting that they occurred in biallelic configuration. AML patients with biallelic DNMT3A inactivation (n = 52) presented with older age (P = 0.029), higher leukocytes (P < 0.0001) and peripheral blast counts (P = 0.0001) and significantly poorer survival rate (5.6% vs. 47.6% at 2 years; P = 0.002) than monoallelic DNMT3A^MT. Multivariate analysis identified biallelic DNMT3A^MT (HR 2.65; P = 0.001), male gender (HR 2.05; P = 0.014) and adverse genetic alteration according to the European LeukemiaNet 2022 classification (HR 1.84; P = 0.028) as independent adverse factors for survival, whereas intensive chemotherapy (HR 0.47; P = 0.011) favorably influenced outcomes. Longitudinal molecular analysis of 12 cases with biallelic DNMT3A^MT demonstrated that such clones persisted or expanded in 9 relapsed or transformed cases (75%) suggesting the early origin of biallelic hits with strong leukemogenic potential. Our study describes the likelihood that biallelic DNMT3A^MT, while rare, are indeed compatible with clonal expansion and thus questions the applicability of synthetic lethality strategies.

Keywords: DNMT3A mutation; Acute myeloid leukemia; Myelodysplastic syndrome; Myeloproliferative neoplasms.

Fig. 1

Landscape of single and multiple DNMT3A mutations. (A) Lollipop plot of somatic DNMT3A mutations. Variants identified as single and multiple hits are plotted at the top and bottom. (B) Oncoplot of pathogenic mutations identified in patients with single or multiple DNMT3A mutations. (C) Comparison of frequencies of recurrent somatic mutations in patients with single vs. multiple DNMT3A mutations. (D) Odds ratios and 95% confidential intervals of genes more likely to have single (blue) or multiple (red) DNMT3A mutations. * P < 0.05, ** P < 0.01, where P is based on Fisher’s exact test. (E) Scatter plot of the variant allele frequencies (VAFs) of patients with DNMT3A^MT. The VAF of first hit DNMT3A^MT was plotted on the x-axis and that of the second –hit DNMT3A^MT on the y-axis. Patients were categorized into 5 groups by the sum of VAFs. (F) Percentage of different types of monoallelic (upper) and biallelic (lower) DNMT3A^MT. (G) Overall survival (OS) comparison between monoallelic (blue) vs. biallelic (red) DNMT3A mutants in DNMT3A^MT MDS and AML patients. Kaplan-Meier Curves were compared by Log-Rank test

Fig. 2

Clonal architecture of biallelic DNMT3A^MTcases. (A) Scatter plot shows variant allele frequencies (VAFs) of co-occurring mutations (y-axis) and 2nd hit DNMT3A mutations (x-axis) in biallelic DNMT3A mutant cases. (B) VAFs were used to categorize co-occurring mutations into ancestral, simultaneous, or secondary mutations compared with biallelic DNMT3A mutations. The bar graphs show the percentages of the corresponding genes. (C) The prevalence of patients in each mutational type of co-occurring mutations. (D-G) Fish plots of representative longitudinal clonal hierarchy of biallelic DNMT3A^MT cases are shown. Clonal architecture of AML at diagnosis and following relapse after conventional intensive chemotherapy-induced remission (D) and allo-HSCT (E). (F) AML-MRC at diagnosis and after refractoriness to the initial therapy. (G) MDS at onset and upon progression to secondary AML (sAML). The variant allele frequencies (VAFs) of each variant are shown at the bottom