Genomic and transcriptomic determinants of clinical outcomes in patients with AML and DNMT3A mutations

Abstract

Acute myeloid leukemia (AML) and DNMT3A mutations (DNMT3A^mut) are considered to carry intermediate risk under the 2022 European LeukemiaNet (ELN-2022) classification in the absence of other co-mutations or cytogenetic abnormalities. However, this group is highly heterogeneous. In this study, the genomic and transcriptomic features influencing outcomes in DNMT3A-mutated AML were examined in a cohort of 884 patients with AML receiving standard chemotherapy. Stratification by NPM1 and FLT3-ITD status revealed worse survival among patients with NPM1 mutations and wild-type FLT3-ITD (NPM1^mut/FLT3-ITD^wt) than patients in the ELN-2022 favorable risk group. The other three subgroups (NPM1^mut/FLT3-ITD^mut, NPM1^wt/FLT3-ITD^mut, and NPM1^wt/FLT3-ITD^wt) exhibited worse prognoses than patients in the ELN-2022 intermediate risk group. Additionally, the presence of TET2^mut in patients with AML and DNMT3A^mut/NPM1^mut/FLT3-ITD^wt led to reclassification from favorable risk to intermediate risk in the ELN-2022. RNA-sequencing analysis revealed a distinct transcriptomic profile in patients with TET2^mut, highlighting the enrichment of leukemic stem cell signatures and dendritic cell migration, with MMP14, CD200, and CT45A5 identified as key differentially expressed genes. In conclusion, co-mutation patterns strongly affected AML outcomes in patients with DNMT3A^mut. Patients with TET2^mut constituted a unique subgroup within the ELN-2022 favorable DNMT3A^mut/NPM1^mut/FLT3-ITD^wt group, characterized by distinct transcriptomic features and an unfavorable prognosis.

Fig. 1. Survival outcomes in patients with DNMT3A^mut.

A Comparison of Kaplan–Meier survival curves for OS and EFS among patients with AML stratified according to ELN-2022 risk groups (favorable, intermediate, adverse) and DNMT3A mutation status. OS and EFS for the DNMT3A^mut group closely aligned with those of the ELN-2022 intermediate risk group. B DNMT3A^mut were associated with significantly worse OS and EFS than DNMT3A^wt.

Fig. 2. Prevalence and prognostic implications of concurrent mutations in patients with DNMT3A^mut.

A Oncoprint of recurrent genetic mutations in patients with DNMT3A^mut and AML. Colored bars represent mutations, categorized according to functional gene classes. B Prevalence of concurrent mutations in patients with DNMT3A^mut and DNMT3A^wt. Mutations observed in at least 1% of patients in one subgroup are displayed. Significant differences between DNMT3A^mut and DNMT3A^wt groups are marked as follows: *P < 0.05, **P < 0.01, ***P < 0.001. C OS and EFS of patients with DNMT3A^mut stratified according to NPM1 and FLT3-ITD status. Patients with NPM1^mut/FLT3-ITD^wt exhibited significantly better OS and EFS than those in other groups. D OS and EFS in the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt group, stratified according to concurrent genetic mutations: TET2, IDH2, signaling pathway mutations (PTPN11, FLT3-TKD, and NRAS), and total subgroup patients. The worst outcomes were observed in the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt/TET2^mut subgroup. E OS and EFS comparison between the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt/TET2^mut subgroup and ELN-2022 favorable risk group. Worse outcomes were observed in the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt/TET2^mut subgroup. F OS and EFS comparison between the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt/TET2^wt subgroup and ELN-2022 intermediate risk group. Better outcomes were observed in the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt/TET2^wt subgroup.

Fig. 3. Comparison of transcriptional signatures between patients with DNMT3A^mut and DNMT3A^wt.

A Unsupervised hierarchical clustering of patients with DNMT3A^mut and DNMT3A^wt patients, with the major upregulated and downregulated DEGs displayed. Colors represent normalized gene expression values. B Volcano plot comparison of all RNA-seq genes between patients with DNMT3A^mut and DNMT3A^wt. Positive (logFC > 0) and negative (logFC < 0) fold changes indicate upregulated and downregulated genes, respectively, in patients with DNMT3A^mut. C, D Bubble plots illustrating a comparison of enriched and depleted MSigDB CGP and Hallmark gene sets between patients with DNMT3A^mut and DNMT3A^wt. Bubble size represents gene counts, and colors indicate statistical significance. E Gene Set Enrichment Analysis plots displaying overrepresentation of immune gene set signatures within the DNMT3A^mut transcriptome. F Venn diagram of DEGs identified in initial and updated comparisons between patients with DNMT3A^mut and DNMT3A^wt. An initial analysis included RNA-seq data from 80 patients with DNMT3A^mut and 184 with DNMT3A^wt and normal karyotypes. In an updated analysis, a subset of 63 DNMT3A^mut patients with normal karyotypes were compared with the original 184 patients with DNMT3A^wt.

Fig. 4. Differential transcriptional signatures between patients with TET2^mut and TET2^wt within the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt subgroup.

A Unsupervised hierarchical clustering of TET2^mut and TET2^wt patients within the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt subgroup, displaying the top upregulated and downregulated DEGs. Colors represented normalized gene expression values. B Number of upregulated and downregulated DEGs identified through comparison of transcriptomes in patients with AML with and without TET2, FLT3-TKD, IDH2, NRAS or any other co-mutations. Bubble plots illustrating enriched and depleted MSigDB Hallmark (C) and CGP and Gene Ontology Biological Processes gene sets (D) between patients with TET2^mut and TET2^wt in the DNMT3A^mut/NPM1^mut/FLT3-ITD^wt subgroup. Bubble size represents gene counts, and color indicates statistical significance. E Gene Set Enrichment Analysis plots indicating enrichment of LSC and immune gene set signatures within the TET2^mut transcriptome. F, G Volcano plot of DEGs with genes downregulated (logFC < 0) and upregulated (logFC > 0) in patients with DNMT3A^mut/NPM1^mut/FLT3-ITD^wt based on TET2 mutation status. Key DEGs are highlighted in a heat map, with colors representing normalized gene expression values.