Mutational Analysis of DNMT3A Improves the Prognostic Stratification Using NPM1/FLT3-ITD Genotypes in Patients with Acute Myeloid Leukemia

Background: Nucleophosmin 1 (NPM1) mutations are considered a favorable factor of acute myeloid leukemia (AML). However, their clinical significance in non-European regions remains unclear. DNA methyltransferase 3A (DNMT3A) mutations have been reported as a factor for poor prognosis in many cohort analyses. However, they were excluded among major prognostic factors even in the European Leukemia Net 2017 (ELN2017) classification. In this study, we analyzed the effects of NPM1 and concurrent mutations, particularly DNMT3A mutations, on prognosis.

Methods: All patients in this analysis were enrolled and selected by the gene sequencing of Japanese AML (GS-JAML) conducted by Nippon Medical School. We targeted only patients aged 70 years or younger who were diagnosed after 2010 and who received standard induction therapy consisting of 7 days of standard-dose cytarabine (100-200 mg/m² continuous infusion) and 3 days of an anthracycline antibiotic infusion (idarubicin 12 mg/m² or daunorubicin 60-90 mg/m²). Mutation screening were performed with target-captured sequencing for the AML gene panel. We also conducted agarose gel electrophoresis for the FMS-like tyrosine kinase 3 (FLT3-ITD) mutations and used the Sanger method to screen for CEBPA and NPM1 mutations. This study was reviewed and approved by the Human Subjects Institutional Review Board (project approval number 29-07-783) of the Nippon Medical School (Tokyo, Japan). Informed consent was obtained in accordance with the Declaration of Helsinki from all participants.

Results: We retrospectively analyzed the prognosis in 605 Japanese patients with de novo AML, including 174 patients with NPM1-mutated, 125 patients with DNMT3A-mutated and 127 patients with FLT3-ITD mutated AML. NPM1 mutation was not a prognostic factor either overall or in subgroups based on NPM1/tandem duplication in FLT3-ITD genotypes. Comprehensive gene mutation analysis showed that mutations in codon R882 of DNMT3A(DNMT3A^R882) were a strong factor of poor prognosis for AML overall and NPM1-mutated AML. Furthermore, multivariate analysis of all AML showed that DNMT3A^R882 mutations and the cooccurrence of FLT3-ITD, NPM1 mutations, and DNMT3A^R882 mutations (triple mutation) were independent factors for poor prognosis related to overall survival, with NPM1 mutations being an independent factor for favorable prognosis (hazard ratio: DNMT3A^R882 mutations, 1.946; triple mutation, 1.992, NPM1 mutations, 0.548). Furthermore, we evaluated the prognostic impacts of DNMT3A^R882 and triple mutation and demonstrated that NPM1-mutated AML patients could be more clearly stratified into three risk groups based on DNMT3A^R882/FLT3-ITD genotypes than the ELN 2017 classification.

Conclusion: Our study showed that the addition of DNMT3A^R882 mutations to existing prognostic models allowed for further stratification of NPM1-mutated AML. This new prognostic model might provide important clinical guidance.

Kanda:asclepia: Honoraria; ASAHI KASEI PHARMA CORPORATION: Honoraria; Janssen Pharmaceutical K.K.: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb Co: Honoraria; Novartis Pharma K.K.: Honoraria, Membership on an entity's Board of Directors or advisory committees; TEIJIN PHARMA LIMITED.: Honoraria; CHUGAI PHARMACEUTICAL Co., Ltd.: Honoraria; Takeda Pharmaceutical Company Limited: Honoraria; Sumitomo Dainippon Pharma Co., Ltd.: Honoraria; DAIICHI SANKYO Co., Ltd.: Honoraria, Membership on an entity's Board of Directors or advisory committees; SymBio Pharmaceuticals, Ltd.: Membership on an entity's Board of Directors or advisory committees; Sanofi K.K.: Honoraria; Kyowa Kirin Co., Ltd.: Honoraria; Megakaryon Co: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen Pharmaceutical K.K.: Honoraria; Ono Pharma Inc.: Honoraria; Otsuka Pharmaceutical Co., Ltd.: Honoraria; Amgen Pharma Inc.: Honoraria; AbbVie Inc.: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas Pharma Inc.: Consultancy, Honoraria; MSD K.K.: Honoraria; CSL Behring K.K.: Honoraria; Otsuka Pharmaceutical Co., Ltd.: Honoraria; NIPPON KAYAKU CO．，LTD．: Honoraria; Nippon Shinyaku Co., Ltd.: Honoraria; Eisai: Research Funding. Kuroda:Kyowa Kirin: Research Funding, Speakers Bureau; Chugai Phamaceutical: Research Funding, Speakers Bureau; Japan Blood Products Organization: Research Funding; Daiichi Sankyo: Research Funding, Speakers Bureau; Ono Pharmaceutical: Research Funding, Speakers Bureau; Sanofi: Research Funding, Speakers Bureau; Eisai: Research Funding, Speakers Bureau; Taiho Phamaceutical: Research Funding; Sumitomo Pharmaceutical: Research Funding, Speakers Bureau; Otsuka Pharmaceutical: Research Funding, Speakers Bureau; Asahikasei: Research Funding, Speakers Bureau; Takeda Pharmaceutical: Research Funding, Speakers Bureau; Nippon Shinyaku: Speakers Bureau; Janssen Pharmaceutical: Speakers Bureau; CLS Behring: Research Funding; Bristol Myers Squibb: Research Funding, Speakers Bureau; Abbvie: Research Funding, Speakers Bureau; Fujimoto Pharmaceutical: Research Funding, Speakers Bureau; Sysmex cooporation: Research Funding. Usuki:Bristo-Myers Squibb: Honoraria, Research Funding; Otsuka: Consultancy, Honoraria, Research Funding; Apellis Pharmaceuticals: Research Funding; Sanofi: Consultancy, Honoraria; Sumitomo-Dainippon: Research Funding; Astellas-Amgen-Biopharma: Research Funding; Eisai: Honoraria, Research Funding; Mundi: Research Funding; Yakult: Honoraria, Research Funding; Janssen: Research Funding; AbbVie: Honoraria, Research Funding; Gilead: Research Funding; MSD: Honoraria, Research Funding; Astellas: Consultancy, Honoraria, Research Funding; Alexion: Consultancy, Honoraria, Research Funding; Kyowa-Kirin: Consultancy, Honoraria, Research Funding; Ono: Honoraria, Research Funding; Celgene: Honoraria, Research Funding; SymBio: Consultancy, Research Funding; SynBio: Research Funding; Takeda: Consultancy, Honoraria, Research Funding; Nippon Shinyaku: Consultancy, Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Chugai: Consultancy, Honoraria, Research Funding; Daiichi Sankyo: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Incyte: Research Funding. Kanda:Mundipharma Pharmaceuticals: Research Funding.