Machine Learning Allows the Identification of New Co-Mutational Patterns with Prognostic Implications in NPM1 Mutated AML - Results of the European Harmony Alliance

Background: Mutations of NPM1 are generally considered as a favorable prognostic marker in acute myeloid leukemia (AML), although patients present with distinct co-mutations that might influence outcomes. The recently updated European LeukemiaNet classification (ELN2022) does now group NPM1^mut AML patients with FLT3-ITD (regardless of the allelic ratio) as intermediate prognosis, while NPM1^mut without FLT3-ITD is part of the favorable group. However, the mutational landscape of NPM1^mut AML is more complex and analysis of a large cohort of patients might allow further dissection to identify less frequent co-mutational patterns of prognostic and predictive importance.

Aims: To identify clinically significant co-mutational patterns in NPM1^mut AML to further refine risk stratification models for this subset of patients.

Methods: From the HARMONY Alliance database, a total of 1093 intensively treated NPM1^mut patients were selected. Patients treated with targeted therapies (e.g. FLT3 or IDH1/2 inhibitors) were not included and NPM1 MRD information was not available at this stage of the analysis. A machine learning algorithm was developed in order to identify combinations of up to 4 co-mutated genes with potential impact on overall survival (OS). A heuristic search algorithm was implemented and bootstrap sampling was applied to estimate the impact of all possible gene combinations on OS. In addition, a global dashboard was developed where it was possible to compare mutational combinations with Kaplan Meier and Cox regression models. Finally, clinically significant co-mutational patterns were summarized in a novel risk stratification model for NPM1^mut AML, which was validated using a publicly available external patient cohort (Awada et al, Blood, 2021).

Results: The study population of 1093 NPM1^mut AML patients included 57% females and median age was 53 years. Regarding ELN2022 classification, 57% of patients were classified into the favorable, 42% into intermediate and only 1% into adverse risk groups. The most frequent co-mutations were DNMT3A (54%) and FLT3-ITD (42%), followed by NRAS, FLT3-TKD and TET2 (20% each). Mutations on IDH1 (13%) and IDH2 (15%) showed a similar behavior for all the analyses performed, so for simplification purposes we will refer to IDH^mut when any of them was mutated and to IDH^wt when both were wildtype.

The triple combination of NPM1^mut + FLT3-ITD + DNMT3A^mut identified a subgroup of patients with adverse prognosis (2-year OS of 33%), similar to patients with TP53^mut. Of note, not all FLT3-ITD patients carried an intermediate or adverse prognosis, as we were able to identify a subgroup (FLT3-ITD + IDH^mut + DNMT3A^wt) with excellent prognosis (2-year OS of 80%), which represented 4% of NPM1^mut AML. However, in the absence of FLT3-ITD and the presence of DNMT3A^mut, the addition of IDH^mut decreased OS towards the intermediate risk (2-year OS 59%). Notably, not all DNMT3A^mut patients carried an intermediate or adverse prognosis. In the absence of FLT3-ITD and with IDH^wt, mutations on either NRAS, KRAS, PTPN11 or RAD21 revealed a subgroup with favorable prognosis even when DNMT3A was mutated (2-year OS 80%) and this group represented 11% of NPM1^mut AML. This information is summarized in a 4-category risk stratification model (figure 1).

The revised NPM1^mut favorable group presented with a 3-year OS of 78%, which was 63%, 48% and 29% for intermediate-1, intermediate-2 and adverse risk groups respectively (p<0.001). Regarding 3-year relapse free survival (RFS), it was 71%, 59%, 39% and 26% accordingly (p<0.001).

In the validation cohort, 3-year OS of was 73% for NPM1^mut favorable group, being 59%, 40% and 22% for intermediate-1, intermediate-2 and adverse groups respectively (p<0.001).

Multivariate OS analysis in NPM1^mut AML identified the following independent prognostic factors: revised NPM1^mut model (taking favorable group as reference, HR 1.77 for intermediate-1, HR 2.92 for intermediate-2 and HR 5.13 for adverse group, p<0.001); secondary or therapy-related AML (HR 1.93, p<0.001), age >60 years (HR 1.84, p<0.001), WBC at diagnosis >100x10³/uL (HR 1.59, p<0.001), and male gender (HR 1.21, p=0.04).

Conclusion/summary: Analysis of large NPM1^mut AML cohorts allows the identification of clinically significant co-mutational patterns. We propose a new genetic stratification model for NPM1^mut AML that identifies 4 groups with different OS and RFS.

Heckman:Kronos Bio: Research Funding; Novartis: Research Funding; Celgene: Research Funding; IMI2 projects HARMONY and HARMONY PLUS: Research Funding; Oncopeptides: Research Funding; Orion: Research Funding; WntResearch: Research Funding. Sobas:Celgene/BMS: Honoraria; Novartis: Honoraria. Metzeler:Daiichi Sankyo: Honoraria; AbbVie: Honoraria; Pfizer: Consultancy; Celgene/BMS: Consultancy, Honoraria, Research Funding; Novartis: Consultancy; Jazz Pharmaceuticals: Consultancy; Astellas: Honoraria. Pratcorona:Novartis: Honoraria. Thiede:AgenDix GmbH: Current Employment, Current equity holder in private company; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Janssen Pharmaceuticals: Speakers Bureau; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Kronos Bio, Inc.: Honoraria. Voso:Astellas: Speakers Bureau; Novartis: Research Funding, Speakers Bureau; Celgene/BMS: Consultancy, Honoraria, Research Funding, Speakers Bureau; jazz: Consultancy, Speakers Bureau. Sanz:Novartis Oncology: Consultancy; takeda: Honoraria; Janssen Pharmaceuticals, Inc.: Other: Teaching and Speaking; Celgene Corporation: Consultancy; La Hoffman Roche Ltd.: Other: Advisor or review panel participant; Helsinn: Honoraria, Other: Advisor or review panel participant; Abbvie Pharmaceuticals: Other: Advisor or review panel participant; Takeda Pharmaceuticals Ltd: Other: Advisor or review panel participant. Döhner:AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Kronos: Research Funding; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS/Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Agios: Research Funding; Astellas: Research Funding; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Heuser:Eurocept: Honoraria; Abbvie: Consultancy, Honoraria, Research Funding; Jazz Pharmaceuticals: Consultancy, Honoraria, Research Funding; Janssen: Honoraria; Novartis: Consultancy, Honoraria, Research Funding; Takeda: Honoraria; Agios: Consultancy, Research Funding; BMS: Consultancy; Daiichi Sankyo: Consultancy, Research Funding; Glycostem: Consultancy, Research Funding; Kura Oncology: Consultancy; Pfizer: Consultancy, Research Funding; PinotBio: Consultancy, Research Funding; Roche: Consultancy, Research Funding; Tolremo: Consultancy; Astellas: Research Funding; Bayer Pharma AG: Research Funding; BergenBio: Research Funding; Loxo Oncology: Research Funding. Haferlach:Munich Leukemia Laboratory: Current Employment, Other: Part ownership. Turki:Jazz Pharma: Speakers Bureau; MSD: Speakers Bureau; CSL Behring: Consultancy. van Speybroeck:Janssen: Current Employment. Schulze-Rath:Bayer Pharma AG: Current Employment, Current equity holder in private company. Butler:Bayer Pharma AG: Current Employment. Hernández-Rivas:Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; GSK: Consultancy, Honoraria; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Support, Speakers Bureau; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research support, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Support; Janssen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Roche: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Abbvie: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AstraZeneca: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Beigene: Membership on an entity's Board of Directors or advisory committees; Lilly: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Rovi: Membership on an entity's Board of Directors or advisory committees; Incyte: Membership on an entity's Board of Directors or advisory committees. Ossenkoppele:Novartis: Consultancy, Honoraria; Servier: Consultancy, Honoraria; JAZZ: Consultancy, Honoraria; AMGEN: Consultancy, Honoraria; BMS/Celgene: Consultancy, Honoraria; Astellas: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; AGIOS: Consultancy, Honoraria; Abbvie,: Consultancy, Honoraria. Döhner:Jazz Pharmaceuticals: Consultancy, Honoraria, Research Funding; Kronos Bio, Inc.: Research Funding; Brystol Myers Squibb: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Daiichi Sankyo Co, LTD: Consultancy, Honoraria; Berlin-Chemie: Consultancy, Honoraria; AstraZeneca: Honoraria; Astellas Pharma Inc.: Consultancy, Honoraria, Research Funding; Amgen Inc.: Consultancy, Honoraria, Research Funding; Agios Pharmaceuticals: Consultancy, Honoraria, Research Funding; AbbVie Inc.: Consultancy, Honoraria, Research Funding; Pfizer Inc.: Research Funding; Gilead Sciences, Inc.: Consultancy, Honoraria; Janssen Pharmaceuticals: Consultancy, Honoraria; Servier: Consultancy, Honoraria; Syndax Pharmaceuticals Inc.: Consultancy, Honoraria. Bullinger:Celgene/BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas: Honoraria; Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Bayer Oncology: Research Funding; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees.