Prognostic impact of co-occurring FLT3 mutations across molecular subgroups in intensively treated acute myeloid leukemia: Insights from real-world genomic data

Abstract

Abstract Introduction FLT3 mutations (FLT3MUT) are among the most frequently altered genes in acute myeloid leukemia (AML), and exhibit substantial biological and prognostic heterogeneity, underscoring the importance of evaluating their prognostic implications within distinct molecular subgroups. Given this nature in leukemogenesis, it is critical to investigate the prognostic implications of FLT3MUT across genetically defined AML subtypes, rather than focusing solely on the co-mutation landscape within FLT3MUT cases. Furthermore, beyond genomic alterations, the transcriptomic landscape associated with FLT3MUT remains largely underexplored. Characterizing these transcriptomic alterations may illuminate critical downstream mechanisms involved in leukemogenesis, immune evasion, and treatment resistance. Methods We retrospectively analyzed 1,151 intensively treated patients with de novo AML at National Taiwan University Hospital. FLT3 mutation types, co-mutations, treatment with FLT3 inhibitors, and clinical outcomes were examined. RNA sequencing was performed in 427 cases and validated using the BeatAML cohort. Multivariable Cox models, with transplantation as time-dependent covariates, were applied to assess survival. Results FLT3 ITD, FLT3TKD, FLT3ITD+TKD and FLT3noncanonicalmutations were identified in 19.6%, 5.6%, 1.3% and 1.1% of patients, respectively. Compared with FLT3 wild type (FLT3WT) AML, patients with FLT3ITD exhibited higher frequencies of NPM1, DNMT3A, WT1, KMT2A-PTD, and lower frequencies of RUNX1::RUNX1T1, CBFB::MYH11, and TP53 mutations. Additionally, patients with FLT3TKD had increased frequencies of NPM1 and DNMT3A mutations compared to FLT3WT. Patients with FLT3ITD had shorter OS compared with FLT3WT (median: 16 vs. 33 months; p=0.001), and co-occurrence of FLT3ITD+TKD was associated with even worse outcomes, with significantly shorter OS than both FLT3WT (median: 7.3 vs. 33 months; p=0.001) and FLT3TKD (median: 28 months; p=0.014). FLT3noncanonical had a similar OS compared with FLT3WT (median: 24 vs. 33 months; p>0.99s). Prognostic significance of FLT3ITD varied significantly across molecular subgroups, showing inferior outcomes particularly in patients with mutations in NPM1 (hazard ratio [HR], 2.13; 95%confidence interval [CI], 1.35–3.38; p=0.02), DNMT3A (HR, 1.92; 95% CI, 1.23–3.01; p=0.03), RUNX1 (HR, 3.31; 95% CI, 1.78–6.13; p=0.005), cohesin complex (HR, 3.93; 95% CI, 1.49–10.32; p=0.03), myelodysplasia-related genes (HR, 1.75; 95% CI, 1.17–2.62; p=0.03), NRAS (HR, 2.21; 95% CI, 1.24–3.95; p=0.03), KMT2A-PTD (HR, 4.71; 95% CI, 1.59–13.94; p=0.03) and KMT2A-r (HR, 8.50; 95% CI, 1.90–38.08; p=0.03). In a multivariable Cox regression model adjusting for age, 2022 ELN risk classification and incorporating HSCT in first complete remission as a time-dependent covariate, (HR, 0.44; 95% CI, 0.28–0.68; p<0.001) treatment with a FLT3 inhibitor (HR, 0.39; 95% CI, 0.24–0.66; p<0.001) was independently associated with significantly improved overall survival (OS). FLT3TKD was significantly associated with shorter OS and event-free survival (EFS) in patients with cohesion complex mutations (OS HR, 5.00; 95% CI, 2.06–12.15; p=0.012; EFS HR, 3.76; 95% CI, 1.62–8.72; p=0.066). Among patients with NPM1 mutation and FLT3ITD,co-occurring DNMT3A, TET2, ASXL1 (DTA) mutations had similar survival outcomes as 2022 ELN adverse risk classification (median OS: 17.1 vs. 14.0 months, p=0.32). Transcriptomic analysis of FLT3ITD AML revealed distinct signatures enriched in oxidative phosphorylation (normalized enrichment score [NES]=3.60, false discovery rate [FDR]<0.001), DNA repair (NES=2.69, FDR<0.001), and fatty acid metabolism (NES=2.50, FDR<0.001), alongside suppression of immune-response pathways (inflammatory response: NES=-1.93, FDR<0.001; interferon pathway: NES=-1.83, FDR=0.002). These findings were well externally validated in the BeatAML cohort. Conclusion FLT3 MUT conveys context-dependent prognostic significance across molecular AML subgroups. Integration of co-mutation profiles and transcriptomic features refines risk stratification and highlights the therapeutic benefit of FLT3 inhibition. The NPM1MUT/FLT3ITD/DTA subgroup exhibits an adverse-risk phenotype, warranting potential reclassification under ELN guidelines.