Clinical Significance of <i>FLT3</i> Mutations in a Comprehensive NGS Multicenter Study of AML: HM-Screen-Japan 01

<jats:title>Abstract</jats:title> <jats:p>Background and Methods: FMS-like tyrosine kinase 3 (FLT3) internal tandem duplication (FLT3-ITD) and tyrosine kinase domain mutation (FLT3-TKD) are types of mutations present in approximately 30% of patients with acute myeloid leukemia (AML). Currently, FLT3 inhibitors (FLT3i) are available in clinical practice, and the second-generation FLT3i, gilteritinib and quizartinib, are being used in Japan. However, the actual epidemiology of FLT3 mutations and co-existing gene alterations, particularly resistance mechanisms after FLT3i treatment, have not been thoroughly investigated in a Japanese population. Therefore, we conducted an actionable mutation profiling multicenter study, Hematologic Malignancies (HM)-SCREEN-Japan 01 (UMIN000035233), in which a comprehensive genomic assay was performed using the FoundationOne Heme (F1H) panel for patients with relapsed/refractory (R/R) AML and patients with newly diagnosed AML who were ineligible for standard chemotherapy (ND unfit). Paraffin-embedded bone marrow samples were used for next-generation sequencing (NGS) examination using the F1H panel. We analyzed the relationships between FLT3 gene mutations and other mutations and then chronologically evaluated the variant allele frequency (VAF) of gene mutations in the genomic profiles of patients with AML receiving FLT3i.</jats:p> <jats:p>Results: Of the 171 patients who participated in this study, 49 (28.7%) had FLT3 mutations. FLT3-ITD and FLT3-TKD accounted for 59% and 43% of all cases of FLT3 mutations, respectively. Two patients (4%) were found to have dual mutations: one with FLT3-ITD plus FLT3-TKD and another with FLT3-ITD plus FLT3-F691L. Eight patients (4.5%) were found to have the FLT3-N676K mutation, which is sensitive to gilteritinib but undetectable by currently available PCR-based companion diagnostic tools in Japan. Frequently co-occurring mutations included those of NPM1 (37%), DNMT3A (33%), IDH1/IDH2 (27%), WT1 (24%), and RUNX1 (22%). Mutations in RAS pathway-related genes (e.g., KRAS, NRAS, and PTPN11) were observed in 15 patients (31%). No gene alteration showed statistically significant co-occurrence with the FLT3mutation. However, the median number of mutations that co-exist with FLT3-TKD was slightly higher than that of FLT3-ITD (four genes [3-5] vs. three genes [2-5]). Sequential changes in the VAF of each gene alteration were investigated in nine patients with FLT3 mutations who eventually gained resistance to FLT3i. It was suggested that there were various patterns in clone evolution. Some showed the acquisition of not only CBL or NRAS as RAS pathways, but also other driver mutations: one showed a persistent FLT3mutation, one showed FLT3-ITD plus FLT3-TKD, and one showed a newly acquired FLT3 mutation substituting an existing FLT3 mutation. We also found that founder mutations, such as the DNMT3Amutation, remain even after eradication of FLT3 mutation during treatment with FLT3i, which could be the cause of the outcome of complete remission with incomplete hematologic recovery.</jats:p> <jats:p>Conclusions: This is the first report to analyze R/R and ND unfit AML cases in a Japanese cohort using F1H NGS, revealing a higher incidence of FLT3-ITD/TKD mutations than previously reported. Therefore, F1H mutational analyses for R/R and ND unfit AML patients harboring FLT3-ITD/TKD mutations may reveal novel therapeutic targets that are sensitive to FLT3i. Samples from these patients showed non-canonical gain-of-function mutations, such as N676K, S451F, V592D, and F691L, which could guide the selection of optimal anti-FLT3 therapies. In addition, longitudinal NGS analysis revealed clonal evolution in cases in which resistance to the FLT3i, gilteritinib and quizartinib were observed. Time-dependent analysis of allele frequencies can help evaluate the details of leukemia clonal evolution and provide optimal treatment options.</jats:p> <jats:p>Figure Legends</jats:p> <jats:p>Fig.1 Overview of gene mutations using F1H NGS analyses. The color of each column indicates the type of genetic mutation. Blue column; point mutation/insertion/deletion, green column; fusion gene, purple column; dual mutations.</jats:p> <jats:p>Fig.2 The chronological changes of leukemic cells fractions bearing each gene mutations during treatment with FLT3 inhibitors, gilteritinib and quizartinib.</jats:p> <jats:p>Figure 1 Figure 1.</jats:p> <jats:p /> <jats:sec> <jats:title>Disclosures</jats:title> <jats:p>Shibayama: Otsuka: Honoraria; Pfizer: Honoraria; Bristol-Myers Squibb: Honoraria; Sanofi: Honoraria; Nippon Shinyaku: Honoraria; Fujimoto: Honoraria; Daiichi Sankyo: Speakers Bureau; AstraZeneca: Honoraria, Membership on an entity's Board of Directors or advisory committees; Chugai: Honoraria, Membership on an entity's Bo ...