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847 Prognostic Impact of Subclinical FLT3-ITD Microclones in Patients with Acute Myeloid Leukemia

Program: Oral and Poster Abstracts
Type: Oral
Session: 618. Acute Myeloid Leukemias: Biomarkers and Molecular Marker in Diagnosis and Prognosis: Refining Diagnostic Risk Assessment
Hematology Disease Topics & Pathways:
Research, Acute Myeloid Malignancies, AML, Translational Research, Diseases, Myeloid Malignancies, Technology and Procedures, Study Population, Human, Measurable Residual Disease , Molecular testing
Monday, December 9, 2024: 2:45 PM

Paul Olson1*, Razif Gabdoulline1*, Rabia Shahswar, MD1*, Arnold Kloos1*, Letizia Venturini1*, Isabell Arnhardt1*, Henri C. Hupe1*, Victoria Panagiota, MD2*, Michael Stadler1*, Matthias Eder, MD2*, Gernot Beutel, MD2*, Elke Dammann1*, Piroska Poll, MD2*, Anke Bergmann3*, Nataliya DiDonato3*, Florian H. Heidel, MD2, Felicitas R. Thol, MD1 and Michael Heuser, MD1,4

1Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
2Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
3Department of Human Genetics, Hannover Medical School, Hannover, Germany
4Department of Internal Medicine IV, University Hospital Halle (Saale), Halle, Germany

Background

Patients with acute myeloid leukemia (AML) without FLT3 internal tandem duplication (ITD) at diagnosis often relapse with FLT3-ITD. Therefore, we evaluated the frequency of FLT3-ITD microclones in FLT3-ITD negative patients to evaluate the prognostic impact of subclinical FLT3-ITD microclones in a large cohort of AML patients.

Methods

Patients with AML who underwent allogeneic hematopoietic cell transplantation (alloHCT) at Hannover Medical School between 2000 and 2023 were included, if FLT3-ITD was negative by fragment length analysis at diagnosis (FLT3-ITD mutant to wildtype ratio below 0.05). Ultrasensitive error-corrected next-generation sequencing (NGS) using an established amplicon sequencing approach was used to identify FLT3-ITD clones with high sensitivity. Three different programs using independent methods (filt3r, getITD, custom script) were applied to ensure the reproducibility of results. DNA was sequenced on a MiSeq instrument to achieve coverage of at least 100,000 reads. Diagnostic samples were also sequenced with a panel of 48 recurrently mutated genes. All patients with FLT3-ITD microclones were evaluated for FLT3-ITD before and 2-8 months after alloHCT, and at relapse, if applicable.

Results

A total of 227 FLT3-ITD negative patients were included. The median age was 54 years (range 18-75 years), and 45% were female. 16%, 33%, and 51% were classified to ELN 2022 favorable, intermediate, and adverse risk groups. All patients received intensive induction chemotherapy; none were treated with an FLT3 inhibitor during induction. The median sequencing depth of FLT3 was 202,063 aligned reads. At least one FLT3-ITD sequence read was detected in 57 (25.1%) patients, with a VAF ranging from 0.00041% to 3.28%. In 40 (17.6%) and 17 (7.5%) patients one or more than one FLT3-ITD clones were detected, respectively. We set a threshold of ≥0.01% VAF, corresponding to at least 50 read counts of FLT3-ITD, to define the presence of a microclone for clinical correlations. Using this threshold, 23 (10%) patients had a FLT3-ITD microclone.

Clinical and genetic characteristics of patients with (n=23) and without (n=204) FLT3-ITD microclones were similar, except a higher frequency of patients with ELN 2022 favorable risk (48 vs 12%), a lower proportion of patients with adverse cytogenetic risk (4 vs 24%), and a higher proportion of patients with NPM1 (58 vs 11%) and DNMT3A mutations (37 vs 15%) in the cohort of patients with FLT3-ITD mutations.

After induction complete remission (CR) or CR with incomplete hematologic recovery (CRi) was achieved by 18 (78%) and 138 (68%) patients with and without FLT3-ITD microclones (P=0.28). FLT3-ITD was detected at this time point in one of 18 (6%) patients with microclones with a VAF of 15.4% and a different FLT3-ITD clone from diagnosis. Eight patients with microclones relapsed before undergoing alloHCT and achieved a second CR/CRi with salvage chemotherapy. FLT3-ITD was detected at second CR/CRi in two of these eight (25%) patients with VAFs of 0.32% and 0.003% of the same FLT3-ITD clone from diagnosis. Five patients did not reach CR/CRi; three of these patients showed persisting FLT3-ITD clones from diagnosis with VAF of 20%, 11.9%, and 0.08%, respectively.

Five patients with a VAF ≥0.01% at diagnosis, who relapsed after alloHCT, were further evaluated for FLT3-ITD. Three patients were FLT3-ITD positive at relapse with VAFs of 72.9%, 35.1% and 0.03%; only the latter had reached CR before alloHCT. The identical FLT3-ITD clone from diagnosis was found in the relapse samples of all three patients.

After a median follow-up of 3.2 years, relapse-free survival (RFS) was significantly shorter for patients with FLT3-ITD microclones compared to patients without microclones (HR 1.98, 95% CI 1.04-3.78, P=0.038; 2-year RFS 41% vs 62%). Overall survival (OS) was similar between patients with and without microclones (HR 1.12, 95% CI 0.65-2.05, P=0.7; 2-year OS 65% vs 69%).

Conclusions

FLT3-ITD microclones are frequently found at diagnosis in patients who are considered FLT3-ITD negative by conventional diagnostic methods. FLT3-ITD microclones are associated with NPM1 and DNMT3A mutations, a favorable ELN 2022 risk, and shorter RFS. Microclones with VAFs ≥0.1% at diagnosis may give rise to FLT3-ITD positive relapse. Detection of FLT3-ITD microclones may provide the basis to evaluate the clinical efficacy of FLT3 inhibitors in FLT3-ITD negative AML patients.

Disclosures: Heidel: BMS/Celgene, Novartis, CTI: Research Funding; BMS/Celgene, AOP, Novartis, CTI, Janssen, Abbvie, GSK, Merck, Kartos, Telios: Consultancy. Thol: Astellas: Honoraria; Rigel: Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Menarini: Membership on an entity's Board of Directors or advisory committees. Heuser: Loxo Oncology: Research Funding; Bristol-Myers-Squibb: Honoraria; Karyopharm: Research Funding; Janssen: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; Jazz Pharmaceuticals: Honoraria, Research Funding; Qiagen: Honoraria; Sobi: Honoraria; Abbvie: Consultancy, Honoraria, Research Funding; Glycostem: Consultancy, Research Funding; BergenBio: Research Funding; AvenCell: Consultancy; LabDelbert: Consultancy; Astellas: Consultancy, Research Funding; Miltenyi: Consultancy; Novartis: Consultancy, Research Funding; PinotBio: Consultancy, Research Funding; Servier: Consultancy, Honoraria, Research Funding.

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