Next-Generation Sequencing (NGS)-Based Measurable Residual Disease (MRD) Monitoring in Acute Myeloid Leukemia with FLT3 Internal Tandem Duplication (FLT3-ITD+ AML) Treated with Additional Midostaurin
Authors: Herzig Julia K. , Rücker Frank G. , Schmalbrock Laura K. , Blätte Tamara J. , Weber Daniela , Skambraks Sabrina , Kapp-Schwoerer Silke , Corbacioglu Andrea , Gaidzik Verena I , Paschka Peter , Panina Ekaterina , Jahn Nikolaus , Schrade Anika , Theis Frauke , Cocciardi Sibylle , Fiedler Walter , Salih Helmut R. , Wulf Gerald , Salwender Hans , Schroeder Thomas , Götze Katharina S. , Kindler Thomas , Luebbert Michael , Schlenk Richard F. , Thol Felicitas , Heuser Michael , Ganser Arnold , Döhner Hartmut , Bullinger Lars , Döhner Konstanze 
Published: November 2020

Background: FLT3-ITD occurs in ~25% of adult AML patients (pts) and is associated with poor prognosis. MRD monitoring is of high prognostic relevance, but restricted to certain AML subtypes. FLT3-ITD represents an attractive target for MRD monitoring in particular in pts treated with a tyrosine kinase inhibitor. FLT3-ITD MRD monitoring is hampered by the broad heterogeneity of ITD length and insertion site (IS). NGS may overcome these limitations offering the opportunity for MRD monitoring in FLT3-ITD+ AML.
Aims: To validate our recently established NGS-based FLT3-ITD MRD assay in a defined cohort of FLT3-ITD+ AML pts treated within the AMLSG16-10 trial (NCT01477606) combining intensive chemotherapy with midostaurin followed by midostaurin maintenance and to evaluate the prognostic impact of FLT3-ITD MRD monitoring.
Methods: Using FLT3-ITD paired-end NGS (Illumina MiSeq) with a variant allele frequency (VAF) sensitivity of 10-4-10-5 (Blätte et al., Leukemia 2019), 227 bone marrow (BM) and 17 peripheral blood samples from 61 FLT3-ITD+ AML pts were analyzed at diagnosis (Dx), after two cycles of chemotherapy (Cy2), at the end of treatment (EOT), and during 3-6 months follow-up (FU). All pts achieved complete remission (CR) after Cy2. Allogeneic hematopoietic cell transplantation in first CR was performed in 40 (66%) pts. Mutational status for NPM1 and DNMT3A was available for all pts (NPM1mut, n=48; DNMT3Amut, n=33; NPM1mut/DNMT3Amut, n=31), and NPM1mut MRD data for 41 pts.
Results: At Dx we identified 191 ITDs; median length was 45 nucleotides (range, 9-194) and median VAF 0.279% (range, 0.006-90.21). Of the 191 ITDs, 133 (70%) located in the juxtamembrane domain (JMD) and 58 (30%) in the tyrosine kinase domain-1 (TKD1). There was no correlation of VAF with length or IS, whereas ITD size correlated with IS: the more C-terminal the IS, the longer the ITD (Rho=0.51; p&lt;.001). Total ITD VAF per pt was in median 34.3% (range, 0.007-90.21) and correlated positively with white blood cell count (WBC, Rho=0.314; p=.021) and lactate dehydrogenase serum level (LDH, Rho=0.274; p=.04), and inversely with the number of ITDs (Rho=-0.265; p=.04). Most pts (67%) exhibited &gt;1 ITD at Dx (median 2; range, 1-16). Categorizing pts according to IS as JMDsole (46%), JMD/TKD1 (34%), and TKD1sole (20%) revealed that JMD/TKD1 pts exhibited more ITD subclones (p&lt;.001) and a lower total VAF at Dx (p=.03). There were no correlations with any other clinical or genetic features.
Pts' total ITD VAF significantly decreased after Cy2 and at EOT (median log10 reduction: 4.4 and 4.7; p&lt;.001, each), and MRD negativity (MRD-) was achieved in 67% and 87% of pts, respectively. According to subgroups, pts with JMDsole or TKD1sole showed deeper MRD reduction compared to JMD/TKD1 pts after Cy2 (4.6 vs 4.7 vs 3.7 log10; p=.06) and at EOT (4.8 vs 4.8 vs 4.0 log10; p=.02) but this did not result in a significant difference in achievement of MRD-. Concurrent NPM1mut was of favorable impact for log10 VAF reduction (median, 4.7 for DNMT3Amut/NPM1mut vs 4.6 for NPM1mut vs 2.8 others; p=.003) and MRD- (77 vs 76 vs 31%; p=.01) after Cy2, but exerted no impact at EOT. Correlating NPM1mut and FLT3-ITD MRD course revealed a positive correlation after Cy2 (Rho=0.327; p=.03), but not at EOT (Rho=0.250; p=.10), likely due to the higher sensitivity of the real-time quantitative PCR-based NPM1mut MRD assay.
Median follow-up was 3.4 years (95% CI, 2.6-4.6). Survival analyses with respect to cumulative incidence of relapse (CIR; n=60) and overall survival (OS; n=61) revealed significantly lower CIR for total VAF at Dx &gt;34.3% (p=.03), a VAF reduction &gt;4.7 log10 (MR4.7) at EOT (p=.001), and for MRD- pts at EOT (p=.001). There was no impact on OS. In preliminary exploratory Cox regression (n=48), including BM blasts, WBC, LDH, age, and NPM1mut as covariables, MRD- at EOT was the only consistent favorable variable for CIR (HR, 0.1; p=.001) and OS (HR, 0.27; p=.03). During FU, 5/8 (63%) MRD+ pts at EOT became MRD- and 4/53 (8%) MRD- pts converted to MRD+ resulting in consecutive relapse in 2 pts.
Conclusion: In this first cohort of FLT3-ITD+ AML pts treated with intensive chemotherapy and midostaurin in the prospective AMLSG16-10 trial we could demonstrate that FLT3-ITD NGS-based MRD monitoring is feasible and represents a promising tool to evaluate therapy response and identification of pts at a higher risk of relapse. Further analysis of the study cohort is ongoing.

Disclosures
Kapp-Schwoerer: Jazz Pharmaceuticals: Honoraria, Research Funding. Paschka:Sunesis Pharmaceuticals: Consultancy; BerGenBio ASA: Research Funding; Novartis: Consultancy, Speakers Bureau; Otsuka: Consultancy; Pfizer: Consultancy, Speakers Bureau; Astellas Pharma: Consultancy, Speakers Bureau; Celgene: Consultancy, Other: Travel, accommodations or expenses; Astex Pharmaceuticals: Consultancy; Jazz Pharmaceuticals: Consultancy, Speakers Bureau; Agios Pharmaceuticals: Consultancy, Speakers Bureau; Amgen: Other; Janssen Oncology: Other; AbbVie: Other: Travel, accommodation or expenses, Speakers Bureau. Fiedler:Ariad/Incyte: Membership on an entity's Board of Directors or advisory committees; Celgene: 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, Other: travel accomodations; Novartis: Membership on an entity's Board of Directors or advisory committees; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: support in medical writing; Daiichi Sankyo Oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel accomodations; Morphosys: Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: support in medical writing; Servier: Honoraria, Other; BerGenBio ASA: Research Funding; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: travel accomodations, support in medical writing, Research Funding; Gilead: Honoraria. Salih:Novartis: Consultancy; Pfizer: Consultancy; Philogen: Consultancy; Medigene: Consultancy; Synimmune: Consultancy, Research Funding. Salwender:Bristol-Myers Squibb/Celgene: Honoraria; Janssen-Cilag: Honoraria; Amgen: Honoraria; Takeda: Honoraria; Oncopeptides: Honoraria; Sanofi: Honoraria; GlaxoSmithKline: Honoraria; AbbVie: Honoraria. Götze:Celgene: Research Funding. Luebbert:Janssen: Research Funding. Schlenk:PharmaMar: Research Funding; Daiichi Sankyo: Membership on an entity's Board of Directors or advisory committees, Other: Travel, Accomodations, Expenses, Research Funding, Speakers Bureau; Novartis: Speakers Bureau; Roche: Research Funding; AstraZeneca: Research Funding; Pfizer: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. Thol:Daiichi Sankyo: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Heuser:Daiichi Sankyo: Consultancy, Research Funding; Pfizer: Consultancy, Honoraria, Research Funding; Karyopharm: Research Funding; Abbvie: Consultancy; PriME Oncology: Honoraria; Amgen: Research Funding; Astellas: Research Funding; Roche: Research Funding; Stemline Therapeutics: Consultancy; Novartis: Consultancy, Honoraria, Research Funding; Janssen: Consultancy; BerGenBio ASA: Research Funding; Bayer: Consultancy, Research Funding. Ganser:Novartis: Consultancy; Celgene: Consultancy. Döhner:AstraZeneca: Consultancy, Honoraria; Sunesis: Research Funding; Roche: Consultancy, Honoraria; Pfizer: Research Funding; Oxford Biomedicals: Consultancy, Honoraria; Novartis: Consultancy, Honoraria, Research Funding; Helsinn: Consultancy, Honoraria; Jazz: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Bristol Myers Squibb: Consultancy, Honoraria, Research Funding; Astex: Consultancy, Honoraria; Astellas: Consultancy, Honoraria, Research Funding; AROG: Research Funding; Amgen: Consultancy, Honoraria, Research Funding; Agios: Consultancy, Honoraria, Research Funding; Abbvie: Consultancy, Honoraria; GEMoaB: Consultancy, Honoraria. Bullinger:Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Menarini: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Seattle Genetics: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Daiichi Sankyo: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Hexal: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees. Döhner:Jazz Pharmaceuticals: Consultancy, Honoraria, Research Funding; Daiichi Sankyo: Honoraria; Celgene: Consultancy, Honoraria; Sunesis Pharmaceuticals: Research Funding; Novartis: Honoraria, Research Funding; Pfizer: Research Funding; Bristol-Myers Squibb: Research Funding; Arog: Research Funding; Roche: Consultancy; Astex Pharmaceuticals: Consultancy; Janssen: Consultancy, Honoraria; Amgen: Consultancy, Research Funding; Astellas Pharma: Consultancy; Agios: Consultancy; Abbvie: Consultancy.