Molecular Characterization of Clinical Response and Relapse in Patients with IDH1-Mutant Newly Diagnosed Acute Myeloid Leukemia Treated with Ivosidenib and Azacitidine
Authors: Daigle Scott R. , Choe Sung , DiNardo Courtney D. , Stein Anthony S. , Stein Eytan M. , Fathi Amir T. , Frankfurt Olga , Schuh Andre C. , Döhner Hartmut , Martinelli Giovanni , Patel Prapti A. , Raffoux Emmanuel , Tan Peter , Zeidan Amer M. , De Botton Stephane , Stone Richard M. , Frattini Mark , Franovic Aleksandra , Xu Emily , Winkler Thomas , Wu Bin , Vyas Paresh 
Published: November 2020

Background: Acute myeloid leukemia (AML), a hematologic malignancy characterized by clonal expansion of abnormal myeloid progenitors, is a disease exhibiting a dynamic mutational landscape over time. Somatic mutations in isocitrate dehydrogenase 1 (IDH1) are reported in 6-10% of patients (pts) with AML. Ivosidenib (IVO) is an oral, potent, targeted inhibitor of mutant IDH1 (mIDH1) and is FDA-approved for the treatment of mIDH1 relapsed/refractory (R/R) AML and newly diagnosed (ND) AML in adults ≥ 75 years (yrs) of age or with comorbidities precluding intensive induction chemotherapy (IC). In an ongoing phase 1b study (NCT02677922), 23 pts (11 male; median age 76 yrs [range 61-88]) with mIDH1 ND AML received IVO 500 mg daily and subcutaneous azacitidine (AZA) 75 mg/m2 on Days 1-7 in 28-day cycles. As of 19Feb2019, median number of treatment cycles was 15 (range 1-30); 10 pts remained on treatment. Overall response rate (complete remission [CR] + CRi [incomplete neutrophil recovery] + CRp [incomplete platelet recovery] + morphologic leukemia-free state [MLFS]) was 78% (18/23): including CR in 61% (14/23) and CR with partial hematologic recovery (CRh) in 9% (2/23). mIDH1 clearance assessed in bone marrow mononuclear cells (BMMCs) by BEAMing digital PCR (detection limit 0.02-0.04%) was observed in 11/16 pts (69%) with CR/CRh, including 10/14 (71%) with CR.
Aim: Characterize clonal evolution and resistance in pts with mIDH1 ND AML treated on study with IVO + AZA.
Methods: The secondary efficacy endpoint of CRh was sponsor derived and defined as CR with absolute neutrophil count &gt; 0.5 X 109/L and platelets &gt; 50 X 109/L. Bulk DNA sequencing (DNA-seq, 1400-gene ACE Extended Cancer Panel, 2% variant allele detection limit) was performed on BMMCs and/or peripheral blood mononuclear cells (PBMCs). Single-cell (sc) targeted DNA-seq was performed on PBMCs using a microfluidic platform (Tapestri®) with a 20-gene AML panel capable of detecting rare subclones down to 0.1%.
Results: To identify mechanisms of acquired resistance, longitudinal bulk DNA-seq was analyzed for 22/23 pts, including 5 pts with available samples at relapse or disease progression (3 CR and 1 MLFS with morphological relapse; 1 CRh with disease progression). Mutations not detected at baseline but emerging during therapy were categorized into canonical biological pathways (Table). Emerging mutations were observed in 9/22 (41%) pts, including 4 with multiple mutations. 3/22 (14%) pts had emerging IDH2 mutations, with concurrent rise in plasma 2-hydroxyglutarate (2-HG) levels. Within the relapse/progression cases, emerging mutations were observed in 4/5 pts, including 3 where the emerging mutation appeared to be the predominant mutation at relapse/progression (2 CR pts with IDH2 mutations, and 1 CRh pt with a TET2 mutation). To date, from the bulk DNA-seq analysis, no emergence of an IDH1 second-site or receptor tyrosine kinase pathway (FLT3, KRAS, NRAS, PTPN11) mutation has been observed. To further evaluate clonal evolution of clinical response and disease progression, scDNA-seq was performed, with data available for 15 pts (10 CR, 2 CRh, 1 MLFS, and 2 stable disease), including end-of-study time points for 5 relapse/progression pts. In the 2 relapsed pts with an emerging IDH2 mutation observed by bulk DNA-seq, 1 had a minor IDH2 clone present at baseline that expanded independently from IDH1 during therapy (Fig). In a separate case, a subclonal baseline PTPN11 clone evolved to gain both RUNX1 and IDH2 mutations, becoming the predominant clone at relapse. In 2 other cases, scDNA-seq data showed that non-IDH1 clones were selected from baseline clones ancestral (TP53 n = 1) to or emerged separate from mIDH1 (TET2 n = 1). Clonal architecture and evolution from additional pts will be presented.
Conclusion: IVO + AZA combination treatment in IC-ineligible ND AML led to deep and durable molecular remissions. Although the dataset is small, IDH2 clones appeared to expand or emerge separate from the IDH1 clone, with no observation of an IDH1 second-site mutation to date. Understanding patterns of emerging mutations/pathways at relapse will allow for comparison with mIDH1 R/R AML and ND AML pts treated with IVO monotherapy. These results underline the importance of mutational testing, particularly at progression to determine optimal salvage therapy. Potential combination or sequential therapies should be evaluated prospectively in future clinical trials.

Disclosures
Daigle: Agios: Current Employment, Current equity holder in private company. Choe:Agios Pharmaceuticals: Current Employment, Current equity holder in private company. DiNardo:Syros: Honoraria; MedImmune: Honoraria; Notable Labs: Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria; Jazz: Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Agios: Consultancy, Honoraria, Research Funding; Novartis: Consultancy; Daiichi Sankyo: Consultancy, Honoraria, Research Funding; ImmuneOnc: Honoraria; AbbVie: Consultancy, Honoraria, Research Funding; Calithera: Research Funding. Stein:Stemline: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau. Stein:Astellas Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Agios Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Syros: Membership on an entity's Board of Directors or advisory committees; PTC Therapeutics: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Biotheryx: Consultancy; Bayer: Research Funding; Genentech: Consultancy, Membership on an entity's Board of Directors or advisory committees; Syndax: Consultancy, Research Funding; Seattle Genetics: Consultancy; Abbvie: Consultancy; Amgen: Consultancy; Celgene Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. Fathi:Amphivena: Consultancy, Honoraria; Agios: Consultancy, Research Funding; Forty Seven: Consultancy; Daiichi Sankyo: Consultancy; Celgene: Consultancy, Research Funding; Astellas: Consultancy; Takeda: Consultancy; PTC Therapeutics: Consultancy; Novartis: Consultancy; NewLink Genetics: Consultancy, Honoraria; Kite: Consultancy, Honoraria; Jazz: Consultancy, Honoraria; TrovaGene: Consultancy; Amgen: Consultancy; Bristol-Myers Squibb: Consultancy, Research Funding; Blue Print Oncology: Consultancy; Boston Biomedical: Consultancy; Kura: Consultancy; Pfizer: Consultancy; Seattle Genetics: Consultancy, Research Funding; Trillium: Consultancy; AbbVie: Consultancy. Döhner:Pfizer: Research Funding; Sunesis: Other, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Astex: Consultancy, Honoraria; Jazz: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria; Agios: Consultancy, Honoraria; Novartis: Consultancy, Honoraria, Research Funding; Seattle Genetics: Consultancy, Honoraria; Arog: Research Funding; Amgen: Consultancy, Honoraria, Research Funding; Oxford Biomedicals: Consultancy, Honoraria; Astellas: Consultancy, Honoraria; Roche: Consultancy, Honoraria; Helsinn: Consultancy, Honoraria; Bristol-Myers Squibb: Research Funding. Martinelli:Celgene: Consultancy, Speakers Bureau; Jazz: Consultancy; Incyte: Consultancy; Pfizer: Consultancy, Research Funding, Speakers Bureau; Daichii Sankyo: Consultancy, Research Funding; Janssen: Consultancy; Amgen: Consultancy; AbbVie: Consultancy, Research Funding; Roche: Consultancy. Patel:France Foundation: Honoraria; DAVA Pharmaceuticals: Honoraria; Celgene: Consultancy, Speakers Bureau; Agios: Consultancy. Tan:AbbVie: Other: Investigator on an AbbVie funded clinical trial; Agios: Research Funding; Janssen: Research Funding; NOHLA Therapeutics: Research Funding; Novartis: Other, Research Funding. Zeidan:Astellas: Consultancy, Honoraria; Taiho: Consultancy, Honoraria; Seattle Genetics: Consultancy, Honoraria; BeyondSpring: Consultancy, Honoraria; Epizyme: Consultancy, Honoraria; Ionis: Consultancy, Honoraria; Agios: Consultancy, Honoraria; Trovagene: Consultancy, Honoraria, Research Funding; Pfizer: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Acceleron: Consultancy, Honoraria; Celgene / BMS: Consultancy, Honoraria, Research Funding; Daiichi Sankyo: Consultancy, Honoraria; Cardinal Health: Consultancy, Honoraria; Jazz: Consultancy, Honoraria; Aprea: Research Funding; MedImmune/Astrazeneca: Research Funding; ADC Therapeutics: Research Funding; Cardiff Oncology: Consultancy, Honoraria, Other; Takeda: Consultancy, Honoraria, Research Funding; Astex: Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria, Research Funding; Incyte: Consultancy, Honoraria, Research Funding; Leukemia and Lymphoma Society: Other; CCITLA: Other; Otsuka: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria, Research Funding. De Botton:Forma Therapeutics: Honoraria, Research Funding; Astellas: Consultancy, Honoraria; Daiichi Sankyo: Consultancy, Honoraria; Syros: Consultancy, Honoraria; Abbvie: Consultancy, Honoraria; Agios: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Speakers Bureau; Pfizer: Consultancy; Novartis: Consultancy; Pierre Fabre: Consultancy; Janssen: Consultancy, Honoraria; Seattle Genetics: Honoraria; Bayer: Consultancy, Honoraria; Servier: Consultancy. Stone:Syntrix: Consultancy; Macrogenics: Consultancy; Hoffman LaRoche: Consultancy; Stemline: Consultancy; AbbVie: Consultancy, Research Funding; Takeda: Consultancy; Pfizer: Consultancy; Trovagene: Consultancy; Jazz: Consultancy; Otsuka: Consultancy; Novartis: Consultancy, Research Funding; Argenx: Consultancy, Other: Data and safety monitoring board; Biolinerx: Consultancy; AstraZeneca: Consultancy; Astellas: Consultancy, Membership on an entity's Board of Directors or advisory committees; Arog: Research Funding; Daiichi-Sankyo: Consultancy; Agios: Consultancy, Research Funding; Actinium: Consultancy; Celgene: Consultancy, Other: Data and safety monitoring board; Syros: Consultancy; Syndax: Consultancy; Elevate: Consultancy; Gemoab: Consultancy; Janssen: Consultancy. Frattini:BMS: Current Employment, Current equity holder in private company. Franovic:BMS: Current Employment, Current equity holder in private company. Xu:Agios Pharmaceuticals: Current Employment, Current equity holder in private company. Winkler:Agios Pharmaceuticals: Current Employment, Current equity holder in private company. Wu:Agios Pharmaceuticals: Current Employment, Current equity holder in private company. Vyas:Forty Seven: Research Funding; Celgene: Research Funding, Speakers Bureau; Novartis: Research Funding, Speakers Bureau; AbbVie: Speakers Bureau; Astellas: Speakers Bureau; Daiichi Sankyo: Speakers Bureau; Pfizer: Speakers Bureau.