Molecular mechanisms mediating relapse following ivosidenib monotherapy in IDH1-mutant relapsed or refractory AML

Abstract

Isocitrate dehydrogenase (IDH) 1 and 2 mutations result in overproduction of D-2-hydroxyglutarate (2-HG) and impaired cellular differentiation. Ivosidenib, a targeted mutant IDH1 (mIDH1) enzyme inhibitor, can restore normal differentiation and results in clinical responses in a subset of patients with mIDH1 relapsed/refractory (R/R) acute myeloid leukemia (AML). We explored mechanisms of ivosidenib resistance in 174 patients with confirmed mIDH1 R/R AML from a phase 1 trial. Receptor tyrosine kinase (RTK) pathway mutations were associated with primary resistance to ivosidenib. Multiple mechanisms contributed to acquired resistance, particularly outgrowth of RTK pathway mutations and 2-HG-restoring mutations (second-site IDH1 mutations, IDH2 mutations). Observation of multiple concurrent mechanisms in individual patients underscores the complex biology of resistance and has important implications for rational combination therapy design. This trial was registered at www.clinicaltrials.gov as #NCT02074839.

Conflict of interest statement

Conflict-of-interest disclosure: S.C., H.W., Z.K., L.D., B.N., P.N., G.L., V.Z., H.L., M.G., W.L., K.M., C.B., S.A.B., and B.W. are employees of and have equity ownership in Agios. C.D.D. has received honoraria and research funding from AbbVie, Agios, Celgene, and Daiichi Sankyo, and honoraria from MedImmune. E.M.S. has membership on the board of directors or advisory committee for Agios, Astellas, Celgene, Daiichi Sankyo, Genentech, Novartis, PTC Therapeutics, and Syros, and has acted as consultant for Agios. S.d.B. has acted as consultant for AbbVie, Agios, Astellas, Bayer, Celgene, Daiichi Sankyo, Forma, Janssen, Novartis, Pfizer, Pierre Fabre, Servier, and Syros; has received research funding from Agios and Forma; and is on a speaker bureau for Celgene. G.J.R. has acted as consultant or member of a data and safety monitoring committee for AbbVie, Actinium, Agios, Amphivena, Argenx, Astellas, Astex, Bayer, Celgene, Celltrion, Daiichi Sankyo, Eisai, Janssen, Jazz, MEI Pharma, Novartis, Orsenix, Otsuka, Pfizer, Roche/Genentech, Sandoz, Takeda, and Trovagene, and has received research funding from Cellectis. J.K.A. has acted as a consultant to AbbVie, Agios, Cancer Expert Now, Daiichi Sankyo, Glycomimetics, Novartis, and Theradex; is on a speaker bureau for France Foundation, PeerView, and prIME Oncology; and has received research funding to their institution from Agios, Astellas, Boehringer Ingelheim, Celgene, Fujifilm, and Genentech. A.S.M. has acted as a consultant to AbbVie, Agios, Astellas, Jazz, and PTC Therapeutics. J.W. has membership on the board of directors or advisory committee for Celgene and Pfizer, has received research funding from Takeda, and has acted as consultant and is on a speaker bureau for Jazz. D.A.P. has acted as a consultant to AbbVie, Agios, Argenx, Celgene, Celyad, Curis, Pfizer, and Servier, and has received research funding from Agios and Pfizer. A.T.F. has acted as a consultant for AbbVie, Agios, Amphivena, Astellas, Celgene, Daiichi Sankyo, Forty Seven, Jazz, Kite, NewLink Genetics, Novartis, PTC Therapeutics, Takeda, and Trovagene. M.S.T. has received research funding from AbbVie, ADC Therapeutics, BioSight, Cellerant, and Orsenix; has acted as a consultant and has membership on the board of directors or advisory committee for AbbVie, BioLineRx, Daiichi Sankyo, Delta Fly Pharma, Jazz, KAHR, Nohla, Oncolyze, Orsenix, Rigel, and Tetraphase; and holds patents or royalties with UpToDate. H.M.K. has received research funding from Ariad, Astex, Bristol Myers Squibb, Cyclacel, Daiichi Sankyo, Immunogen, Jazz, Novartis, and Pfizer and honorarium from Actinium, Immunogen, Pfizer, and Takeda. R.M.S. has acted as a consultant for AbbVie, Actinium, Agios, Amgen, Argenx, Arog, Astellas, AstraZeneca, BioLineRx, Celgene, Cornerstone Biopharma, Fujifilm, Jazz, Merck, Novartis, Ono, Orsenix, Otsuka, Pfizer, Sumitomo, and Trovagene; has received research funding from Agios, Arog, and Novartis; and is a member of a data and safety monitoring board for Argenx, Celgene, and Takeda Oncology. L.Q. has received research funding from Agios and Celgene and is on a speaker bureau for Celgene. E.C.A. was an employee of and had equity ownership in Agios at the time of the study and is currently an employee of Aprea Therapeutics.

© 2020 by The American Society of Hematology.

Figures

Graphical abstract

Figure 1.

Patient flow diagram summarizing analysis sets. Analyses did not include all patients treated in this population because of several factors, including lack of complete sample availability for all protocol-designated time points and/or suboptimal quantity and/or quality of some samples, resulting in failure to obtain valid data. BMMC, bone marrow mononuclear cell; CDx, companion diagnostic test; DNAseq, DNA sequencing; FDA, US Food and Drug Administration; IDH, isocitrate dehydrogenase; IVO, ivosidenib; PBMC, peripheral blood mononuclear cell; PK, pharmacokinetics; VAF, variant allele frequency.

Figure 2.

Baseline co-occurring mutation analysis. (A) Heat map showing co-occurring mutations at baseline by best overall response category (NGS; whole bone marrow; n = 167 patients). Merge of dose-escalation and dose-expansion data (VAF cutoff, 1%-5%). Cytogenetic risk was classified according to the National Comprehensive Cancer Network Clinical Practice Guidelines for AML, version 1.2015. The bar graph depicts the frequency of genes with co-occurring mutations. A similar heat map with detected mutations by VAF level is provided in supplemental Figure 1. (B) Association between mutation status and best response. P value is based on Fisher’s exact test examining the association between specific pathway or gene mutations and best overall response of CR/CRh vs non-CR/CRh responders and nonresponders. NC denotes P value not calculated because of small number of patients with mutation. FLT3-TKD+ denotes FLT3-TKD or juxtamembrane domain point mutations. Data source: 167 patients with baseline NGS data from whole bone marrow. IDH1-MC, IDH1 mutation clearance; ITD, internal tandem duplication; mut, mutant; wt, wild-type.

Figure 3.

Clonal hierarchy of mIDH1 and co-occurring mutations. (A) Association of clinical response and mIDH1 clonal/subclonal status. mIDH1 was defined as subclonal in a sample if any comutation VAF was greater than mIDH1 VAF +5%; otherwise, it was defined as clonal. See details in the supplemental Methods. (B) Plot showing the tally of how often a co-occurring gene VAF is observed to be lower (red) or higher (blue) than mIDH1 VAF by NGS. Only genes that were mutated in at least 5% of patients are shown. Per-gene VAFs are detailed in supplemental Figure 4. For each gene X, the subset of patients with a mutation in gene X is selected (n in parentheses) and plotted, with the x-axis showing the percentage of patients where gene X VAF > mIDH1 VAF +5% and the y-axis showing the percentage of patients where gene X VAF < mIDH1 VAF −5%.

Figure 4.

Mutations in genes and pathways detected at relapse and progression. (A) Gene mutations detected at relapse/progressive disaease (RL/PD) in patients with paired baseline and RL/PD data (n = 74), with genes organized by pathway and patients sorted by best overall response. Blue squares indicate new mutations at RL/PD that were not detected at baseline. Blue squares in the IDH1 mutation row indicate emergent second-site IDH1 mutations at time of RL/PD. Orange squares indicate mutations identified at RL/PD that were also detected at baseline. An X indicates that a variant in that gene that was detected at baseline is no longer detected at relapse. (B) Frequency of emergence of mutations by pathway in patients with data at baseline and at RL/PD (n = 74). CRi, complete remission with incomplete hematologic recovery; CRp, complete remission with incomplete platelet recovery; MLFS, morphologic leukemia-free state; SD, stable disease.

Figure 5.

2-HG–restoring mutations emerging at relapse or disease progression. (A) Second-site IDH1 mutations emerging during ivosidenib treatment (n = 20). Each circle represents a single patient with detection of the mutation. Direct denotes that the mutation makes contact with the ivosidenib or cofactor (NADPH) binding pocket by 3-dimensional modeling. Indirect denotes that it induces structural changes in vicinity of ivosidenib or cofactor binding pockets (hypothesized). Novel mutations (not previously published) are mostly the indirect type. (B) Crystal structure of IDH1-R132H in the inactive, open conformation. The cocrystal structure of IDH1-R132H with inhibitor 20a (PBD accession no. 5L57) was obtained at 2.7 Ao resolution and used to develop the model for the ivosidenib analog AGI-14686 (supplemental Methods). The homodimeric protein structure is shown with the inhibitor (AGI-14686) in yellow, occupying the middle of the tetra-helical domain. The protein monomers are shown in green and cyan, the mutated 132H residue in magenta and cofactor NADPH in orange. (C) The mIDH1-AGI-14686 binding model for the IDH1-R132H-S280F mutation places the di-F cyclopentane of AGI-14686 near Ser280 (left). Mutation of Ser280 to Phe (right) will create a steric interference with ivosidenib (or its analogs), and thus will no longer bind to mIDH1. The mIDH1 protein is depicted in cartoon (green and blue for each monomer), the ivosidenib analog AGI-14686 in yellow sticks, and residue 280 in spheres (Ser in the left panel, Phe in the right panel). R132H is shown in magenta. (D) Biochemical 50% inhibitory concentration (IC50) for second-site IDH1 mutations. We expressed various combinations of IDH1 mutants with second-site mutations and examined biochemically whether they were still inhibited by ivosidenib.

Figure 6.

Polyclonal relapse mechanisms. Single-cell analysis showing clonal evolution in individual patients. (A) mIDH2 acquired in the same clone as mIDH1, with elevation of 2-HG at relapse. Two distinct mIDH1 clones were present at baseline: 1 harboring NPM1/NRAS and the other harboring NPM1/FLT3-TKD comutations. After ivosidenib treatment, the IDH1/NPM1/NRAS clone was no longer detected. Reduction in the IDH1/NPM1/FLT3-TKD clone was observed at cycle 2 day 1, but it ultimately expanded at relapse with the acquisition of mIDH2. (B) mIDH2 was not detected at baseline, but emergence of mIDH2 in a separate clone than mIDH1 was observed at cycle 12 day 1, with elevation of 2-HG. (C) mIDH2 was present at baseline (though not detected by bulk NGS) in a distinct clone to mIDH1, with clinical relapse associated with detection of an NRAS clone. In this case of NRAS-driven clinical relapse, the 2-HG levels remained low at relapse. Additional details on these cases shown in supplemental Figure 7. NS, not specified.