The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate

Abstract

The somatic mutations in cytosolic isocitrate dehydrogenase 1 (IDH1) observed in gliomas can lead to the production of 2-hydroxyglutarate (2HG). Here, we report that tumor 2HG is elevated in a high percentage of patients with cytogenetically normal acute myeloid leukemia (AML). Surprisingly, less than half of cases with elevated 2HG possessed IDH1 mutations. The remaining cases with elevated 2HG had mutations in IDH2, the mitochondrial homolog of IDH1. These data demonstrate that a shared feature of all cancer-associated IDH mutations is production of the oncometabolite 2HG. Furthermore, AML patients with IDH mutations display a significantly reduced number of other well characterized AML-associated mutations and/or associated chromosomal abnormalities, potentially implicating IDH mutation in a distinct mechanism of AML pathogenesis.

Figure 1. IDH1 R132 and IDH2 R172 are analogous residues that both interact with the β-carboxyl of isocitrate

(A) Active site of crystallized human IDH1 with isocitrate. (B) Active site of human IDH2 with isocitrate, modeled based on the highly homologous and crystallized pig IDH2 structure. For (A) and (B), carbon 6 of isocitrate containing the β-carboxyl is highlighted in cyan, with remaining isocitrate carbons shown in yellow. Carbon atoms of amino acids (green), amines (blue), and oxygens (red) are also shown. Hydrogen atoms are omitted from the figure for clarity. Dashed lines depict interactions < 3.1 angstroms, corresponding to hydrogen and ionic bonds. Residues coming from the other monomer of the IDH dimer are denoted with a prime (') symbol.

Figure 2. Expression of R172K mutant IDH2 results in enhanced α-ketoglutarate-dependent consumption of NADPH

(A) 293T cells transfected with wild-type or R172K mutant IDH2, or empty vector, were lysed and subsequently assayed for their ability to generate NADPH from NADP⁺ in the presence of 0.1 mM isocitrate. (B) The same cell lysates described in (A) were assayed for their consumption of NADPH in the presence of 0.5 mM α-ketoglutarate. Data for (A) and (B) are each representative of 3 independent experiments. Data are presented as the mean ± SEM from 3 independent measurements at the indicated time points. (C) Expression of wild-type and R172K mutant IDH2 was confirmed by Western blotting of the lysates assayed in (A) and (B). Re-probing of the same blot with IDH1 antibody as a control is also shown.

Figure 3. Expression of R172K mutant IDH2 elevates 2HG levels within cells and in culture medium

293T cells transfected with IDH2 wild-type (A) or IDH2 R172K (B) were provided fresh culture medium the day following transfection. 24 hours later, the medium was collected, from which organic acids were extracted, purified, and derivatized with MTBSTFA. Shown are representative gas chromatographs for the derivatized organic acids eluting between 30 to 34 minutes, including aspartate (Asp) and glutamate (Glu). The arrows indicate the expected elution time of 32.5 minutes for MTBSTFA-derivatized 2HG, based on similar derivatization of a commercial R(-)-2HG standard. Metabolite abundance refers to GC-MS signal intensity. (C) Mass spectrum of the metabolite peak eluting at 32.5 minutes in (B), confirming its identity as MTBSTFA-derivatized 2HG. The structure of this derivative is shown in the inset, with the tert-butyl dimethylsilyl groups added during derivatization highlighted in green. m/e⁻ indicates the mass (in atomic mass units) to charge ratio for fragments generated by electron impact ionization (D) Cells were transfected as in (A) and (B), and after 48 hours intracellular metabolites were extracted, purified, MTBSTFA-derivatized, and analyzed by GC-MS. Shown is the quantitation of 2HG signal intensity relative to glutamate for a representative experiment. See also Figure S1.

Figure 4. Both IDH1 and IDH2 are critical for cell proliferation

(A) SF188 cells were treated with either of two unique siRNA oligonucleotides against IDH1 (siIDH1-A and siIDH1-B), either of two unique siRNA oligonucleotides against IDH2 (siIDH2-A and siIDH2-B), or control siRNA (siCTRL), and total viable cells were counted five days later. Data are the mean ± SEM of four independent experiments. In each case, both pairs of siIDH nucleotides gave comparable results. A representative Western blot from one of the experiments, probed with antibody specific for either IDH1 or IDH2 as indicated, is shown on the right-hand side. (B) Model depicting the pathways for citrate +4 (blue) and citrate +5 (red) formation in proliferating cells from [¹³C-U]-L-glutamine (glutamine +5). (C) Cells were treated with two unique siRNA oligonucleotides against IDH2 or control siRNA, labeled with [¹³C-U]-L-glutamine, and then assessed for isotopic enrichment in citrate by LC-MS. Citrate +5 and Citrate +4 refer to citrate with five or four ¹³C-enriched atoms, respectively. Reduced expression of IDH2 from the two unique oligonucleotides was confirmed by Western blot. Blotting with actin antibody is shown as a loading control. (D) Cells were treated with two unique siRNA oligonucleotides against IDH3 (siIDH3-A and siIDH3-B) or control siRNA, and then labeled and assessed for isotopic citrate enrichment by GC-MS. Shown are representative data from three independent experiments. Reduced expression of IDH3 from the two unique oligonucleotides was confirmed by Western blot. In (C) and (D), data are presented as mean ± SD of 3 replicates per experimental group.

Figure 5. Primary human AML samples with IDH1 or IDH2 mutations display marked elevations of 2HG

(A) and (B) AML patient peripheral blood, bone marrow, or pheresis samples were extracted for analysis of intracellular metabolites. Organic acids were purified, derivatized with MTBSTFA, and then analyzed by GC-MS as in Figure 4. Shown are representative gas chromatograms from samples subsequently determined to lack IDH1 or IDH2 mutations (A) or to have a R140Q mutation in IDH2 (B). (C) 2HG signal intensity relative to the intrasample glutamate signal was quantified in a total of 27 serial samples where adequate tumor tissue was available, and then segregated by IDH mutation status. Horizontal bars depict the group mean.

Figure 6. Structural modeling of R140Q mutant IDH2

(A) Active site of human wild-type IDH2 with isocitrate replaced by α-ketoglutarate (α-KG). R140 is well positioned to interact with the β-carboxyl group that is added as a branch off carbon 3 when α-ketoglutarate is reductively carboxylated to isocitrate. (B) Active site of R140Q mutant IDH2 complexed with α-ketoglutarate, demonstrating the loss of proximity to the substrate in the R140Q mutant. This eliminates the charge interaction from residue 140 that stabilizes the addition of the β-carboxyl required to convert α-ketoglutarate to isocitrate.