Molecular mechanisms of isocitrate dehydrogenase 1 (IDH1) mutations identified in tumors: The role of size and hydrophobicity at residue 132 on catalytic efficiency

Abstract

Edited by John M. Denu Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP؉ -dependent conversion of isocitrate (ICT) to ␣-ketoglutarate (␣KG) in the cytosol and peroxisomes. Mutations in IDH1 have been implicated in >80% of lower grade gliomas and secondary glioblastomas and primarily affect residue 132, which helps coordinate substrate binding. However, other mutations found in the active site have also been identified in tumors. IDH1 mutations typically result in a loss of catalytic activity, but many also can catalyze a new reaction, the NADPH-dependent reduction of ␣KG to D-2-hydroxyglutarate (D2HG). D2HG is a proposed oncometabolite that can competitively inhibit ␣KG-dependent enzymes. Some kinetic parameters have been reported for several IDH1 mutations, and there is evidence that mutant IDH1 enzymes vary widely in their ability to produce D2HG. We report that most IDH1 mutations identified in tumors are severely deficient in catalyzing the normal oxidation reaction, but that D2HG production efficiency varies among mutant enzymes up to ϳ640-fold. Common IDH1 mutations have moderate catalytic efficiencies for D2HG production, whereas rarer mutations exhibit either very low or very high efficiencies. We then designed a series of experimental IDH1 mutants to understand the features that support D2HG production. We show that this new catalytic activity observed in tumors is supported by mutations at residue 132 that have a smaller van der Waals volume and are more hydrophobic. We report that one mutation can support both the normal and neomorphic reactions. These studies illuminate catalytic features of mutations found in the majority of patients with lower grade gliomas.Metabolic changes in tumors have been described for nearly a century (1-3), but only relatively recently have enzymes involved in metabolic processes been established as tumor suppressors or oncoproteins. One of the more striking examples of metabolic enzymes playing a role in tumorigenesis includes isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2).3 These homodimeric enzymes are responsible for the reversible NADP ϩ -and Mg 2ϩ -dependent conversion of ICT to ␣KG (Fig. 1A) in the cytosol and peroxisomes (IDH1), or mitochondria (IDH2). IDH3 is responsible for the same reaction within the context of the TCA cycle, although the oxidative decarboxylation catalyzed by this enzyme is non-reversible and NAD ϩ -dependent. Mutations in IDH1 and IDH2 were identified in glioblastoma multiforme in a large sequencing effort (4), and soon Ͼ80% of adult grade II/III gliomas and secondary glioblastomas were found to have IDH1 mutations, commonly R132H or R132C IDH1 (5, 6) (reviewed in Refs. 7-9). Subsequently ϳ10 -20% of acute myeloid leukemias were shown to have primarily IDH2 mutations, typically R140Q or R172K IDH2 (10). Early mechanisms of tumorigenesis focused on deficient conversion of ICT to ␣KG (11), suggesting that IDH serves as a tumor suppressor, in part through altering levels of hypoxia-inducible transcription factor-1␣ (12). However,...

Lack of evidence for substrate channeling or flux between wildtype and mutant isocitrate dehydrogenase to produce the oncometabolite 2-hydroxyglutarate

“…Others, however, have found no advantage for the recombinant IDH1 heterodimer (22). Alternatively, the WT dependence might be due to substrate channeling or some other form of cooperativity between the WT and mutant subunits as proposed previously (17,23). Pietrak et al (24) demonstrated that both the WT activity for oxidative decarboxylation of isocitrate and the mutant activity for reduction of ␣-KG to 2-HG remain intact in a WT-mutant IDH1 heterodimer, suggesting that channeling could be involved.…”

Computational Analysis of IDH1, IDH2, and TP53 Mutations in Low-Grade Gliomas Including Oligodendrogliomas and Astrocytomas

“…6,30 The IDH mutations ( Figure 3A and B) occurring in the catalytic site are likely to cause a loss of catalytic activity; these mutated genes encode for D2HG which is proposed to be an oncometabolite in the cytoplasm for IDH1 and in the mitochondria for IDH2; it competitively inhibits KG-dependent enzymes, including the TET family of 5-methylcytosine hydroxylases and the JmjC family of histones lysine Cancer Informatics demethylases, resulting in cell differentiation. 27,28,31,32 Thirumal Kumar et al 27,28 reveal that the drug therapeutics for D-2hydroxyglutarate dehydrogenase are very limited; therefore, understanding the nature of molecular structure caused by these mutations will serve as platform for the development of novel targets for new drug therapy for D-2-hydroxyglutaric aciduria.…”

Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors

“…Particular mutations in isocitrate dehydrogenase 1 (IDH1), predominantly at amino acid R132, result in both loss of function of its normal NADPH-generating activity, as well as gain of function of a neomorphic NADPH-consuming activity that produces the oncometabolite 2-hydroxyglutarate (Dang et al, 2009). This change in function was implemented by adding the IDH1-catalyzed neomorphic reaction to Recon3D and imposing turnover numbers of the normal and neomorphic reactions measured by Avellaneda Matteo et al based on the IDH1 mutation status of each tumor (Table S3) (Avellaneda Matteo et al, 2017).…”