IDH1 Human

What is IDH1 and what is its normal function in human cells?

IDH1 is a cytosolic NADP-dependent enzyme that catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (αKG). It is located in the cytoplasm and peroxisomes where it participates in lipid metabolism and glucose sensing . The normal enzyme functions as part of cellular metabolic pathways, with the wild-type protein maintaining critical roles in cellular redox status and energy production.

What is the structural basis for IDH1 function?

IDH1 functions through conformational changes between different states. Research has revealed an initial isocitrate (ICT)-binding state that transitions to a closed pre-transition state required for catalytic activity. This conformational change is essential for normal enzymatic function, with specific residues like Arg132 playing multiple functional roles in the catalytic reaction . Crystal structures of both wild-type and mutant IDH1 have provided significant insights into these mechanisms.

How does IDH1 differ from other isocitrate dehydrogenase enzymes?

Human cells express three distinct IDH enzymes: cytosolic NADP-dependent IDH1, mitochondrial NADP-dependent IDH2, and mitochondrial NAD-dependent IDH3 . Unlike its mitochondrial counterparts, IDH1 is primarily cytosolic and uses NADP+ as a cofactor. This localization difference contributes to its distinct role in cellular metabolism.

What types of IDH1 mutations are commonly observed in human cancers?

The most prevalent tumor-specific mutation of IDH1 consists of a missense mutation at amino acid 132 that replaces an active-site arginine residue with histidine (R132H) . While R132H is the most common variant, other substitutions at this position can occur. These mutations are somatic and heterozygous, first discovered through genome-wide analysis of central nervous system tumors.

In which cancer types are IDH1 mutations most frequently found?

IDH1 mutations have been described in WHO Grade IV secondary glioblastomas (GBMs), WHO Grade II diffuse astrocytomas, WHO Grade II oligodendrogliomas, WHO Grade III anaplastic astrocytomas, WHO Grade III anaplastic oligodendrogliomas, and WHO Grade III anaplastic oligoastrocytomas . Approximately 70% of lower-grade gliomas harbor IDH1 mutations, making it a critical biomarker in neuro-oncology .

What is the molecular mechanism by which mutant IDH1 contributes to tumorigenesis?

Mutant IDH1 has a neomorphic activity that converts α-ketoglutarate into 2-hydroxyglutarate (2HG) instead of the normal conversion of isocitrate to α-ketoglutarate . This altered enzyme consists of a dimer between wild-type and mutant proteins. The accumulated oncometabolite D-2-HG leads to epigenetic dysregulation, oncogenesis, and subsequent clonal expansion . Specifically, 2HG may inhibit various dioxygenases including PHD (prolyl hydroxylase), TET2, and histone demethylases, triggering aberrant angiogenesis and gene expression .

How does the R132H mutation specifically alter IDH1 function at the molecular level?

The R132H mutation hinders the conformational changes from the initial ICT-binding state to the pre-transition state, leading to impairment of the normal IDH activity . Additionally, the mutation renders a new reduction function that converts α-ketoglutarate to 2-hydroxyglutarate. Tyr139 has been shown to play a vital role in this gained reduction activity by compensating for the increased negative charge on the C2 atom of αKG during hydride anion transfer from NADPH .

What are the current laboratory methods for detecting IDH1 mutations in clinical samples?

Several methods have proven useful for diagnosing IDH1 mutation-bearing gliomas:

• DNA genotyping of tumor specimens, involving sequencing of DNA extracted from brain tumor samples, which many clinical molecular diagnostic laboratories use to detect IDH1 and IDH2 mutations.

• Immunohistochemical analysis using specific monoclonal antibodies targeting mutant IDH1, such as Imab-1, an anti-IDH1-R132H-specific antibody that reacts with mutated IDH1 .

• Magnetic resonance spectrometry to detect 2HG, the downstream metabolite of mutant IDH1, which enables non-invasive molecular characterization of IDH1-mutated gliomas .

How can researchers optimize immunohistochemical detection of IDH1 mutations?

For optimal immunohistochemical detection, researchers should consider:

• Selection of appropriate antibodies (e.g., Imab-1) that specifically recognize the R132H mutant protein.

• Standardization of staining protocols, including fixation methods, antigen retrieval techniques, and detection systems.

• Implementation of appropriate controls to validate staining specificity.

• Analysis of staining patterns – notably, in immunohistochemical studies, every glioma cell in IDH1-positive samples stains positive for mutated IDH1, even along the infiltrating edge of the tumor into cortex .

What are the advantages and limitations of MR spectroscopy for detecting 2HG in IDH1-mutant tumors?

Magnetic resonance spectrometry offers several unique advantages:

• Non-invasive detection that doesn't require tissue sampling.

• Ability to identify 2HG "hot spots" that can guide biopsy procedures.

• Utility in assisting diagnostic workup and monitoring response to targeted therapies .

Limitations include technical challenges in distinguishing 2HG from other brain metabolites, variability in detection sensitivity, and the need for specialized equipment and expertise. Currently, no reports exist of increased 2HG in blood, urine, or cerebrospinal fluid of glioma patients harboring IDH1 mutations .

What inhibitor drugs have been developed specifically for IDH1-mutant cancers?

Several IDH1 inhibitors have been developed and evaluated clinically:

• DS-1001: An oral brain-penetrant mutant IDH1 selective inhibitor that has shown efficacy in reducing D-2-HG levels and tumor size in preclinical studies .

• Ivosidenib: An IDH1 inhibitor used for the treatment of IDH1-mutant gliomas, grades 2-4, which has demonstrated clinical benefit in both newly diagnosed and recurrent settings .

These inhibitors aim to reduce the production of the oncometabolite 2HG by targeting the neomorphic activity of mutant IDH1.

What clinical evidence supports the efficacy of IDH1 inhibitors in glioma treatment?

Clinical studies have shown promising results:

• DS-1001: In a multicenter, open-label, dose-escalation phase I study for recurrent/progressive IDH1-mutant glioma, objective response rates were 17.1% for enhancing tumors and 33.3% for non-enhancing tumors. DS-1001 was well tolerated with favorable brain distribution .

• Ivosidenib: Real-world data on ivosidenib treatment has shown concordance with controlled trials like INDIGO. The heterogeneous population evaluated in these studies provides insight into real-world IDH inhibitor use outside the strict confines of clinical trials .

What are the methodological considerations for evaluating response to IDH1 inhibitors?

Researchers evaluating IDH1 inhibitor response should consider:

• Appropriate imaging protocols to assess tumor response, accounting for potential pseudoprogression.

• Measurement of 2HG levels in tumors as a pharmacodynamic biomarker.

• Standardized response criteria appropriate for gliomas.

• Accounting for confounding factors such as concurrent treatments.

• Distinguishing between prognostic effects (reflecting underlying disease characteristics) and predictive effects (truly reflective of response to therapy) .

How can researchers investigate the structural and conformational changes of wild-type versus mutant IDH1?

Researchers can employ several sophisticated approaches:

• X-ray crystallography to determine three-dimensional structures of wild-type and mutant IDH1 with and without substrates bound, as demonstrated in studies revealing the initial ICT-binding state and pre-transition state .

• Site-directed mutagenesis coupled with biochemical assays to assess the functional impact of specific residues, such as the studies establishing Tyr139's role in the reduction activity of mutant IDH1 .

• Molecular dynamics simulations to model protein dynamics and conformational changes that occur during catalysis.

• Hydrogen-deuterium exchange mass spectrometry to map regions of conformational flexibility.

What experimental systems are optimal for studying IDH1 mutation effects on cellular metabolism?

Researchers should consider multiple experimental systems:

• Isogenic cell line models with wild-type and mutant IDH1 to isolate the specific effects of the mutation.

• Patient-derived cell lines and xenografts that maintain the genetic background of IDH1-mutant tumors.

• Genetically engineered mouse models expressing mutant IDH1 in relevant cell types.

• Metabolomic profiling using mass spectrometry and NMR to comprehensively characterize metabolic alterations.

• 13C-labeled substrate tracing experiments to track metabolic flux through different pathways.

How can epigenetic effects of IDH1 mutations be comprehensively characterized?

To investigate epigenetic changes induced by IDH1 mutations:

• Chromatin immunoprecipitation sequencing (ChIP-seq) to map histone modification patterns.

• Whole-genome bisulfite sequencing or reduced representation bisulfite sequencing to assess DNA methylation.

• ATAC-seq to examine chromatin accessibility changes.

• RNA-seq to correlate epigenetic alterations with gene expression changes.

• Single-cell approaches to resolve cellular heterogeneity within tumors.

• Functional assays to test the reversibility of epigenetic changes upon IDH1 inhibitor treatment.

What are promising approaches for developing next-generation IDH1 inhibitors?

Future IDH1 inhibitor development might focus on:

• Structure-based drug design utilizing crystallographic data of the mutant enzyme to optimize binding and specificity.

• Development of inhibitors that can target multiple IDH1 mutation variants beyond R132H.

• Designing molecules with improved blood-brain barrier penetration for glioma treatment.

• Creating dual inhibitors that can target both IDH1 and IDH2 mutations simultaneously.

• Exploring combination strategies with other targeted therapies or standard treatments.

How might mutant IDH1 enzyme properties inform protein engineering applications?

The neomorphic catalytic activities associated with IDH1 mutations may provide useful insights for metabolic engineering:

• Knowledge of the structural changes that confer new catalytic activities can guide rational enzyme design.

• Understanding the molecular basis for substrate specificity shifts can inform protein engineering strategies.

• Mutant IDH1 has already contributed to the rapid design of enzymes for industrial applications, such as the large-scale production of adipic acid, a precursor in nylon synthesis .

This represents an example of how cancer-derived mutations can have broad applications beyond oncology research.