IDI1 Human

What is IDI1 and what is its primary function in human cells?

IDI1 (isopentenyl-diphosphate delta isomerase 1) is a peroxisomally-localized enzyme that catalyzes the interconversion of isopentenyl diphosphate (IPP) to its highly electrophilic isomer dimethylallyl diphosphate (DMAPP) . This isomerization reaction represents a critical step in the isoprenoid biosynthetic pathway, which ultimately leads to the synthesis of farnesyl diphosphate and cholesterol .

The enzyme contains specific functional domains including:

IDI1 is predicted to localize to the cytoplasm and has isopentenyl-diphosphate delta-isomerase activity that is essential for the isopentenyl diphosphate biosynthetic process . The proper functioning of this enzyme is critical, as demonstrated by the reduction in IPP isomerase activity observed in peroxisomal deficiency diseases such as Zellweger syndrome and neonatal adrenoleukodystrophy .

What cellular pathways involve IDI1?

IDI1 is primarily involved in two major cellular pathways:

• Cholesterol Biosynthesis Pathway: IDI1 participates in the "superpathway of cholesterol biosynthesis," working alongside other enzymes like HMGCS2 (HMG-CoA synthase 2) . Within this pathway, IDI1 catalyzes a critical isomerization step needed for the synthesis of sterols and other isoprenoid compounds.

• Immune Signaling Regulation: Recent research has identified IDI1's unexpected role in modulating the cGAS-Sting signaling pathway, a critical component of innate immunity . Through this interaction, IDI1 can influence immune responses, particularly in the context of cancer development.

The dual involvement of IDI1 in both metabolic and immune pathways represents an important connection between cellular metabolism and immune function, demonstrating how metabolic enzymes can have pleiotropic effects beyond their canonical roles.

What experimental methods are recommended for studying IDI1 expression?

Researchers investigating IDI1 expression should consider the following methodological approaches:

Transcriptional Analysis:

• Quantitative PCR (qPCR) to measure IDI1 mRNA levels in different tissues or under various experimental conditions

• RT² Profiler PCR Arrays specifically designed for fatty acid metabolism, lipoprotein signaling, and cholesterol metabolism pathways

• Gene expression analysis using established housekeeping genes like Glucuronidase beta (Gusb) as endogenous controls

Protein Analysis:

• Western blotting to quantify IDI1 protein levels and confirm transcriptional findings

• Immunofluorescence to determine subcellular localization, potentially with co-staining of peroxisomal markers

Functional Assays:

• Oil Red O staining for visualization and quantification of lipid accumulation

• Flow cytometry with lipophilic dyes like Nile Red to measure intracellular lipid content

Genetic Manipulation:

• RNA interference (siRNA) to knockdown IDI1 expression and assess functional consequences

• Plasmid transfection for overexpression studies

When designing experiments to study IDI1 expression, researchers should consider including appropriate controls and validating findings at both the transcriptional and translational levels, as demonstrated in studies of IDI1 in stretched cardiac myocytes .

How does IDI1 interact with the cGAS-Sting signaling pathway in hepatocellular carcinoma?

IDI1 functions as a negative regulator of the cGAS-Sting signaling pathway in hepatocellular carcinoma (HCC) through direct protein-protein interactions. This relationship represents a novel connection between metabolism and immune regulation in cancer.

The mechanism of this interaction has been elucidated through several experimental approaches:

• Direct Binding to cGAS: IDI1 physically interacts with cGAS (cyclic GMP-AMP synthase), a key DNA sensor in the innate immune system. This interaction was confirmed through:

  • GST pull-down experiments demonstrating binding between GST-cGAS fusion protein and endogenously expressed IDI1

  • Co-immunoprecipitation experiments confirming the interaction between endogenous IDI1 and cGAS

• Recruitment of E3 Ligase: IDI1 recruits the E3 ligase TRIM41 to cGAS, promoting its ubiquitination and subsequent degradation . Overexpression of IDI1 enhances the interaction between cGAS and TRIM41 and increases cGAS ubiquitination .

• Inhibition of Downstream Signaling: IDI1-mediated degradation of cGAS inhibits phosphorylation of downstream factors including TBK1 and IRF3, and reduces expression of the chemokines CCL5 and CXCL10 . These effects collectively suppress innate immune signaling.

• Dynamic Regulation: The interaction between IDI1 and cGAS is not static but responsive to cellular conditions. When the cGAS-Sting-TBK1 pathway is activated by stimuli such as HT-DNA or IR exposure, the interaction between IDI1 and cGAS is weakened .

• Clinical Correlation: In HCC samples, an inverse relationship between IDI1 and cGAS expression has been observed, supporting the relevance of this regulatory mechanism in human cancer .

This dual role of IDI1 as both a metabolic enzyme and an immune regulator makes it a particularly interesting therapeutic target in HCC, where it appears to promote cancer progression primarily through immune evasion rather than direct effects on cancer cell growth or invasion .

How does mechanical stretching affect IDI1 expression in cardiac myocytes?

Mechanical stretching significantly affects IDI1 expression in cardiac myocytes, revealing an important connection between mechanical stress and metabolic adaptation in cardiac cells. Research using HL-1 atrial myocytes has demonstrated several key findings:

Morphological and Lipid Changes in Stretched Myocytes:

• Stretched HL-1 atrial myocytes exhibit significantly increased cell sizes (1200.1 ± 35.1 μm² vs. 637.2 ± 13.9 μm² in controls)

• Nuclear sizes also increase substantially (263.2 ± 13.6 μm² vs. 135.6 ± 4.2 μm² in controls)

• Lipid accumulation is enhanced, with:

  • Increased Oil Red O-stained area per myocyte (5.1% ± 0.2% vs. 2.3% ± 0.1%)

  • Higher fraction of myocytes expressing Nile red (80.9% ± 2.2% vs. 48.2% ± 2.1%)

Differential Gene Expression:
PCR array analysis of fatty acid metabolism, lipoprotein signaling, and cholesterol metabolism genes revealed differential expression patterns in stretched myocytes:

Canonical pathway analysis using Ingenuity Pathway Analysis identified IDI1 and Hmgcs2 as the only two genes in the dataset involved in the "superpathway of cholesterol biosynthesis" .

Validation at Multiple Levels:

• These expression changes were confirmed at both transcriptional (mRNA) and translational (protein) levels through qPCR and Western blot analysis

• Functional validation through RNA interference targeting IDI1 demonstrated that its expression is causally related to the lipid accumulation phenotype observed in stretched myocytes

This research suggests that mechanical stretching, as might occur in conditions like atrial fibrillation or heart failure, triggers a specific metabolic adaptation involving IDI1 upregulation. This finding provides insight into potential mechanisms of stretch-induced lipid accumulation in cardiac tissue and might have implications for understanding and treating cardiac pathologies associated with mechanical stress.

What methodological considerations are important when investigating IDI1-protein interactions?

Investigating IDI1-protein interactions requires careful experimental design and attention to several methodological considerations to ensure reliable results:

1. Interaction Detection Methods:

2. Experimental Variables to Consider:

• Cellular Stimulation: The IDI1-cGAS interaction was weakened after HT-DNA stimulation or IR exposure, indicating that interaction dynamics can change under different cellular conditions

• Cell Type Selection: Different cell types may exhibit different interaction patterns based on expression levels and subcellular distribution of IDI1

• Subcellular Fractionation: Given IDI1's peroxisomal localization, separating cellular compartments may help determine where specific interactions occur

3. Functional Validation Approaches:

• RNA Interference: Knockdown of IDI1 to assess effects on binding partner function and downstream pathways

• Overexpression Studies: Using plasmid transfection to examine how increased IDI1 affects interactions and related pathways

• Ubiquitination Assays: Essential when studying interactions involving protein degradation (as with IDI1-TRIM41-cGAS)

4. Clinically Relevant Validation:

• Expression Correlation: Examining the relationship between IDI1 and interaction partners in clinical samples, as demonstrated by the inverse correlation between IDI1 and cGAS in HCC tissues

• Pathway Analysis: Using tools like Ingenuity Pathway Analysis to identify potential relationship networks involving IDI1

How can IDI1 be targeted for potential therapeutic interventions in cancer?

IDI1 presents a promising therapeutic target in cancer, particularly hepatocellular carcinoma (HCC), based on its dual role in metabolism and immune evasion. Several targeting strategies can be considered:

1. Approaches to Target IDI1:

2. Rationale for Targeting in Different Contexts:

• Hepatocellular Carcinoma: IDI1 is significantly upregulated in liver cancer and promotes cancer development in mice . Its primary mechanism appears to be inhibition of the cGAS-Sting pathway rather than direct effects on cancer cell growth or invasion .

• Immune Modulation: Targeting IDI1 could restore cGAS-Sting signaling, enhancing innate immune responses against cancer cells. IDI1 inhibition would prevent the recruitment of TRIM41 to cGAS, thereby preventing cGAS degradation .

• Metabolic Targeting: As part of the cholesterol biosynthesis pathway, IDI1 inhibition might disrupt cancer cell metabolism, potentially creating synergistic effects when combined with other metabolic inhibitors.

3. Biomarker Considerations:

• Expression Analysis: IDI1 expression levels could serve as a predictive biomarker for therapy response.

• Pathway Assessment: The inverse relationship between IDI1 and cGAS expression in tumors might inform patient stratification .

4. Combination Approaches:

• With Immunotherapies: IDI1 inhibition could potentially enhance responses to immune checkpoint inhibitors by boosting innate immunity.

• With Metabolic Therapies: Combining with other inhibitors of the cholesterol biosynthesis pathway might yield synergistic effects.

The therapeutic potential of IDI1 targeting is particularly interesting because it addresses two hallmarks of cancer simultaneously: metabolic reprogramming and immune evasion. While promising, further preclinical research is needed to fully validate IDI1 as a therapeutic target and develop effective targeting strategies.

What contradictions exist in the current research regarding IDI1's role in different cancer types?

Current research on IDI1 reveals several notable contradictions and context-dependent differences in its role across cancer types:

1. Growth vs. Immune Evasion Functions:
A significant paradox is observed in liver cancer, where IDI1 "has no significant effect on the growth or invasion of liver cancer cells but significantly promotes liver cancer development in mice" . This suggests that direct cellular effects versus host-tumor interactions may be distinctly regulated by IDI1.

2. Cancer-Type Specific Mechanisms:

These differences suggest that IDI1's oncogenic functions may be highly context-dependent, possibly reflecting tissue-specific metabolic requirements or immune microenvironments.

3. Metabolic vs. Non-metabolic Functions:
A conceptual contradiction exists between IDI1's canonical role as a metabolic enzyme in cholesterol biosynthesis and its newly discovered function in immune regulation through cGAS interaction . This dual functionality raises questions about compartment-specific functions or potential shuttling mechanisms that aren't fully understood.

4. In Vitro vs. In Vivo Effects:
The discrepancy between IDI1's minimal effect on cancer cell growth in vitro versus its significant promotion of cancer development in mice highlights important limitations of cell culture models and emphasizes the importance of studying IDI1 in intact physiological systems where immune interactions are preserved.

5. Expression Regulation:
While IDI1 upregulation is observed in multiple cancer types, the driving mechanisms differ:

• In some contexts, it may be driven by increased demand for cholesterol biosynthesis

• In others, it might be specifically upregulated through oncogenic signaling like the beta-catenin/TCF pathway

• In cardiac myocytes, mechanical stretching increases IDI1 expression , suggesting yet another regulatory mechanism

These contradictions illustrate the complex and context-dependent nature of IDI1's role in cancer biology and underscore the need for cancer type-specific investigation when considering IDI1 as a therapeutic target.