NRIP3 Human is produced recombinantly in Escherichia coli with high purity (>85%) and tagged for purification. Key structural details include:
| Property | Details |
|---|---|
| Molecular Weight | 29.4 kDa |
| Amino Acid Range | 1–241 (with a 23-amino-acid His-tag at the N-terminus) |
| Purity | >85% (verified by SDS-PAGE) |
| Storage Conditions | 4°C (short-term) or -20°C (long-term); avoid freeze-thaw cycles |
| Buffer Composition | 20 mM Tris-HCl (pH 8.0), 0.15 M NaCl, 20% glycerol, 1 mM DTT |
The protein sequence includes conserved domains involved in nuclear receptor interactions and replication stress management :
Key Motifs: Aspartic-type endopeptidase activity (predicted) .
Interacting Partners: DDI1 (DNA-damage-inducible 1 homolog 1) and RTF2 (Replication Termination Factor 2) .
NRIP3 facilitates resistance to DNA damage induced by chemoradiotherapy (CRT) via:
DDI1 Upregulation: NRIP3 increases DDI1 expression through PPARα activation, promoting RTF2 removal to recover stalled replication forks .
Lipid Metabolism Modulation: Overexpression reduces ceramide (Cer) levels, which are linked to apoptosis and cell cycle arrest .
Overexpression: Enhances esophageal squamous cell carcinoma (ESCC) cell growth, S-phase progression, and xenograft tumor formation .
Knockdown: Arrests cells at the G1/S checkpoint and increases DNA damage markers (e.g., γH2AX, phosphorylated ATR/Chk1) .
| Parameter | NRIP3 Overexpression | NRIP3 Knockdown |
|---|---|---|
| Cell Proliferation | Increased (EdU+ cells ↑) | Decreased (EdU+ cells ↓) |
| Colony Formation | Enhanced (p < 0.01) | Suppressed |
| Lipid Levels | Ceramide ↓, Triglycerides ↓ | Ceramide ↑ |
| DNA Damage Markers | Phospho-ATR/Chk1 ↓, γH2AX ↓ | Phospho-ATR/Chk1 ↑, γH2AX ↑ |
NRIP3 is implicated in 13 CRISPR screens related to cancer pathways, highlighting its role in replication stress management and tumor survival .
Cancer: Linked to poor prognosis in ESCC patients receiving CRT . Elevated NRIP3 correlates with resistance to cisplatin and radiotherapy .
Leukemia: Fusions like MLL-NRIP3 are reported in acute leukemia .
NRIP3 (Nuclear Receptor Interacting Protein 3) is a protein-coding gene that produces a transcript of 567 nucleotides in length with cytosolic subcellular localization . The protein functions as an interactor with nuclear receptors and demonstrates context-dependent regulatory roles in cellular processes. NRIP3 protein can be detected in both nuclear and cytoplasmic compartments, suggesting potential shuttling between these cellular locations .
The functional impact of NRIP3 varies significantly between cancer types, with evidence suggesting opposing roles in different tissues. For example, in esophageal squamous cell carcinoma (ESCC), NRIP3 appears to promote tumor growth and therapy resistance , while in colorectal cancer (CRC), it exhibits tumor-suppressive properties by inhibiting cell proliferation, colony formation, invasion, and migration .
NRIP3 expression is primarily regulated through epigenetic mechanisms, particularly DNA methylation of its promoter region. Research demonstrates an inverse correlation between NRIP3 expression and promoter methylation status. In colorectal cancer studies, immunohistochemistry assays reveal higher NRIP3 expression in normal margin tissue compared to cancer tissues (p < 0.001), with reduced expression significantly associated with promoter methylation (p < 0.001) .
The methylation pattern of NRIP3 shows progressive changes during cancer development, with methylation observed in 2.7% of resected margin samples, 32.2% of colorectal adenomatous polyps, and 50.6% of colorectal cancer samples . This progressive increase suggests that NRIP3 methylation may represent an early event in carcinogenesis.
In stress response studies, NRIP3 shows variable methylation patterns (hypomethylation and mixed methylation) in response to different stressors, indicating another layer of epigenetic regulation in non-cancer contexts .
NRIP3 interacts with several critical cellular signaling pathways:
PI3K-AKT Signaling: In colorectal cancer, NRIP3 has been demonstrated to suppress the PI3K-AKT pathway. Microarray analysis and subsequent validation showed that reexpression of NRIP3 in CRC cell lines (DLD1, RKO, and HCT116) reduced levels of PI3K, phosphorylated AKT (p-AKT), and phosphorylated mTOR (p-mTOR), while knockdown of NRIP3 in DKO cells increased these signaling molecules .
PPARα-Mediated Signaling: In esophageal squamous cell carcinoma, NRIP3 increases DDI1 expression via PPARα, establishing a NRIP3-PPARα-DDI1-RTF2 axis that mediates resistance to chemoradiotherapy .
DNA Damage Response: NRIP3 has been implicated in replication stress management through its interaction with RTF2 (homologous to Schizosaccharomyces pombe Rtf2), which is involved in cellular responses to DNA damage induced by chemoradiotherapy .
Matrix Metalloproteinase Regulation: In functional studies, NRIP3 expression has been shown to affect levels of MMP2, MMP7, and MMP9, which are involved in extracellular matrix remodeling and cancer cell invasion .
Researching NRIP3 methylation requires a multi-modal approach to capture both site-specific and global methylation patterns:
Methylation-Specific PCR (MS-PCR): This technique has been effectively employed in multiple studies to analyze the methylation status of the NRIP3 promoter region. In colorectal cancer research, MS-PCR successfully detected NRIP3 methylation in various sample types including resected margins, adenomatous polyps, and cancer tissues .
Bisulfite Sequencing: For more comprehensive analysis of CpG islands within the NRIP3 promoter, bisulfite sequencing provides base-pair resolution of methylation status. This approach can identify specific CpG sites that may be most critical for expression regulation.
Whole-Genome Methylation Arrays: Technologies such as the Illumina Infinium arrays can assess genome-wide methylation patterns, providing context for NRIP3 methylation within the broader epigenetic landscape.
Combined Approaches: When investigating NRIP3 methylation in relation to stress responses, researchers have employed combined approaches to evaluate both global and gene-specific methylation changes. This includes evaluation of 5-hydroxymethylcytosine (5-hmC) modifications, which represent an intermediate in the demethylation process .
When designing methylation studies, researchers should carefully consider cell type specificity, as methylation patterns can vary significantly across tissues. Additionally, correlation of methylation data with expression analysis (RNA and protein levels) strengthens the functional interpretation of methylation changes.
To comprehensively characterize NRIP3's function in cancer cells, researchers should employ a multi-faceted experimental strategy:
Expression Modulation:
RNA interference (siRNA) for NRIP3 knockdown in cells with high endogenous expression
Overexpression vectors for reintroduction in cells with low expression or methylated NRIP3
CRISPR-Cas9 for complete knockout studies
Inducible expression systems for temporal control
Phenotypic Assays:
Proliferation assays (MTT, BrdU incorporation)
Colony formation assays to assess clonogenic potential
Cell cycle analysis using flow cytometry (particularly for G1/S transition given NRIP3's role in cell cycle arrest)
Transwell migration and invasion assays
Scratch/wound healing assays for cell migration
Molecular Pathway Analysis:
Western blotting to assess signaling pathway components (PI3K, AKT, mTOR)
Co-immunoprecipitation to identify protein-protein interactions
Gene expression profiling (RNA-seq or microarray) following NRIP3 modulation
Chromatin immunoprecipitation to identify potential DNA binding sites
In Vivo Models:
Xenograft models using cells with modified NRIP3 expression
Metastasis models to assess NRIP3's impact on cancer spread
This methodological framework has successfully revealed NRIP3's role in colorectal cancer, where it was shown to suppress migration and invasion. In NRIP3-silenced versus NRIP3-expressing DLD1, RKO, and HCT116 cells, significant differences were observed in migratory cell counts (224.00 ± 13.74 vs 178.08 ± 7.97, 176.92 ± 6.69 vs 102.5 ± 9.71, and 232.63 ± 11.55 vs 181.40 ± 18.65, respectively) .
Detecting NRIP3 protein in clinical samples presents several technical challenges that researchers should address through careful methodological design:
Antibody Specificity and Validation:
Challenge: Limited specificity of available antibodies can lead to false positive signals
Solution: Validate antibodies using positive and negative controls, including cells with NRIP3 knockdown or overexpression
Recommendation: Use multiple antibodies targeting different epitopes to confirm findings
Subcellular Localization:
Tissue Heterogeneity:
Challenge: Variable NRIP3 expression across different cell types within a tissue
Solution: Laser capture microdissection to isolate specific cell populations
Recommendation: Use serial sections for correlation with cell type-specific markers
Quantification Methods:
Challenge: Establishing consistent scoring systems for immunohistochemistry
Solution: Digital pathology with automated scoring algorithms
Recommendation: Implement H-score or Allred scoring systems for semi-quantitative assessment
Sample Preservation:
Challenge: Protein degradation in archived samples
Solution: Optimize protocols for protein extraction from FFPE tissues
Recommendation: When possible, utilize fresh-frozen tissue for more reliable protein detection
These approaches have been successfully implemented in colorectal cancer research, where immunohistochemistry assays demonstrated significant differences in NRIP3 expression between tumor and margin tissues, with correlation to methylation status .
NRIP3 exhibits remarkably distinct functions across different cancer types, highlighting the importance of tissue context in determining its role:
Esophageal Squamous Cell Carcinoma (ESCC):
Oncogenic Function: NRIP3 promotes tumor cell growth
Therapy Resistance: Confers resistance to chemoradiotherapy (CRT)
Molecular Mechanism: Functions through a NRIP3-PPARα-DDI1-RTF2 axis
NRIP3 increases and binds to DDI1 and RTF2, accelerating RTF2 removal
Clinical Correlation: Elevated NRIP3 levels associate with poor outcomes in patients receiving radiotherapy and/or cisplatin-based chemotherapy
Colorectal Cancer (CRC):
Tumor-Suppressive Function: Inhibits cell proliferation, colony formation, invasion, and migration
Cell Cycle Regulation: Induces G1/S arrest
Signaling Pathway: Suppresses tumor growth by inhibiting PI3K-AKT signaling
Molecular Evidence: Reexpression of NRIP3 reduces levels of MMP2, MMP7, and MMP9
Clinical Correlation: NRIP3 methylation (leading to reduced expression) associates with poor prognosis
Multivariate analysis confirms NRIP3 methylation as an independent poor prognostic marker (HR: 2.256, 95% CI: 1.069–4.761, P=0.033)
This functional dichotomy suggests that NRIP3's role is highly context-dependent and likely influenced by tissue-specific interaction partners, signaling networks, and epigenetic landscapes. Researchers must carefully consider this context-dependency when designing studies and interpreting results across different cancer types.
NRIP3 methylation shows a progressive pattern during cancer development and correlates with several clinicopathological features:
| Clinical parameter | Univariate analysis | Multivariate analysis |
|---|---|---|
| HR (95% CI) | P value | HR (95% CI) |
| NRIP3 (methylation vs unmethylation) | 2.396 (1.203–4.773) | 0.013 |
| TNM stage (III/IV vs I/II) | 4.831 (2.384–9.791) | <0.001 |
| Differentiation (low vs high or middle) | 2.420 (1.231–4.757) | 0.010 |
| Lymph node metastasis (positive vs negative) | 3.358 (1.727–6.530) | <0.001 |
This data demonstrates that NRIP3 methylation remains a significant prognostic factor even after adjusting for other clinical variables .
Therapeutic Implications:
These findings collectively suggest that NRIP3 methylation is not merely a passenger event but plays a functional role in cancer progression and could serve as a valuable biomarker.
NRIP3 significantly influences therapeutic responses through distinct mechanisms in different cancer types:
In Esophageal Squamous Cell Carcinoma (ESCC):
Therapy Resistance: NRIP3 upregulation confers resistance to chemoradiotherapy (CRT)
Molecular Mechanism: NRIP3 promotes resistance through the NRIP3-PPARα-DDI1-RTF2 axis
DNA Damage Response: NRIP3 accelerates the removal of RTF2, a key determinant for managing replication stress
Replication Stress Protection: This pathway represents a protective mechanism against DNA damage induced by chemoradiotherapy
Clinical Impact: Elevated NRIP3 correlates with poor outcomes in patients receiving radiotherapy and/or cisplatin-based chemotherapy
In Colorectal Cancer (CRC):
Synthetic Lethality: NRIP3 methylation (which reduces expression) sensitizes cells to combined PI3K and ATR/ATM inhibitors
Signaling Pathway Involvement: NRIP3 suppresses PI3K-AKT signaling, which may influence cellular response to targeted therapies
Cell Cycle Effects: NRIP3's role in G1/S arrest may affect sensitivity to cell cycle-targeted therapies
Potential Therapeutic Strategy: Restoring NRIP3 expression might enhance therapeutic efficacy in certain contexts
Stress Response Connection:
Epigenetic Stress Response: NRIP3 shows altered methylation patterns in response to various stressors
Potential Mechanism: This epigenetic plasticity may contribute to adaptive responses to therapeutic stress
Connection to Other Stress-Response Genes: NRIP3 methylation changes may occur alongside modifications to genes like Nr3c1, OXTR, SLC6A4, and BDNF, which are involved in stress response pathways
These findings highlight NRIP3's potential as both a predictive biomarker for therapy response and a therapeutic target for enhancing treatment efficacy. The context-dependent nature of NRIP3's effects emphasizes the need for cancer type-specific assessment when considering its role in therapeutic strategies.
The contrasting functions of NRIP3 across cancer types suggest several mechanisms that warrant investigation:
Tissue-Specific Protein Interactions:
Signaling Pathway Integration:
Cell Type-Specific Epigenetic Regulation:
Subcellular Localization Differences:
NRIP3 has been detected in both nuclear and cytoplasmic compartments
Different cancer types might exhibit different patterns of NRIP3 localization, affecting its functional interactions
Nuclear localization could promote transcriptional regulatory functions while cytoplasmic localization might favor signaling pathway interactions
Post-Translational Modifications:
Cancer type-specific patterns of phosphorylation, ubiquitination, or other modifications could alter NRIP3 function
These modifications might affect protein stability, binding partner preferences, or enzymatic activity
Understanding these mechanisms requires integrated approaches combining proteomics, transcriptomics, and functional studies across multiple cancer types using standardized methodologies.
Evidence suggests potential connections between NRIP3 and cellular stress response pathways:
Epigenetic Regulation in Stress Conditions:
Connection to DNA Damage Response:
Potential Relationship to Glucocorticoid Signaling:
As a nuclear receptor interacting protein, NRIP3 might modulate the function of stress-related nuclear receptors
Studies have identified altered methylation in the glucocorticoid receptor gene (Nr3c1) in response to stress
NRIP3 might function within this broader network of stress-responsive epigenetic regulation
Association with Other Stress-Response Genes:
Further investigation into NRIP3's role in stress responses could reveal new insights into how cellular stress influences cancer development and therapy response, potentially identifying novel intervention points for cancer treatment.
NRIP3 shows considerable promise as both a prognostic and predictive biomarker across different cancer types:
Prognostic Value in Colorectal Cancer:
NRIP3 methylation independently predicts poor prognosis (HR: 2.256, 95% CI: 1.069–4.761, P=0.033)
Associates with clinicopathological features including late onset, poor differentiation, and lymph node metastasis
The progressive increase in methylation frequency from normal tissue (2.7%) to adenomas (32.2%) to cancer (50.6%) suggests utility as an early detection marker
Predictive Value for Therapy Response:
Clinical Implementation Considerations:
Methylation-specific PCR provides a practical method for clinical testing
NRIP3 methylation assessment could be integrated into existing molecular testing panels
Immunohistochemistry for NRIP3 protein offers a complementary approach accessible to most pathology laboratories
Potential in Liquid Biopsy:
DNA methylation markers can often be detected in circulating cell-free DNA
NRIP3 methylation might serve as a non-invasive biomarker for monitoring disease progression or treatment response
Validation Requirements:
Large-scale multicenter validation studies with standardized methodologies
Prospective clinical trials evaluating NRIP3 status as a stratification factor
Establishment of standardized cutoff values for clinical interpretation
The development of NRIP3 as a clinical biomarker would benefit from considering cancer type-specific contexts and potentially combining NRIP3 status with other molecular markers for enhanced prognostic or predictive power.
The context-dependent role of NRIP3 across different cancer types necessitates specific methodological approaches:
Comprehensive Tissue Analysis:
Systematic evaluation of NRIP3 expression, methylation, and function across multiple tissue types
Use of tissue microarrays to efficiently assess multiple samples
Inclusion of normal, pre-malignant, and malignant tissue from the same organ to track progressive changes
Standardized Experimental Systems:
Establish a panel of cell lines from different tissue origins for parallel testing
Employ identical methodologies across different cancer types to eliminate technical variability
Use isogenic cell line pairs differing only in NRIP3 status to isolate its specific effects
Context-Specific Interaction Analysis:
Perform proteomics studies to identify tissue-specific NRIP3 interactors
Use proximity ligation assays or BioID approaches to capture interactions in their native cellular context
Validate key interactions through co-immunoprecipitation and functional studies
Pathway-Specific Analyses:
Conduct focused pathway analyses (e.g., PI3K-AKT in CRC, PPARα-DDI1-RTF2 in ESCC)
Use pathway inhibitors to validate the functional significance of identified interactions
Employ reporter assays to quantify pathway activity in response to NRIP3 modulation
In Vivo Models:
Develop tissue-specific transgenic models to study NRIP3 function in different organs
Use orthotopic xenograft models to maintain appropriate tissue microenvironment
Compare systemic versus tissue-specific effects through careful experimental design
These methodological approaches can help distinguish genuine biological differences from technical artifacts and provide a more coherent understanding of NRIP3's complex, context-dependent biology.
Addressing contradictory findings about NRIP3 requires systematic approaches to distinguish biological variation from methodological differences:
Meta-Analysis and Systematic Review:
Comprehensive review of existing literature with attention to methodological details
Statistical meta-analysis where appropriate data exists
Identification of patterns in contradictions (e.g., cancer type-specific differences)
Reproducibility Studies:
Direct replication of key experiments using identical methodologies
Multi-center collaborative studies with standardized protocols
Pre-registration of study designs to reduce reporting bias
Methodological Standardization:
Development of reference materials and standards for NRIP3 detection
Validation of antibodies and primers across multiple laboratories
Establishment of common cell line models for comparative studies
Comprehensive Molecular Profiling:
Integrate transcriptomic, proteomic, and epigenomic analyses
Profile multiple cancer types using identical platforms
Identify molecular contexts associated with different NRIP3 functions
Direct Comparison Studies:
Design experiments specifically to test competing hypotheses
Include multiple cancer types within the same experimental framework
Control for variables that might explain contradictions (genetic background, experimental conditions)
Isoform-Specific Analysis:
Identify and characterize potential NRIP3 isoforms
Develop isoform-specific detection methods
Test whether different isoforms explain contradictory functional observations
These approaches can help resolve contradictions and develop a more unified understanding of NRIP3's biology that accommodates legitimate context-dependent variations in function.
Translating NRIP3 research into clinical applications requires addressing several challenges:
Biomarker Development:
Analytical Validation:
Establish reproducible, standardized assays for NRIP3 methylation and expression
Determine analytical sensitivity, specificity, and reproducibility
Validate across multiple laboratories and platforms
Clinical Validation:
Conduct large-scale studies correlating NRIP3 status with clinical outcomes
Establish clinically meaningful cutoff values
Validate in prospective clinical trials
Therapeutic Target Development:
Target Validation:
Confirm NRIP3's role in appropriate disease models
Identify patient populations most likely to benefit from NRIP3-targeted therapies
Develop pharmacodynamic biomarkers to confirm target engagement
Context-Specific Approaches:
Design inhibition strategies for contexts where NRIP3 promotes disease (e.g., ESCC)
Develop approaches to restore NRIP3 function where it acts as a tumor suppressor (e.g., CRC)
Consider combination strategies targeting NRIP3-related pathways
Clinical Trial Design:
Biomarker-Guided Patient Selection:
Stratify patients based on NRIP3 status (expression or methylation)
Consider cancer type-specific enrollment criteria
Include companion diagnostic development
Appropriate Endpoints:
Select endpoints relevant to NRIP3's biological effects
Consider intermediate biomarker endpoints (e.g., pathway activation)
Design trials with sufficient statistical power for biomarker-defined subgroups
Regulatory Considerations:
Companion Diagnostic Development:
Coordinate therapeutic and diagnostic development
Address regulatory requirements for biomarker validation
Ensure analytical performance meets clinical needs
Evidence Generation:
Design pivotal studies to meet regulatory standards
Consider accelerated approval pathways where appropriate
Plan post-approval studies to address remaining questions
These best practices can help facilitate the translation of NRIP3 research into clinical applications that meaningfully impact patient care.
NRIP3 research holds significant promise in several key areas that warrant further investigation:
Mechanistic Understanding:
Elucidation of the molecular mechanisms underlying NRIP3's context-dependent functions in different cancer types
Identification of tissue-specific interaction partners and regulatory networks
Characterization of potential NRIP3 isoforms and their functional significance
Epigenetic Regulation:
Detailed mapping of the regulatory elements controlling NRIP3 expression
Investigation of dynamic changes in NRIP3 methylation during disease progression
Exploration of potential epigenetic therapies to modulate NRIP3 expression in disease contexts
Clinical Applications:
Development and validation of NRIP3 as a prognostic biomarker in colorectal cancer
Evaluation of NRIP3 as a predictive biomarker for targeted therapy response
Investigation of NRIP3 status in non-invasive liquid biopsy approaches
Therapeutic Targeting:
Development of strategies to inhibit NRIP3 in contexts where it promotes disease
Exploration of approaches to restore NRIP3 function where it acts as a tumor suppressor
Investigation of synthetic lethal interactions, particularly in NRIP3-methylated cancers
Broader Disease Relevance:
Extension of NRIP3 research beyond the currently studied cancer types
Investigation of NRIP3's role in non-cancer diseases, particularly stress-related disorders
Exploration of potential germline variations affecting NRIP3 function
Advancing these research directions will require multidisciplinary approaches combining molecular biology, epigenetics, clinical oncology, and computational biology to fully understand and leverage NRIP3's complex biology for improved patient care.
Several methodological innovations could significantly advance NRIP3 research:
Advanced Genomic Technologies:
CRISPR-based epigenome editing to precisely modify NRIP3 methylation status
Single-cell multi-omics to characterize NRIP3 regulation and function at cellular resolution
Spatial transcriptomics and proteomics to map NRIP3 expression patterns within tissue contexts
Protein Structure and Interaction Analysis:
Cryo-EM or X-ray crystallography of NRIP3 protein complexes
Hydrogen-deuterium exchange mass spectrometry to map dynamic protein interactions
Proximity labeling approaches (BioID, APEX) to identify context-specific interactors
In Vivo Models:
Development of conditional knockout/knockin models with tissue-specific NRIP3 modulation
Patient-derived organoids to study NRIP3 function in near-native contexts
Humanized mouse models to better recapitulate human-specific aspects of NRIP3 biology
Computational Approaches:
Systems biology models integrating multi-omics data to predict NRIP3 function
Machine learning approaches to identify patterns in NRIP3 regulation across cancer types
Network analysis to contextualize NRIP3 within broader cellular processes
Translational Tools:
Development of standardized assays for clinical assessment of NRIP3 status
Digital pathology approaches for automated quantification of NRIP3 in tissue samples
Liquid biopsy methods to detect NRIP3 methylation in circulating DNA
These methodological innovations would enable more comprehensive, precise, and clinically relevant characterization of NRIP3, accelerating both basic understanding and translational applications.
The NRIP3 gene encodes a protein that is involved in the interaction with nuclear receptors. These receptors are a class of proteins found within cells that are responsible for sensing steroid and thyroid hormones and certain other molecules. The interaction between NRIP3 and these receptors is essential for the regulation of gene expression .
NRIP3 is predicted to enable aspartic-type endopeptidase activity, which means it is involved in the breakdown of proteins by cleaving peptide bonds. This activity is crucial for various cellular processes, including protein degradation and processing . The protein is predominantly localized in the cytoplasm but can shuttle between the nucleus and cytoplasm, depending on specific signals .
Mutations or dysregulation of the NRIP3 gene have been associated with several diseases, including Familial Behcet-Like Autoinflammatory Syndrome and Cone-Rod Dystrophy 20 . These conditions highlight the importance of NRIP3 in maintaining normal cellular functions and its potential role in disease pathogenesis.
Human recombinant NRIP3 is used in various research applications to study its function and role in disease. Recombinant proteins are proteins that are artificially made through the expression of recombinant DNA within living cells. These proteins are crucial for understanding the molecular mechanisms of diseases and for developing potential therapeutic interventions.