PRTFDC1 Human

What is PRTFDC1 and what are its primary functions?

PRTFDC1 (Phosphoribosyl Transferase Domain Containing 1) is a protein-coding gene that enables protein homodimerization activity and is predicted to be involved in purine ribonucleoside salvage pathways . The gene produces a protein with low, barely detectable phosphoribosyltransferase activity in vitro. It has binding affinity for GMP, IMP, and alpha-D-5-phosphoribosyl 1-pyrophosphate (PRPP), though it is not expected to significantly contribute to purine metabolism or GMP salvage under normal physiological conditions . Gene Ontology (GO) annotations related to PRTFDC1 include protein homodimerization activity and magnesium ion binding .

Where is the PRTFDC1 gene located in the human genome?

The PRTFDC1 gene is located on chromosome 10, specifically at position 10:25226229-25231340 according to PCR validation data . Previous GeneCards identifiers for this genomic location include GC10M025141, GC10M025177, and GC10M024799 . This chromosomal location information is particularly important when designing genomic studies or when investigating potential regulatory elements in the region surrounding the gene.

What protein isoforms of PRTFDC1 exist and how do they differ functionally?

At least three isoforms of PRTFDC1 are known to exist . While the complete functional differences between these isoforms have not been fully characterized in the provided sources, molecular studies of the protein indicate that all variants contain the phosphoribosyltransferase domain. Different isoforms may exhibit tissue-specific expression patterns or possess altered enzymatic efficiencies, but detailed comparative analyses of their specific functions would require targeted studies comparing their biochemical properties, cellular localization, and interaction partners.

What is the evolutionary relationship between PRTFDC1 and HPRT1?

PRTFDC1 is highly homologous to hypoxanthine phosphoribosyltransferase (HPRT1) and may have arisen from a gene duplication event of a common ancestor gene . This evolutionary relationship explains their structural similarities and partially overlapping functions. HPRT1 is considered an important paralog of PRTFDC1 . The divergence between these genes likely resulted in functional specialization, with HPRT1 maintaining stronger phosphoribosyltransferase activity compared to the weaker activity observed in PRTFDC1. This evolutionary context is important for understanding the potential redundancy and complementary roles these genes may play in purine metabolism.

How does PRTFDC1 function as a tumor suppressor gene in cancer biology?

Recent studies have shown that PRTFDC1 can act as a tumor suppressor gene, particularly in oral squamous cell carcinomas (OSCC) . The tumor suppressive function of PRTFDC1 has been demonstrated through several experimental approaches. CpG islands in the PRTFDC1 promoter can become hypermethylated in ovarian cancers and OSCC, leading to gene silencing . When PRTFDC1 expression is experimentally restored in OSCC cells, a significant inhibition of cell growth is observed in colony-formation assays . Conversely, knockdown of PRTFDC1 expression in OSCC cells that normally express the gene promotes cell growth .

These findings suggest that PRTFDC1 may regulate cell proliferation pathways, potentially through its involvement in nucleotide metabolism or through other cellular signaling mechanisms that remain to be fully characterized. The epigenetic silencing of PRTFDC1 through promoter hypermethylation represents a potential biomarker for cancer detection and prognosis, particularly in oral and ovarian cancers.

What is the relationship between PRTFDC1 and Lesch-Nyhan Syndrome?

PRTFDC1 has been associated with Lesch-Nyhan Syndrome , a rare genetic disorder typically caused by mutations in the HPRT1 gene. Given that PRTFDC1 is a paralog of HPRT1 and shares similar domain structure, it may play a compensatory or modulatory role in the pathophysiology of this syndrome. The relationship likely stems from the involvement of both genes in purine metabolism pathways, though PRTFDC1's specific contribution to the disease mechanism requires further investigation.

Methodologically, researchers investigating this relationship should consider:

• Conducting genetic association studies to identify potential PRTFDC1 variants in Lesch-Nyhan patients without HPRT1 mutations

• Examining potential interactions between PRTFDC1 and HPRT1 proteins

• Investigating whether PRTFDC1 expression changes in response to HPRT1 dysfunction

• Developing animal models with both PRTFDC1 and HPRT1 modifications to assess combined effects

What regulatory mechanisms control PRTFDC1 expression?

The regulation of PRTFDC1 expression involves epigenetic mechanisms, particularly DNA methylation. The CpG islands in the PRTFDC1 promoter can become hypermethylated in certain cancer types, leading to gene silencing . This epigenetic control suggests that PRTFDC1 expression may be dynamically regulated during development and in response to cellular stress or disease states.

To comprehensively study PRTFDC1 regulation, researchers should:

• Perform chromatin immunoprecipitation (ChIP) assays to identify transcription factors binding to the PRTFDC1 promoter

• Use bisulfite sequencing to map methylation patterns across the promoter region in different cell types

• Investigate the effects of histone modifications on PRTFDC1 expression using ChIP-seq

• Examine potential microRNA regulation using prediction algorithms followed by luciferase reporter assays

What are the most reliable methods for detecting PRTFDC1 expression in human samples?

For reliable detection of PRTFDC1 expression in human samples, researchers have several validated methodological options:

• RT-qPCR Analysis: PrimePCR assays for PRTFDC1 have been validated with high specificity (100%) and efficiency (98%) . The validated assay (qHsaCIP0032857) can detect multiple transcript variants (ENST00000320152, ENST00000376378, ENST00000376376, ENST00000358336) . When performing RT-qPCR, researchers should use intron-spanning primers to avoid genomic DNA amplification, as the gDNA Cq (39.53) is significantly higher than the cDNA Cq (21.95) .

• ELISA: Commercially available ELISA kits can detect human PRTFDC1 protein . When using this approach, optimization of sample dilutions is crucial for accurate quantification.

• Western Blotting: While not specifically mentioned in the search results, antibody-based detection of PRTFDC1 would typically employ GST-tagged recombinant proteins as positive controls.

For comprehensive expression analysis, combining nucleic acid and protein detection methods is recommended to account for potential post-transcriptional regulation.

How can I design efficient experiments to study PRTFDC1's role in tumor suppression?

To effectively investigate PRTFDC1's tumor suppressive function, a multi-faceted experimental approach is recommended:

• Expression Modulation Studies:

  • Overexpression experiments using validated expression vectors containing the PRTFDC1 coding sequence in cancer cell lines with low endogenous expression

  • RNA interference (siRNA or shRNA) to knockdown PRTFDC1 in cells with high endogenous expression

  • CRISPR-Cas9 gene editing to create isogenic cell lines with PRTFDC1 knockout

• Functional Assays:

  • Colony formation assays to assess clonogenic potential (as previously validated)

  • Cell proliferation assays (MTT, BrdU incorporation)

  • Cell cycle analysis using flow cytometry

  • Apoptosis assays (Annexin V/PI staining, caspase activity)

  • Migration and invasion assays to assess metastatic potential

• Methylation Analysis:

  • Bisulfite sequencing of the PRTFDC1 promoter region in tumor vs. normal samples

  • Treatment with demethylating agents (5-aza-2′-deoxycytidine) to restore expression

• In vivo Studies:

  • Xenograft models using cell lines with modulated PRTFDC1 expression

  • Patient-derived xenografts to maintain tumor heterogeneity

This comprehensive approach allows for validation of findings across multiple experimental systems and provides stronger evidence for PRTFDC1's role in tumor suppression.

What considerations are important when using recombinant PRTFDC1 proteins in research?

When working with recombinant PRTFDC1 proteins, several important considerations should guide experimental design:

• Protein Stability: Recombinant PRTFDC1 proteins should be stored at -80°C and aliquoted to avoid repeated freeze-thaw cycles which could compromise protein activity .

• Buffer Compatibility: The storage buffer (typically 50 mM Tris-HCl, 10 mM reduced Glutathione, pH 8.0) may affect downstream applications and should be considered when designing binding or activity assays.

• Tag Influence: Common tags such as GST can affect protein folding, activity, and interactions. Control experiments with tag-only proteins should be included to account for potential tag-specific effects.

• Shelf Life: Best results are typically obtained when using the protein within three months from the date of receipt .

• Quality Control: Verification of protein purity and integrity by SDS-PAGE is recommended before use in sensitive applications .

• Functional Validation: Given PRTFDC1's low phosphoribosyltransferase activity, sensitive assays may be required to detect enzymatic function. Controls with the more active HPRT1 paralog can provide a reference point for activity levels.

How should researchers interpret PRTFDC1 expression data in the context of cancer studies?

When interpreting PRTFDC1 expression data in cancer studies, researchers should consider several contextual factors:

• Tissue-Specific Expression Patterns:

  • Compare expression levels to matched normal tissue rather than relying on absolute values

  • Consider the normal expression pattern of PRTFDC1 across different tissue types as a baseline

• Epigenetic Context:

  • Integrate methylation data of the PRTFDC1 promoter with expression data

  • Low expression coupled with high promoter methylation strengthens evidence for epigenetic silencing

• Isoform-Specific Analysis:

  • Distinguish between expression of different PRTFDC1 isoforms when possible

  • The three known isoforms may have distinct functions or expression patterns in cancer

• Functional Correlation:

  • Correlate expression levels with functional outcomes like proliferation, invasion, or patient survival

  • Low PRTFDC1 expression correlated with increased cell growth supports its tumor suppressor role

• Statistical Considerations:

  • For PCR-based quantification, reference genes should be carefully selected and validated

  • The high efficiency (98%) of validated PRTFDC1 assays allows for accurate quantification using the ΔΔCt method

A comprehensive interpretation should integrate expression data with functional studies and clinical outcomes to establish the biological and clinical significance of PRTFDC1 alterations in specific cancer types.

What are the potential confounding factors when studying PRTFDC1 in relation to HPRT1?

Due to the evolutionary relationship and functional similarity between PRTFDC1 and HPRT1, several confounding factors must be considered:

• Sequence Homology Issues:

  • High sequence similarity may lead to cross-reactivity of antibodies

  • PCR primers must be carefully designed to ensure specificity for either gene

  • The validated PCR assay for PRTFDC1 demonstrates 100% specificity , minimizing this concern

• Functional Redundancy:

  • HPRT1 may compensate for PRTFDC1 deficiency, masking phenotypes

  • Double knockdown experiments may be necessary to reveal functions

• Differential Expression:

  • HPRT1 and PRTFDC1 may have different tissue-specific expression patterns

  • Changes in one gene may affect expression of the other through feedback mechanisms

• Pathway Complexity:

  • Both genes function within complex purine metabolism pathways

  • Effects attributed to PRTFDC1 might be indirect through alterations in nucleotide pools

• Evolutionary Conservation:

  • Cross-species comparisons must account for different evolutionary trajectories of these paralogs

  • Model organism studies should verify the presence and function of both genes

To address these confounding factors, researchers should:

• Use multiple detection methods with validated specificity

• Include controls for both genes in expression and functional studies

• Consider compensatory mechanisms in data interpretation

• Design experiments that can distinguish direct from indirect effects

How might PRTFDC1 methylation be developed as a cancer biomarker?

PRTFDC1 promoter hypermethylation has been observed in ovarian cancers and oral squamous cell carcinomas (OSCC) , suggesting potential utility as a cancer biomarker. To develop this as a clinically relevant biomarker, researchers should consider the following methodological approach:

• Biomarker Validation Strategy:

  • Conduct large-scale methylation analysis across diverse cancer cohorts

  • Compare methylation patterns in tumor vs. adjacent normal tissue

  • Correlate methylation status with clinical outcomes (survival, treatment response)

  • Determine sensitivity and specificity metrics for diagnostic applications

• Sample Collection Considerations:

  • Evaluate methylation in readily accessible samples (liquid biopsies, saliva for OSCC)

  • Assess concordance between tissue methylation and detection in circulating cell-free DNA

• Analytical Method Development:

  • Optimize methylation-specific PCR protocols for clinical laboratory implementation

  • Develop standardized cutoff values for positive/negative results

  • Ensure reproducibility across different testing platforms

• Clinical Integration:

  • Determine the appropriate clinical context for testing (screening, diagnosis, prognosis)

  • Develop testing algorithms that incorporate PRTFDC1 methylation with other biomarkers

  • Conduct prospective clinical validation studies

• Therapeutic Implications:

  • Investigate whether PRTFDC1 methylation status predicts response to demethylating agents

  • Explore targeted approaches to restore PRTFDC1 expression in hypermethylated tumors

This systematic approach would establish whether PRTFDC1 methylation can serve as a reliable and clinically actionable biomarker in specific cancer types.

What therapeutic strategies could target PRTFDC1 dysregulation in cancer?

Based on the understanding that PRTFDC1 functions as a tumor suppressor gene that is often silenced through promoter hypermethylation , several therapeutic strategies could be developed:

• Epigenetic Therapy:

  • DNA methyltransferase inhibitors (DNMTi) like 5-azacytidine or decitabine to reverse hypermethylation

  • Combination with histone deacetylase inhibitors (HDACi) for synergistic reactivation of silenced genes

  • Targeted delivery systems to enhance specificity for cancer cells

• Gene Therapy Approaches:

  • Viral vector-mediated PRTFDC1 gene delivery to restore expression

  • CRISPR-based epigenetic editing to specifically demethylate the PRTFDC1 promoter

  • mRNA therapeutics for transient expression in tumor cells

• Metabolic Pathway Modulation:

  • Targeting purine metabolism pathways to exploit vulnerabilities created by PRTFDC1 deficiency

  • Synthetic lethal approaches focusing on parallel metabolic pathways

• Combination Therapies:

  • Integrating PRTFDC1-targeted approaches with conventional chemotherapy

  • Sequencing strategies to prime tumors for enhanced response to immunotherapy

• Biomarker-Guided Treatment:

  • Using PRTFDC1 methylation status to select patients for epigenetic therapy

  • Monitoring PRTFDC1 expression as a pharmacodynamic marker of treatment efficacy

Each approach requires preclinical validation in appropriate model systems before advancing to clinical investigation. The optimal strategy may vary depending on cancer type, molecular context, and patient-specific factors.

What are the knowledge gaps in understanding PRTFDC1 function?

Despite growing recognition of PRTFDC1's importance, several significant knowledge gaps remain:

• Detailed Biochemical Function:

  • The precise substrates and reaction kinetics of PRTFDC1 remain poorly characterized

  • While it has low phosphoribosyltransferase activity in vitro , its actual physiological activity and regulation need further investigation

  • Structural studies comparing PRTFDC1 and HPRT1 could reveal differences in substrate binding and catalysis

• Cellular Signaling Roles:

  • Beyond its enzymatic function, potential roles in cellular signaling pathways remain unexplored

  • How PRTFDC1 contributes to growth suppression independent of its predicted enzymatic activity needs clarification

  • Protein interaction networks of PRTFDC1 have not been comprehensively mapped

• Isoform-Specific Functions:

  • Functional differences between the three known PRTFDC1 isoforms are not well characterized

  • Tissue-specific expression patterns and regulation of these isoforms remain to be mapped

• Physiological Relevance:

  • The role of PRTFDC1 in normal development and tissue homeostasis is unclear

  • While disease associations exist with Acute Laryngitis and Lesch-Nyhan Syndrome , the mechanistic basis of these links requires investigation

• Regulatory Mechanisms:

  • Beyond promoter methylation, other regulatory mechanisms controlling PRTFDC1 expression and function are poorly understood

  • Post-translational modifications that might regulate PRTFDC1 activity have not been extensively characterized

Addressing these knowledge gaps will require multidisciplinary approaches combining biochemistry, structural biology, cell signaling, and in vivo models.

How might single-cell analysis techniques advance PRTFDC1 research?

Single-cell analysis technologies offer powerful new approaches to address unresolved questions about PRTFDC1:

• Cell Type-Specific Expression Patterns:

  • Single-cell RNA sequencing (scRNA-seq) can reveal cell populations with distinct PRTFDC1 expression levels

  • This approach could identify specific cell types where PRTFDC1 plays critical roles in normal and disease states

  • Spatial transcriptomics can map PRTFDC1 expression within tissue architecture

• Tumor Heterogeneity Analysis:

  • Characterizing PRTFDC1 expression across diverse cell populations within tumors

  • Identifying resistant subpopulations with altered PRTFDC1 methylation or expression

  • Tracking clonal evolution of PRTFDC1 alterations during disease progression

• Epigenetic Profiling:

  • Single-cell ATAC-seq can map chromatin accessibility at the PRTFDC1 locus

  • Single-cell bisulfite sequencing can reveal heterogeneity in PRTFDC1 promoter methylation

  • Integrating these data with expression analysis to establish direct regulatory relationships

• Protein-Level Analysis:

  • Single-cell proteomics and phosphoproteomics to assess PRTFDC1 protein levels and modifications

  • Mass cytometry (CyTOF) with PRTFDC1-specific antibodies to track protein expression in relation to other cellular markers

• Metabolic Analysis:

  • Single-cell metabolomics to correlate PRTFDC1 expression with purine metabolite levels

  • Identifying metabolic signatures associated with PRTFDC1 function or deficiency

These technologies would enable researchers to move beyond bulk tissue analysis to understand the context-specific functions of PRTFDC1 at unprecedented resolution, potentially revealing new therapeutic opportunities and biomarker applications.