PDGFRA Human

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

PDGFRA is a receptor tyrosine kinase (RTK) encoded by the PDGFRA gene located on chromosome 4q12. It functions as a cell surface receptor that transmits signals into the cell through signal transduction when platelet-derived growth factor binds to it. This activation triggers phosphorylation of intracellular proteins, initiating multiple signaling pathways that control critical cellular processes including proliferation, differentiation, migration, and survival .

PDGFRA signaling is particularly important for the development of numerous cell types throughout the body. The receptor is expressed in various tissues and plays crucial roles in embryonic development, tissue homeostasis, and wound healing. In the adult organism, PDGFRA continues to function in tissue maintenance and repair processes .

How are PDGFRA alterations implicated in human diseases?

PDGFRA alterations manifest in several human diseases through diverse mechanisms:

• Oncogenic mutations: PDGFRA mutations are commonly found in gastrointestinal stromal tumors (GISTs), inflammatory fibroid polyps, and gliomas .

• Gene amplifications: PDGFRA gene amplification occurs in approximately 11% of glioblastomas (GBMs), making it the second most frequently amplified receptor tyrosine kinase gene in these tumors after EGFR .

• Gene rearrangements: Chromosomal rearrangements involving PDGFRA can cause myeloid neoplasms associated with hypereosinophilia, such as PDGFRA-associated chronic eosinophilic leukemia .

• Pediatric high-grade gliomas: PDGFRA alterations have been identified in nearly 15% of pediatric high-grade glioma patients, with significantly elevated PDGFRA expression in tumors harboring PDGFRA mutation or amplification .

What methodologies are recommended for detecting PDGFRA expression in tissues?

For reliable detection of PDGFRA expression in tissues, researchers should consider the following methodological approaches:

Transcriptional analysis:

• RT-PCR for targeted gene expression analysis

• RNA sequencing for comprehensive transcriptomic profiling

• qPCR for quantitative measurement of PDGFRA mRNA levels

Protein detection:

• Immunohistochemistry (IHC) using specific anti-PDGFRA antibodies

• Western blotting for protein size and expression level assessment

• Immunofluorescence for cellular localization studies

Validation methods:

• Inclusion of appropriate positive and negative controls

• Preabsorption tests with recombinant PDGFRA to confirm antibody specificity

• Secondary antibody controls to assess background staining

When working with mouse models, researchers studying PDGFRA expression may utilize the Pdgfratm11(EGFP)Sor/J mice (PDGFRα-eGFP mice), which express enhanced green fluorescent protein (eGFP) driven by the endogenous Pdgfra promoter, allowing for direct visualization of PDGFRα+ cells .

How do PDGFRA alterations contribute to glioma development and progression?

PDGFRA alterations contribute to glioma development through multiple mechanisms that enhance tumor cell proliferation, survival, and invasiveness:

Genetic alterations:

• Gene amplification occurs in 11% of glioblastomas, creating multiple copies of the PDGFRA gene

• Intragenic deletions, such as PDGFRAΔ8,9 (deletion of exons 8 and 9), have been identified in 40% of PDGFRA-amplified GBMs

• Complex rearrangements between PDGFRA and neighboring genes like KDR can create fusion proteins with constitutive kinase activity

Histological correlations:

• PDGFRA amplification significantly correlates with oligodendroglioma histological features (p=0.0075), suggesting a role in determining tumor cell phenotype

• Tumors with PDGFRA amplification often display increased PDGFRA and Olig2 immunopositivity

Signal activation:

• PDGFRA gene rearrangements create constitutively phosphorylated tyrosine kinases that activate downstream signaling pathways independent of ligand binding

• This aberrant activation drives uncontrolled cell proliferation and survival mechanisms in tumor cells

What are the latest findings regarding PDGFRA as a therapeutic target in pediatric high-grade gliomas?

Recent research has identified PDGFRA as a promising therapeutic target for pediatric high-grade gliomas, particularly H3K27M diffuse midline gliomas (DMG), which are aggressive malignant brain tumors with poor prognosis:

Prevalence of alterations:

• A multicenter study led by Dr. Mariella Filbin analyzed genomic data from 217 pediatric high-grade glioma samples and identified PDGFRA alterations in nearly 15% of patients

• Transcriptomic data revealed significantly elevated PDGFRA expression in tumors with PDGFRA mutation or amplification

Oncogenic role:

• Elevated PDGFRA expression has been shown to drive growth of DMG tumors

• PDGFRA appears to play a multifaceted role in the pathogenesis of both adult and pediatric high-grade gliomas

Therapeutic implications:

• The study provides the first real-world clinical data supporting the use of PDGFRA inhibitors in treating certain pediatric patients with high-grade gliomas

• Tyrosine kinase inhibitors targeting PDGF receptors, such as imatinib, have shown preclinical validation for conditions involving PDGFRA alterations

How should researchers analyze PDGFRA gene amplification in tumor samples?

Proper analysis of PDGFRA gene amplification in tumor samples requires a multi-method approach for reliable results:

Quantitative PCR (qPCR):

• Design primers specific to different regions of the PDGFRA gene

• Use reference genes (e.g., 18S) for normalization

• Consider gene amplification when average DNA quantities are greater than 4-fold relative to reference samples

Array comparative genomic hybridization (aCGH):

• Provides high-resolution detection of copy number variations

• Can identify complex amplicons and rearrangements

• Particularly useful for detecting intragenic alterations within PDGFRA

Fluorescence in situ hybridization (FISH):

• Offers direct visualization of gene amplification in tissue sections

• Enables assessment of tumor heterogeneity

• Can detect focal amplifications that might be missed by other methods

Next-generation sequencing (NGS):

• Provides comprehensive analysis of genomic alterations

• Can detect both amplifications and mutations simultaneously

• Allows for analysis of the entire PDGFRA locus and adjacent regions

Data interpretation considerations:

• Complex amplicons may involve adjacent genes (e.g., KDR)

• Gene rearrangements often accompany amplifications

• The pattern of amplification across different exons can suggest potential functional consequences

What experimental models are most appropriate for investigating PDGFRA function?

Several experimental models are available for investigating PDGFRA function, each with specific advantages for different research questions:

Cell culture models:

• Primary cells expressing endogenous PDGFRA (e.g., fibroblasts, glial cells)

• Cell lines with characterized PDGFRA expression levels

• Genetically modified cells with PDGFRA knockdown, knockout, or overexpression

• Patient-derived cells harboring specific PDGFRA mutations or amplifications

Animal models:

• PDGFRα-eGFP mice (Pdgfratm11(EGFP)Sor/J) that express eGFP in nuclei of PDGFRα+ cells, enabling visualization and isolation of cells expressing PDGFRA

• Conditional knockout mice for tissue-specific PDGFRA deletion

• Patient-derived xenograft models that maintain the genetic characteristics of human tumors

• CRISPR-engineered mice carrying specific PDGFRA mutations found in human diseases

Ex vivo systems:

• Organoid cultures that better represent tissue architecture and cellular interactions

• Tissue explants maintaining the native microenvironment of PDGFRA-expressing cells

• Co-culture systems to study interactions between PDGFRA+ cells and other cell types

How can researchers investigate PDGFRA-associated cellular senescence?

Recent research has identified links between PDGFRA expression and cellular senescence, providing methodological approaches for investigating this relationship:

Senescence induction methods:

• Irradiation-induced senescence models (particularly effective in nucleus pulposus cells)

• Oxidative stress-induced senescence

• Replicative senescence through extended passaging

Key findings from recent research:

• PDGFRA gene expression is significantly reduced in irradiation-induced senescent nucleus pulposus (NP) cells compared to non-irradiated cells

• PDGF-AB/BB treatment can modulate gene expression in senescent cells, affecting clusters related to cell cycle regulation, mesenchymal cell differentiation, and response to reduced oxygen levels

• PDGFRA appears to be a top hub gene in treated NP cells according to network analysis

Analytical approaches:

• Transcriptomic analysis to identify changes in PDGFRA and related gene expression

• Network analysis to determine the position of PDGFRA in senescence-associated gene networks

• Functional assays measuring senescence-associated phenotypes (e.g., β-galactosidase activity, cell cycle arrest)

• Assessment of senescence-associated secretory phenotype (SASP) in relation to PDGFRA expression

What techniques are optimal for studying PDGFRA signaling pathways?

Investigating PDGFRA signaling pathways requires specialized techniques to capture the complex dynamics of receptor activation and downstream effects:

Receptor activation analysis:

• Phospho-specific antibodies to detect activated PDGFRA

• Immunoprecipitation followed by western blotting for phosphotyrosine detection

• Proximity ligation assays to visualize protein-protein interactions in situ

• FRET/BRET techniques for real-time monitoring of receptor activation

Downstream signaling assessment:

• Phospho-proteomics to identify phosphorylation events triggered by PDGFRA activation

• Kinase activity assays for key downstream effectors

• Transcriptional profiling to identify genes regulated by PDGFRA signaling

• Pathway inhibitors to dissect specific branches of PDGFRA-activated pathways

Functional readouts:

• Proliferation assays (e.g., EdU incorporation, Ki67 staining)

• Migration assays (e.g., wound healing, transwell)

• Survival assays under stress conditions

• Differentiation markers to assess cell fate decisions

How do PDGFRA mutations correlate with clinical outcomes in different human diseases?

The relationship between PDGFRA mutations and clinical outcomes varies across different human diseases:

Gastrointestinal stromal tumors (GISTs):

• PDGFRA mutations are found in approximately 5-10% of GISTs

• D842V mutation in exon 18 is associated with resistance to imatinib therapy

• Non-D842V mutations generally confer better prognosis and response to targeted therapies

Glioblastoma (GBM):

• PDGFRA amplification occurs in 11% of GBMs, making it the second most frequent RTK gene amplified in these tumors

• PDGFRA amplification is associated with oligodendroglioma histological features

• The PDGFRAΔ8,9 mutant is found in 40% of PDGFRA-amplified GBMs

Pediatric high-grade gliomas:

• PDGFRA alterations are present in nearly 15% of pediatric high-grade glioma patients

• Elevated PDGFRA expression is a key driver of diffuse midline glioma (DMG) tumor growth

• Recent clinical data supports targeting PDGFRA as a therapeutic approach in these devastating tumors

PDGFRA-associated chronic eosinophilic leukemia:

• Often involves FIP1L1-PDGFRA fusion gene resulting from deletion of material from chromosome 4

• Patients typically respond well to imatinib therapy

• Response to therapy correlates with the specific fusion partner and breakpoint location

What are the current approaches for targeting PDGFRA in cancer therapy?

Several approaches are being employed to target PDGFRA in cancer therapy, with varying degrees of success:

Tyrosine kinase inhibitors (TKIs):

• Imatinib has been preclinically validated for conditions involving PDGFRA alterations

• Crenolanib demonstrates activity against the imatinib-resistant D842V mutation

• Avapritinib is highly potent against PDGFRA exon 18 mutations

• Dasatinib and nilotinib show activity against certain PDGFRA mutants

Resistance mechanisms:

• Point mutations in the kinase domain (especially gatekeeper mutations)

• Activation of alternative signaling pathways

• Increased drug efflux via ABC transporters

• Epigenetic alterations affecting drug sensitivity

Emerging therapeutic strategies:

• Antibody-drug conjugates targeting PDGFRA

• Combination therapies targeting multiple RTKs simultaneously

• PROTAC-based approaches for PDGFRA degradation

• Immunotherapies directed against PDGFRA-altered cells

How should researchers design clinical trials targeting PDGFRA alterations?

Effective clinical trial design for targeting PDGFRA alterations requires careful consideration of several factors:

Patient selection criteria:

• Comprehensive molecular profiling to identify specific PDGFRA alterations

• Stratification based on mutation type, amplification status, or fusion variants

• Consideration of co-occurring genomic alterations that may affect response

• Analysis of PDGFRA expression levels in addition to genetic alterations

Biomarker development:

• Establish reliable assays for detecting PDGFRA alterations in tissue and liquid biopsies

• Develop pharmacodynamic markers of target engagement

• Identify predictive biomarkers of response and resistance

• Monitor clonal evolution during treatment

Trial design considerations:

• Basket trials enrolling patients based on PDGFRA alterations across tumor types

• Umbrella trials testing multiple agents against different PDGFRA alterations

• Incorporation of adaptive designs to modify treatment based on early response signals

• Inclusion of crossover options to maintain patient access to experimental therapies

What emerging technologies might advance PDGFRA research?

Several cutting-edge technologies hold promise for advancing PDGFRA research:

Single-cell technologies:

• Single-cell RNA sequencing to define heterogeneity in PDGFRA expression

• Single-cell proteomics to characterize PDGFRA signaling at the individual cell level

• Spatial transcriptomics to map PDGFRA expression within tissue architecture

• CRISPR screening at single-cell resolution to identify modifiers of PDGFRA function

Advanced imaging:

• Super-resolution microscopy for visualizing PDGFRA distribution and clustering

• Live-cell imaging with fluorescent biosensors to track PDGFRA activation in real-time

• Intravital microscopy to observe PDGFRA+ cells in their native environment in vivo

• Correlative light and electron microscopy to link PDGFRA localization with ultrastructure

Computational approaches:

• AI-driven analysis of PDGFRA signaling networks

• Systems biology modeling of PDGFRA pathway dynamics

• Integration of multi-omics data to comprehensively characterize PDGFRA function

• Virtual screening and molecular dynamics simulations for drug discovery

What are the unexplored aspects of PDGFRA function that warrant investigation?

Despite extensive research, several aspects of PDGFRA biology remain underexplored:

Non-canonical functions:

• Nuclear localization and potential transcriptional regulation

• Ligand-independent signaling mechanisms

• Interactions with non-traditional binding partners

• Potential roles in cellular metabolism regulation

Developmental roles:

• Fine-grained spatiotemporal mapping of PDGFRA expression during embryogenesis

• Cell fate decisions influenced by PDGFRA signaling

• Interaction with other developmental pathways (e.g., Hedgehog, Wnt)

• Role in tissue repair and regeneration in adults

Microenvironmental interactions:

• Communication between PDGFRA+ cells and immune components

• Role in extracellular matrix remodeling and tissue architecture

• Contribution to formation of specialized niches (e.g., perivascular, subepithelial)

• Response to mechanical forces and tissue stiffness

Translational opportunities:

• Exploration of PDGFRA as a target in diseases beyond cancer

• Development of PDGFRA-targeted cellular therapies

• Investigation of PDGFRA in aging and age-related diseases

• Potential for PDGFRA modulation in regenerative medicine approaches