PDLIM1 Human

What is PDLIM1 and what are its alternative names?

PDLIM1, also known as CLP36 (36 kDa carboxy-terminal LIM domain protein), Elfin, or CLIM1, is a member of the PDZ-LIM protein family. It is a cytoskeletal protein composed of 329 amino acids that functions as a platform for protein complex formation . The protein exhibits high conservation and homology in structure across species, indicating its evolutionary importance .

What domains are present in PDLIM1 and what are their functions?

PDLIM1 contains two primary functional domains:

• PDZ domain: Located at the amino-terminal region, this domain shares 55% identity with human ALP and 66% identity with human RIL . The PDZ domain mediates interactions with cytoskeletal components, particularly α-actinin.

• LIM domain: Located at the carboxy-terminal region, this domain consists of two zinc finger domains with a consistent cysteine-rich sequence: (Cys-X₂-Cys-X₁₇±₁-His-X₂-Cys)-X₂-(Cys-X₂-Cys-X₁₇±₁-Cys-X₂-His/Asp/Cys) . The LIM domain facilitates interactions with various proteins, including kinases and actin cytoskeletal components .

What are the primary cellular functions of PDLIM1?

PDLIM1 serves multiple cellular functions:

• Acts as a scaffold to promote protein complex formation, thereby regulating signaling pathways

• Participates in cytoskeleton regulation through interaction with α-actinin and stress fibers

• Contributes to neurite outgrowth and growth cone movements

• Recruits signaling molecules to stress fibers, as evidenced by its interaction with CLP-36 interacting kinase 1 (Clik1)

• Localizes to actin-rich structures induced by invasive bacterial pathogens

How is PDLIM1 expression regulated at the post-transcriptional level?

PDLIM1 expression is regulated by microRNAs, particularly miR-3940-5p in the context of diffuse large B-cell lymphoma (DLBCL). This was identified through a dual approach combining computational prediction and expression analysis . The computational prediction using TargetScan resources identified 154 miRNAs that potentially interact with PDLIM1, while analysis of GSE173080 microarray data from the Gene Expression Omnibus (GEO) identified 75 miRNAs with reduced expression in DLBCL . The intersection of these approaches revealed four potential regulatory miRNAs: hsa-miR-107, hsa-miR-141-3p, hsa-miR-4763-3p, and hsa-miR-3940-5p .

What is the tissue distribution pattern of PDLIM1 in humans?

PDLIM1 exhibits a widespread distribution in human tissues, including the lung, heart, spleen, and liver . Its function varies across tissues due to its interactions with different proteins in a tissue-specific manner . In the nervous system, PDLIM1 is expressed in sensory ganglia of adult rats but not in the central nervous system, with increased expression in peripheral sensory neurons and motor neurons following sciatic nerve transection .

How can PDLIM1 expression be experimentally manipulated in cellular models?

Based on the research methodologies described in the literature:

• RNA interference: Short hairpin RNA (shRNA) has been successfully used to knock down PDLIM1 expression in DLBCL cells, resulting in reduced cell proliferation and increased apoptosis .

• Overexpression systems: Plasmid-based overexpression of PDLIM1 or its specific domains (e.g., PDZ domain) has been utilized to study gain-of-function effects in various cell types .

• microRNA modulation: Upregulation of miR-3940-5p has been shown to negatively modulate PDLIM1 expression and function, affecting the malignant phenotype of DLBCL cells .

What is the expression pattern of PDLIM1 in diffuse large B-cell lymphoma (DLBCL)?

PDLIM1 shows elevated expression in DLBCL cells and tissues compared to non-carcinoma samples, as demonstrated by multiple analytical approaches:

• Gene Expression Profiling Interactive Analysis (GEPIA) revealed high PDLIM1 expression in DLBCL samples .

• Real-time quantitative PCR (qRT-PCR) analysis of 76 DLBCL and 76 matched non-carcinoma clinical samples confirmed significantly increased PDLIM1 expression in tumor samples .

• Western blot analysis further confirmed elevated PDLIM1 protein levels in DLBCL samples compared to non-carcinoma samples .

How does PDLIM1 expression correlate with clinical outcomes in DLBCL patients?

PDLIM1 expression levels correlate significantly with clinical outcomes in DLBCL patients:

These correlations indicate that high PDLIM1 expression is associated with more advanced disease and worse prognostic indicators .

What functional effects result from PDLIM1 knockdown in DLBCL cells?

Knockdown of PDLIM1 in DLBCL cells results in several significant functional changes:

• Reduced cell proliferation, indicating PDLIM1's role in promoting cancer cell growth .

• Increased DLBCL cell apoptosis, suggesting PDLIM1's involvement in cell survival mechanisms .

• Diminished tumorigenesis of DLBCL cells in nude mice models, demonstrating PDLIM1's role in tumor development in vivo .

These findings suggest that PDLIM1 has a critical effect on DLBCL cell growth and survival, highlighting its potential as a therapeutic target for DLBCL treatment .

What are the key protein interaction partners of PDLIM1?

PDLIM1 interacts with multiple proteins through its PDZ and LIM domains:

• α-actinin family members: PDLIM1 forms complexes with α-actinin-1/4 in colonic epithelial cells and localizes to actin stress fibers . It also interacts with α-actinin-2 in human myocardium .

• Cytoskeletal proteins: Through immunoprecipitation and mass spectrometric analysis, PDLIM1 has been shown to interact with the cytoskeleton cross-linking protein ACTN4 in hepatocellular carcinoma (HCC) cells .

• Kinases: PDLIM1 interacts with CLP-36 interacting kinase 1 (Clik1) through its LIM domain, causing a dramatic relocation of Clik1 from the nucleus to actin stress fibers .

• Other interaction partners: Paladin, FHL1, and EGFR have also been identified as PDLIM1 interaction partners .

How does PDLIM1 regulate the Hippo signaling pathway in cancer cells?

In hepatocellular carcinoma (HCC), PDLIM1 regulates the Hippo signaling pathway through the following mechanism:

• PDLIM1 competitively binds to ACTN4 through Asn145 (N145), weakening the interaction between ACTN4 and F-actin and preventing overgrowth of F-actin .

• Loss of PDLIM1 in HCC cells leads to excessive F-actin formation, which induces LATS1 dephosphorylation .

• Dephosphorylated LATS1 inactivates the Hippo pathway, promoting HCC metastasis .

• Low expression of PDLIM1 is associated with poor prognosis in HCC patients, consistent with its role in suppressing metastasis through this pathway .

What is the functional relationship between PDLIM1 and miR-3940-5p in DLBCL?

The miR-3940-5p/PDLIM1 axis plays a crucial role in DLBCL pathogenesis:

• miR-3940-5p has been identified as an upstream regulator of PDLIM1 in DLBCL cells .

• PDLIM1 expression and function are negatively modulated by the upregulation of miR-3940-5p .

• This negative regulation affects the malignant phenotype of DLBCL cells, influencing cell proliferation, apoptosis, and tumorigenesis .

• The miR-3940-5p/PDLIM1 regulatory axis could potentially be exploited for therapeutic interventions in DLBCL .

What techniques are recommended for analyzing PDLIM1 expression in patient samples?

Based on successful approaches documented in the literature:

• Gene expression analysis: Utilizing databases like Gene Expression Omnibus (GEO) and tools like Gene Expression Profiling Interactive Analysis (GEPIA) to analyze PDLIM1 expression patterns across different tissues and cancer types .

• Real-time quantitative PCR (qRT-PCR): For quantifying PDLIM1 mRNA levels in clinical samples and cell lines. This method has successfully demonstrated elevated PDLIM1 expression in DLBCL compared to non-carcinoma samples .

• Western blot analysis: For determining PDLIM1 protein levels in tissues and cells, confirming expression patterns observed at the mRNA level .

• Immunohistochemistry: Although not explicitly mentioned in the provided sources, immunohistochemistry would be an appropriate method for visualizing PDLIM1 expression in tissue sections.

What in vivo models can be used to study PDLIM1 function in cancer?

The literature describes the use of nude mice models to study PDLIM1 function in DLBCL:

• Xenograft models: DLBCL cells with shRNA-mediated PDLIM1 knockdown can be implanted in nude mice to assess the effect on tumorigenesis .

• DLBCL mouse model: This model has been used to explore the interaction between PDLIM1 and miR-3940-5p and its effects on DLBCL cellular activities and cancer development .

These models allow researchers to assess the impact of PDLIM1 manipulation on tumor growth, invasion, and metastasis in a physiologically relevant environment.

What approaches can identify microRNA regulators of PDLIM1?

A dual approach combining computational prediction and expression analysis has been successful in identifying miRNA regulators of PDLIM1:

• Computational prediction: Using resources like TargetScan (https://www.targetscan.org/) to identify potential miRNAs that may interact with PDLIM1 based on sequence complementarity .

• Expression analysis: Analyzing microarray data from databases like the Gene Expression Omnibus (GEO) to identify miRNAs with altered expression patterns in relevant cancer types .

• Intersection analysis: Finding the overlap between computationally predicted miRNAs and those showing differential expression in cancer vs. normal tissues .

• Experimental validation: Confirming miRNA-PDLIM1 interactions through luciferase reporter assays, site-directed mutagenesis, and functional studies examining the effects of miRNA overexpression or inhibition on PDLIM1 levels and cellular phenotypes .

How might PDLIM1 serve as a therapeutic target in cancer?

PDLIM1 shows potential as a therapeutic target in cancer, particularly DLBCL, based on several findings:

What are the context-dependent roles of PDLIM1 in different cancer types?

PDLIM1 exhibits context-dependent functions across different cancer types:

• Diffuse Large B-cell Lymphoma (DLBCL): PDLIM1 is upregulated and promotes cell growth and survival. Its high expression correlates with poor clinical outcomes .

• Colorectal Cancer (CRC): PDLIM1 may serve as a marker of tumor aggressiveness and as a predictor of survival in CRC patients . Interestingly, PDLIM1 in neonatal human foreskin fibroblasts (neoHFFs) can act as a pro-invasive regulator when activated by late-stage colorectal cancer-exosomes .

• Hepatocellular Carcinoma (HCC): PDLIM1 appears to have a tumor-suppressive role in HCC by preventing excessive F-actin formation and inhibiting the metastatic potential of HCC cells through regulation of the Hippo pathway .

These divergent roles highlight the importance of understanding the tissue-specific and context-dependent functions of PDLIM1 in cancer biology.

What are the key unresolved questions about PDLIM1 in human disease?

Several important questions about PDLIM1 remain to be fully addressed:

• Mechanism of action in different tissues: While PDLIM1 interacts with different proteins across diverse tissues, the precise mechanisms by which it exerts its functions in a tissue-specific manner are not entirely understood .

• Functional consequences of Clik1 relocation: Although PDLIM1 interaction causes Clik1 to relocate from the nucleus to actin stress fibers, whether this relocation leads to changes in Clik1 function remains to be explored .

• Role in bacterial pathogen interaction: PDLIM1 resides in actin-rich structures induced by invasive bacterial pathogens, but the specific mechanism and significance of this localization need further study .

• Therapeutic targeting strategies: The optimal approaches for targeting PDLIM1 or its regulatory pathways in cancer therapy remain to be determined.

• Comprehensive interactome: A complete map of PDLIM1 interaction partners across different tissues and disease states would provide valuable insights into its multifaceted roles.