Browse PDLIM4

Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Isoform 1: Cytoplasm, cytoskeleton Nucleus Cytoplasm Cytoplasm, perinuclear region Cell projection, lamellipodium Cell projection, dendritic spine Early endosome membrane Peripheral membrane protein Cytoplasmic side Recycling endosome membrane Peripheral membrane protein Cytoplasmic side Cell junction, synapse, synaptosome Note=Localizes to actin stress fibers in nonmuscle cells. Colocalizes with GRIA1 in early endosomes. Enriched in numerous but not all spine-like structures along dendritic branches. Colocalizes with actin and enriched at sites containing larger amounts of actin and alpha-actinin. Targeted efficiently to spines via its PDZ domain-mediated interaction with the alpha-actinin/actin cytoskeletal complex. Localizes to synaptosomes in brain (By similarity). Colocalizes with F-actin (PubMed:10826496). Colocalizes with TRIP6 at cell-cell contacts and lamellipodia (PubMed:10826496). In the cytoplasm, displays a fibrillar pattern with characteristic thick fibers and occasional clusters. Colocalizes with the actin stress fibers. Oxidative stress induces redistribution from cytoskeleton to cytosol (PubMed:21636573). Colocalizes with SRC at the perinuclear region, but not at focal adhesions (PubMed:19307596). ; SUBCELLULAR LOCATION: Isoform 2: Cytoplasm Note=Stains more diffusely in the cytoplasm with thin fibers forming a dense mesh-like pattern.
Domain PF15936 Domain of unknown function (DUF4749)
PF00412 LIM domain
PF00595 PDZ domain (Also known as DHR or GLGF)
Function

Isoform 1: Suppresses SRC activation by recognizing and binding to active SRC and facilitating PTPN13-mediated dephosphorylation of SRC 'Tyr-419' leading to its inactivation. Inactivated SRC dissociates from this protein allowing the initiation of a new SRC inactivation cycle (PubMed:19307596). Involved in reorganization of the actin cytoskeleton (PubMed:21636573). In nonmuscle cells, binds to ACTN1 (alpha-actinin-1), increases the affinity of ACTN1 to F-actin (filamentous actin), and promotes formation of actin stress fibers. Involved in regulation of the synaptic AMPA receptor transport in dendritic spines of hippocampal pyramidal neurons directing the receptors toward an insertion at the postsynaptic membrane. Links endosomal surface-internalized GRIA1-containing AMPA receptors to the alpha-actinin/actin cytoskeleton. Increases AMPA receptor-mediated excitatory postsynaptic currents in neurons (By similarity). ; FUNCTION: Isoform 2: Involved in reorganization of the actin cytoskeleton and in regulation of cell migration. In response to oxidative stress, binds to NQO1, which stabilizes it and protects it from ubiquitin-independent degradation by the core 20S proteasome. Stabilized protein is able to heterodimerize with isoform 1 changing the subcellular location of it from cytoskeleton and nuclei to cytosol, leading to loss of isoforms 1 ability to induce formation of actin stress fibers. Counteracts the effects produced by isoform 1 on organization of actin cytoskeleton and cell motility to fine-tune actin cytoskeleton rearrangement and to attenuate cell migration.

> Gene Ontology
 
Biological Process -
Molecular Function -
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG -
Reactome -
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between PDLIM4 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.

Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of PDLIM4 in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of PDLIM4 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.0520.943
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-0.7240.67
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)870.4380.746
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.6970.198
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-1.1540.496
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47-0.1220.954
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.6230.399
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.0330.978
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11121.3060.303
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 48-0.0840.947
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 28-0.1080.948
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.6710.000436
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of PDLIM4 in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 141705.9-5.91
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 103033.3-33.30.231
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27730001
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27590001
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21174.804.81
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13117.707.71
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of PDLIM4. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of PDLIM4. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by PDLIM4.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of PDLIM4. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of PDLIM4 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between PDLIM4 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolPDLIM4
NamePDZ and LIM domain 4
Aliases RIL; LIM protein RIL; reversion-induced LIM protein; PDZ and LIM domain protein 4
Chromosomal Location5q31.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting PDLIM4 collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.