Browse PDLIM7

Summary
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
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 Cytoplasm Cytoplasm, cytoskeleton Note=Colocalizes with RET to the cell periphery and in some cytoskeletal components. Colocalizes with TPM2 near the Z line in muscle. Colocalizes with TBX4 and TBX5 to actin filaments (By similarity).
Domain PF00412 LIM domain
PF00595 PDZ domain (Also known as DHR or GLGF)
Function

May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway (By similarity).

> Gene Ontology
 
Biological Process GO:0001503 ossification
GO:0001649 osteoblast differentiation
GO:0006898 receptor-mediated endocytosis
GO:0030278 regulation of ossification
GO:0045667 regulation of osteoblast differentiation
GO:0045669 positive regulation of osteoblast differentiation
GO:0045778 positive regulation of ossification
Molecular Function -
Cellular Component GO:0001725 stress fiber
GO:0001726 ruffle
GO:0005924 cell-substrate adherens junction
GO:0005925 focal adhesion
GO:0015629 actin cytoskeleton
GO:0030055 cell-substrate junction
GO:0031252 cell leading edge
GO:0032432 actin filament bundle
GO:0042641 actomyosin
GO:0097517 contractile actin filament bundle
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-422475: Axon guidance
R-HSA-1266738: Developmental Biology
R-HSA-8853659: RET signaling
Summary
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between PDLIM7 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
 
  Literatures describing the relation between PDLIM7 and anti-tumor immunity in human cancer.
PMID Cancer type Relation to immunity Evidence sentences
22588558Nasopharyngeal CarcinomaPromote immunityThese findings raise the possibility that c-Myc activation in nasopharyngeal carcinoma (NPC) might antagonise the effect of LMP1 on HLA class I expression thus contributing to immune escape of tumour cells.
29360818EBV-positive malignanciesPromote immunity (T cell function); Essential for immunotherapyBoth human CD8 and CD4 T-cells expressing the LMP1-TCR provoked high levels of cytokine secretion and cytolytic activity towards peptide-pulsed and LMP1-expressing tumour cells.
16479544Hodgkin Lymphoma; Nasopharyngeal Carcinoma; Primary EBV-Positive Nodal T-Cell or NK-Cell Lymphoma; Chronic Active EBV Infection of T-and NK-Cell Type, Systemic FormPromote immunity (T and NK cell function); essential for immunotherapyEpstein-Barr virus (EBV) latent membrane protein-1-specific cytotoxic T lymphocytes targeting EBV-carrying natural killer cell malignancies. Epstein-Barr virus (EBV)-encoded latent membrane protein (LMP) 1 is a potential target for immunotherapy of some proportion of Hodgkin's disease cases, nasopharyngeal carcinomas, EBV-associated natural killer (NK)/T lymphomas, and chronic active EBV infection (CAEBV).
29675003Gastric CarcinomaInhibit immunityIn addition, a growing body of evidence demonstrates that exosomes contain genetic material of viruses and viral miRNAs and proteins such as EBV latent membrane protein 1 (LMP1) which are delivered into recipient cells.
28732079Nasopharyngeal CarcinomaInhibit immunityLMP1-mediated glycolysis induces myeloid-derived suppressor cell expansion in nasopharyngeal carcinoma. LMP1 promotes the expression of multiple glycolytic genes, including GLUT1. This metabolic reprogramming results in increased expression of the Nod-like receptor family protein 3 (NLRP3) inflammasome, COX-2 and P-p65 and, consequently, increased production of IL-1β, IL-6 and GM-CSF. This work indicates that LMP1-mediated glycolysis regulates IL-1β, IL-6 and GM-CSF production through the NLRP3 inflammasome, COX-2 and P-p65 signaling pathways to enhance tumor-associated MDSC expansion, which leads to tumor immunosuppression in NPC.
28077657LymphomaInhibit immunityLatent Membrane Protein 1 (LMP1) and LMP2A Collaborate To Promote Epstein-Barr Virus-Induced B Cell Lymphomas in a Cord Blood-Humanized Mouse Model but Are Not Essential. Thus, the expression of either LMP1 or LMP2A may be sufficient to promote early-onset EBV-induced tumors in this model. The simultaneous deletion of both LMP1 and LMP2A results in fewer tumors and a further delay in tumor onset.
24344220LymphomaImmunotherapy targetTumor cells from approximately 40% of patients with Hodgkin or non-Hodgkin lymphoma express the type II latency Epstein-Barr virus (EBV) antigens latent membrane protein 1 (LMP1) and LMP2, which represent attractive targets for immunotherapy. Autologous T cells directed to the LMP2 or LMP1 and LMP2 antigens can induce durable complete responses without significant toxicity.
Summary
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
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 PDLIM7 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
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
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 PDLIM7 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.7290.0515
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-1.1530.642
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.4220.822
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.7320.208
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.380.89
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47-1.1750.74
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.1110.801
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.1670.899
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.440.758
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.8780.615
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 281.7850.467
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.5440.000112
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of PDLIM7 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) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 41407.1-7.11
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27730001
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27590001
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91606.2-6.21
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59011.1-11.11
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38275.305.30.507
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22134.504.51
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16146.206.21
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
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of PDLIM7. 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
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of PDLIM7. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by PDLIM7.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of PDLIM7. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of PDLIM7 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between PDLIM7 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolPDLIM7
NamePDZ and LIM domain 7 (enigma)
Aliases ENIGMA; LMP1; LMP3; 1110003B01Rik; LMP; Lim mineralization protein 3; protein enigma; LIM mineralization pro ......
Chromosomal Location5q35.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting PDLIM7 collected from DrugBank database.
> Drugs from DrugBank database
 

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