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NGFR (nerve growth factor receptor)

Written2015-12Nobuyuki Tanaka
Cancer Immunobiology, Miyagi Cancer Center Research Institute; tanaka@med.tohoku.ac.jp

Abstract Review on NGFR, with data on DNA, on the protein encoded, and where the gene is implicated.

(Note : for Links provided by Atlas : click)

Identity

Alias_namesnerve growth factor receptor (TNFR superfamily
Alias_symbol (synonym)TNFRSF16
CD271
p75NTR
Other aliasp75(NTR)
Gp80-LNGFR
HGNC (Hugo) NGFR
LocusID (NCBI) 4804
Atlas_Id 41535
Location 17q21.33 Size: 19,728 bases; orientation: plus strand.  [Link to chromosome band 17q21]
Location_base_pair Starts at 47572655 and ends at 47592382 bp from pter ( according to hg19-Feb_2009)  [Mapping NGFR.png]
Fusion genes
(updated 2016)
CD248 (11q13.2) / NGFR (17q21.33)NGFR (17q21.33) / SPAG9 (17q21.33)SMURF2 (17q23.3) / NGFR (17q21.33)
SPAG9 (17q21.33) / NGFR (17q21.33)

DNA/RNA

Note NGFR is a member of the Tumor Necrosis Factor receptor (TNFR) superfamily. It serves as a low-affinity common receptor subunit for multiple neurotrohins (NGF, BDNF, NTF3 (NT-3) and NTF4 (NT-4/5)) (Tomellini et al. et al., 2014). It lacks any enzymatic activity, and mediates signals through interacting protein partners.
Transcription The transcript encodes 427 amino acids, including a signal peptide sequence.

Protein

Description Nerve growth factor receptor (NGFR) is a low affinity cell surface receptor for NGF. It is a member of the Tumor Necrosis Factor receptor (TNFR) superfamily, and thus anonymously called TNFRSF16. NGFR not only serves as a common receptor subunit for neurotrophins (NGF, BDNF, NT-3 and NT-4/5), but also binds their precursors (pro-neurotrophins), pro-NGF, pro-BDNF, pro-NT-3 and pro-NT-4/5. It also works as a co-receptor with other receptor partners, such as SORT1 (Sortilin), LINGO1 and RTN4R (Nogo receptor/NOGO-R)(Wang et al. et al., 2002; Bronfman et al. et al., 2004; Mi et al. et al., 2004; Meabon et al. et al., 2015).
NGFR consists of 427-amino-acid in overall length, and possesses an extracellular region with four 40 amino acid repeats with 6 cysteins at conserved positions followed by a serine/threonine-rich region, a single transmembrane domain, and a 155 amino acid cytoplasmic domain. The extracellular receives N- and O- glycosylations, and the cysteine-rich region conserved among the TNFR superfamily is licensing it as a similar receptor. The intracellular region lacks any catalytic domain, instead it possesses a death domain implicated in protein-protein interaction. Therefore, its signaling potential is dependent on protein-protein interactions.
NGFR receives proteolytic processing. Extracellular cleavage is mediated by ADAM17/TACE, which modifies NGFR to a smaller 28-kDa membrane-bound C-terminal fragment (p75-CTF). Further processing of p75-CTF by γ-secretase releases the intracellular domain (p75-ICD), which is implicated in cell death (Underwood et al. et al., 2008). Recent report indicates that the most abundant homotypic arrangement for NGFR is a trimer, and both of the monomers and trimers coexist (Anastasia et al. et al., 2015). In neurons, the trimers are not required for NGFR activation irrespective of ligand stimulation, whereas monomers are capable of conferring acute responses. Activation of NGFR is context-dependent, where the oligomerization status and expression amount determine the biological effect, and the trimers seem to sequester NGFR from an active form.
Expression NGFR is expressed in a wide variety of tissues, such as brain, peripheral neurons, schwann cells, liver, esophagus and oral epithelium and the mesenchyme. In development, it is expressed in neural crest stem cells, and is regarded as a neural crest stem (NCS) cell marker. NGFR is also expressed in adult tissue stem cells and cancer stem cells, derived from ectoderm, neural crest and mesoderm.
 
  NGFR is localized on cellular membrane, either as a monomer or a trimer. NGFR forms a receptor heterodomer complex with TrkA, TrkB and TrkC. Also, NGFR associates with cell surface receptors such as Lingo-1, NogoR and Sortilin.
Localisation NGFR is localized on the cell surface, endosomes and caveolae (Bilderback et al. et al., 1999; Huang et al. et al., 1999). It also shows cytoplasmic and nuclear localization. Intracellular domain (ICD), a cleaved product of NGFR, is present in intracellular compartments (Parkhurst et al. et al., 2010).
Function NGFR forms disulfide-linked dimers independently of ligand binding (Vilar et al. et al., 2009). Variety of functions mediated by NGFR owes to co-receptors. NGFR cooperates with tyrosine kinase receptors of neurophilins; NTRK1 (TrkA) for NGF binding, NTRK2 (TrkB) for BDNF and NT-4/5 and NTRK3 (TrkC) for NT-3. NGFR also cooperates with non-tyrosine kinase receptors, sortilin, Lingo-1 and NOGO-R. A trimetric receptor complex with Lingo-1 and NOGO-R binds RTN4 (Nogo-66), MAG (myelin associated glycoprotein) and OMG (oligodendrocyte myelin glycoprotein).
NGFR confers diverse functions to cells, which is totally dependent on cell types, differentiation status, binding to neurotrophins, neurotrophin maturation status, availability of co-receptors, accessibility to intracytoplasmic effectors, post-translation modification and cleavages. A variety of NGFR-mediated signals mediate cell proliferation and survival (Gentry et al. et al., 2000), differentiation, cell cycle progression (Chittka et al. et al., 2004), apoptosis (Rabizadeh et al. et al., 1993) (Nykjaer et al. et al., 2004), neurite outgrowth and retraction (Rabizadeh et al. et al., 1999), myelination (Notterpek et al., 2003), cell migration and invasion.
Signaling:
NGFR lacks its own enzymatic activity. Instead, it associates with a variety of intracellular proteins to mediate signals. TRAF2 , TRAF4 and TRAF6 mediate NF-κB activation (Khursigara et al. et al., 1999; Ye et al. et al., 1999). NGFR, through its death domain (DD), binds RIPK2 (RIP2) by a neurotrophin-dependent manner, activates NF-κB and supports Schwann cell survival (Khursigara et al. et al., 2001). Similarly, PTPN13 (Fas-associated phosphatase-1/FAP-1) and FAIM (Fas apoptosis inhibitory molecule) associate NGFR, and activates NF-κB and mediate neurite outgrowth (Irie et al. et al., 1999) (Sole et al. et al., 2004). NGFR activates RAC1, which leads to JNK activation and cell death (Harrington et al. et al., 2002). Pro-neurotrophin such as pro-BDNF activates CASP3 (Caspase-3) and JNK, leading to neuronal cell death (Charalampopoulos et al. et al., 2012). JNK is necessary but not sufficient for NGFR-mediated cell death. NGFR constitutively associates with ARHGDIA (RhoGDI), preventing its inhibition towards RHOA. RIP2 recruitment to DD and RhoGDI release from it, is mechanistically linked, and RhoGDI prevents RhoA activity upon release from NGFR. RIP2 has another competitor BEX1 for NGFR binding; BEX1 inhibits NF-κB activation and cell cycle progression. Association of MAGED1 (Neurotrophin receptor-interacting MAGE homolog/NRAGE), NGFRAP1 (p75NTR-associated cell death executor/NADE) and neurotrophin receptor interacting factor (NRIF) is related with pro-apoptotic signaling (Sasaki et al. et al., 2005; Bertrand et al. et al., 2008) (Mukai et al. et al., 2000) (Linggi et al. et al., 2005). Other binding partners include Schwann cell factor 1 (SC1) (Chittka et al. et al., 2004) and SALL2 (Pincheira et al. et al., 2009) both inducing cell cycle arrest, PARD3 (Par-3) which is involved in polarized myelination, and PDE4A4/5 implicated in enhanced cAMP degradation (Sachs et al. et al., 2007). NGFR also binds MAGI1 , which induces neurite outgrowth (Ito et al. et al., 2013). SHC1 is constitutively bound with NGFR, which may play a role in activation of phosphoinositide 3-kinase (PI3K) and Akt (protein kinase B) (Epa et al. et al., 2004). PI3K-Akt pathway supports survival of many types of cells (So et al. et al., 2013). Rab5 Family GTPases RAB5A and RAB31 directly associate with the DD of NGFR, and NGFR regulates glucose homeostasis and insulin sensitivity.
Stem cell Marker:
A variety of stem/progenitor cells express NGFR (Tomellini et al. et al., 2014). Inner cell mass of blastocysts is NGFR-positive, indicating that embryonic stem cells express NGFR. Later in the development, neural crest stem cells (NCSC) express NGFR (Schuldiner et al. et al., 2000), where three neutrophins, BDNF, NT-3 and NT-4, mediate their survival (Pyle et al. et al., 2006). NGFR also marks adult stem cells. Tissue stem cells originating from NCSCs express NGFR, and NGFR seemingly maintains their undifferentiated phenotypes and survival via NT-3(Kruger et al. et al., 2002) (Chalazonitis et al., 2004). Mesenchymal stem cells (MSCs) also express NGFR, where NGFR inhibits the differentiation of MSCs into osteogenic, adipogenic, chondrogenic and myogenic lineages (Mikami et al. et al., 2011). NGFR is a marker for precursors of hepatic stellate cells and portal fibloblast in the liver (Suzuki et al. et al., 2008). Likewise, keratinocyte of the basal layer of epidermis, and esophageal and oropharyngeal mucosa's basal layer cells possessing tissue stem cell properties, are NGFR-positive.

Implicated in

Note
  
Entity Melanoma
Note Tumor tissues are often heterogeneous and contain a population of cells with stem-like properties, referred as cancer stem cells (CSCs). NGFR is a CSC-marker of Melanoma which arise from Melanocytes, neural crest derived cells (Boiko et al. et al., 2010). NGFR+ Melanoma CSCs are not only tumorigenic, but also prone to make metastasis.
  
  
Entity Hypopharyngeal cancer
Note Squamous cell carcinoma (SCS) is also tightly associated with NGFR. NGFR defines CSC-like cells in hypopharyngeal cancer (Imai et al. et al., 2013).
Prognosis The degree of NGFR+ cells within a tumor is significantly associated with patients' prognosis
  
  
Entity Head and neck squamous cancer and esophageal cancer
Note Squamous cell carcinoma arising in the oral cancer is also tightly associated with NGFR. Higher NGFR expression is also associated with poor prognosis of other SCCs such as esophageal, oral and head and neck cancers, suggesting its CSC-like phenotypes (Okumura et al. et al., 2006; Murillo-Sauca et al. et al., 2014).
  
  
Entity Breast cancer
Note GFR mediates breast CSC self-renewal by regulating the expression of pluripotency transcription factors (Tomellini et al. et al., 2015).
  

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Citation

This paper should be referenced as such :
Tanaka N
NGFR (nerve growth factor receptor);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/NGFRID41535ch17q21.html


External links

Nomenclature
HGNC (Hugo)NGFR   7809
Cards
AtlasNGFRID41535ch17q21
Entrez_Gene (NCBI)NGFR  4804  nerve growth factor receptor
AliasesCD271; Gp80-LNGFR; TNFRSF16; p75(NTR); 
p75NTR
GeneCards (Weizmann)NGFR
Ensembl hg19 (Hinxton)ENSG00000064300 [Gene_View]  chr17:47572655-47592382 [Contig_View]  NGFR [Vega]
Ensembl hg38 (Hinxton)ENSG00000064300 [Gene_View]  chr17:47572655-47592382 [Contig_View]  NGFR [Vega]
ICGC DataPortalENSG00000064300
TCGA cBioPortalNGFR
AceView (NCBI)NGFR
Genatlas (Paris)NGFR
WikiGenes4804
SOURCE (Princeton)NGFR
Genetics Home Reference (NIH)NGFR
Genomic and cartography
GoldenPath hg19 (UCSC)NGFR  -     chr17:47572655-47592382 +  17q21-q22   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)NGFR  -     17q21-q22   [Description]    (hg38-Dec_2013)
EnsemblNGFR - 17q21-q22 [CytoView hg19]  NGFR - 17q21-q22 [CytoView hg38]
Mapping of homologs : NCBINGFR [Mapview hg19]  NGFR [Mapview hg38]
OMIM162010   
Gene and transcription
Genbank (Entrez)AK303278 AK313654 BC050309 BC052797 BQ639556
RefSeq transcript (Entrez)NM_002507
RefSeq genomic (Entrez)NC_000017 NC_018928 NT_010783 NW_004929407
Consensus coding sequences : CCDS (NCBI)NGFR
Cluster EST : UnigeneHs.681726 [ NCBI ]
CGAP (NCI)Hs.681726
Alternative Splicing GalleryENSG00000064300
Gene ExpressionNGFR [ NCBI-GEO ]   NGFR [ EBI - ARRAY_EXPRESS ]   NGFR [ SEEK ]   NGFR [ MEM ]
Gene Expression Viewer (FireBrowse)NGFR [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4804
GTEX Portal (Tissue expression)NGFR
Protein : pattern, domain, 3D structure
UniProt/SwissProtP08138   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP08138  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP08138
Splice isoforms : SwissVarP08138
PhosPhoSitePlusP08138
Domaine pattern : Prosite (Expaxy)DEATH_DOMAIN (PS50017)    TNFR_NGFR_1 (PS00652)    TNFR_NGFR_2 (PS50050)   
Domains : Interpro (EBI)DEATH-like_dom    Death_domain    TNFR/NGFR_Cys_rich_reg    TNFR_16   
Domain families : Pfam (Sanger)Death (PF00531)    TNFR_c6 (PF00020)   
Domain families : Pfam (NCBI)pfam00531    pfam00020   
Domain families : Smart (EMBL)DEATH (SM00005)  TNFR (SM00208)  
Conserved Domain (NCBI)NGFR
DMDM Disease mutations4804
Blocks (Seattle)NGFR
PDB (SRS)2N80    2N83    2N97    3EWV   
PDB (PDBSum)2N80    2N83    2N97    3EWV   
PDB (IMB)2N80    2N83    2N97    3EWV   
PDB (RSDB)2N80    2N83    2N97    3EWV   
Structural Biology KnowledgeBase2N80    2N83    2N97    3EWV   
SCOP (Structural Classification of Proteins)2N80    2N83    2N97    3EWV   
CATH (Classification of proteins structures)2N80    2N83    2N97    3EWV   
SuperfamilyP08138
Human Protein AtlasENSG00000064300
Peptide AtlasP08138
HPRD01197
IPIIPI00027436   IPI00964934   IPI00964654   
Protein Interaction databases
DIP (DOE-UCLA)P08138
IntAct (EBI)P08138
FunCoupENSG00000064300
BioGRIDNGFR
STRING (EMBL)NGFR
ZODIACNGFR
Ontologies - Pathways
QuickGOP08138
Ontology : AmiGObeta-amyloid binding  signal transducer activity  receptor activity  transmembrane signaling receptor activity  tumor necrosis factor-activated receptor activity  neurotrophin TRKA receptor binding  protein binding  extracellular region  nucleus  nuclear envelope  nucleoplasm  endosome  rough endoplasmic reticulum  Golgi apparatus  cytosol  plasma membrane  integral component of plasma membrane  intracellular protein transport  activation of cysteine-type endopeptidase activity involved in apoptotic process  inflammatory response  immune response  axon guidance  response to wounding  external side of plasma membrane  cell surface  negative regulation of neuron projection development  Rab GTPase binding  sensory perception of pain  membrane protein intracellular domain proteolysis  ubiquitin protein ligase binding  positive regulation of myelination  positive regulation of synaptic transmission, cholinergic  response to lipopolysaccharide  dendrite membrane  neuronal cell body membrane  circadian regulation of gene expression  tumor necrosis factor-mediated signaling pathway  cellular response to oxidative stress  positive regulation of Rho protein signal transduction  skeletal muscle cell differentiation  regulation of cell proliferation  glucose homeostasis  regulation of apoptotic process  neuron projection  positive regulation of apoptotic process  negative regulation of apoptotic process  negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  perikaryon  regulation of cysteine-type endopeptidase activity involved in apoptotic process  positive regulation of MAPK cascade  negative regulation of neuron apoptotic process  membrane raft  clathrin-coated endocytic vesicle  neurotrophin TRK receptor signaling pathway  nerve growth factor binding  negative regulation of axonogenesis  positive regulation of axonogenesis  positive regulation of protein kinase B signaling  negative regulation of mitochondrial depolarization  positive regulation of synaptic transmission, glutamatergic  preprotein binding  apoptotic signaling pathway  positive regulation of neuron death  regulation of reactive oxygen species metabolic process  regulation of glucose import in response to insulin stimulus  
Ontology : EGO-EBIbeta-amyloid binding  signal transducer activity  receptor activity  transmembrane signaling receptor activity  tumor necrosis factor-activated receptor activity  neurotrophin TRKA receptor binding  protein binding  extracellular region  nucleus  nuclear envelope  nucleoplasm  endosome  rough endoplasmic reticulum  Golgi apparatus  cytosol  plasma membrane  integral component of plasma membrane  intracellular protein transport  activation of cysteine-type endopeptidase activity involved in apoptotic process  inflammatory response  immune response  axon guidance  response to wounding  external side of plasma membrane  cell surface  negative regulation of neuron projection development  Rab GTPase binding  sensory perception of pain  membrane protein intracellular domain proteolysis  ubiquitin protein ligase binding  positive regulation of myelination  positive regulation of synaptic transmission, cholinergic  response to lipopolysaccharide  dendrite membrane  neuronal cell body membrane  circadian regulation of gene expression  tumor necrosis factor-mediated signaling pathway  cellular response to oxidative stress  positive regulation of Rho protein signal transduction  skeletal muscle cell differentiation  regulation of cell proliferation  glucose homeostasis  regulation of apoptotic process  neuron projection  positive regulation of apoptotic process  negative regulation of apoptotic process  negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  perikaryon  regulation of cysteine-type endopeptidase activity involved in apoptotic process  positive regulation of MAPK cascade  negative regulation of neuron apoptotic process  membrane raft  clathrin-coated endocytic vesicle  neurotrophin TRK receptor signaling pathway  nerve growth factor binding  negative regulation of axonogenesis  positive regulation of axonogenesis  positive regulation of protein kinase B signaling  negative regulation of mitochondrial depolarization  positive regulation of synaptic transmission, glutamatergic  preprotein binding  apoptotic signaling pathway  positive regulation of neuron death  regulation of reactive oxygen species metabolic process  regulation of glucose import in response to insulin stimulus  
Pathways : BIOCARTANerve growth factor pathway (NGF) [Genes]    Erk1/Erk2 Mapk Signaling pathway [Genes]    Phosphorylation of MEK1 by cdk5/p35 down regulates the MAP kinase pathway [Genes]   
Pathways : KEGGRas signaling pathway    Rap1 signaling pathway    Cytokine-cytokine receptor interaction    PI3K-Akt signaling pathway    Neurotrophin signaling pathway    Transcriptional misregulation in cancer   
REACTOMEP08138 [protein]
REACTOME Pathways193634 [pathway]   193648 [pathway]   193670 [pathway]   193681 [pathway]   193692 [pathway]   205017 [pathway]   205025 [pathway]   205043 [pathway]   209543 [pathway]   209560 [pathway]   209563 [pathway]   
NDEx NetworkNGFR
Atlas of Cancer Signalling NetworkNGFR
Wikipedia pathwaysNGFR
Orthology - Evolution
OrthoDB4804
GeneTree (enSembl)ENSG00000064300
Phylogenetic Trees/Animal Genes : TreeFamNGFR
HOVERGENP08138
HOGENOMP08138
Homologs : HomoloGeneNGFR
Homology/Alignments : Family Browser (UCSC)NGFR
Gene fusions - Rearrangements
Fusion : MitelmanSMURF2/NGFR [17q23.3/17q21.33]  [t(17;17)(q21;q24)]  
Fusion: TCGASMURF2 17q23.3 NGFR 17q21.33 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNGFR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NGFR
dbVarNGFR
ClinVarNGFR
1000_GenomesNGFR 
Exome Variant ServerNGFR
ExAC (Exome Aggregation Consortium)NGFR (select the gene name)
Genetic variants : HAPMAP4804
Genomic Variants (DGV)NGFR [DGVbeta]
DECIPHER (Syndromes)17:47572655-47592382  ENSG00000064300
CONAN: Copy Number AnalysisNGFR 
Mutations
ICGC Data PortalNGFR 
TCGA Data PortalNGFR 
Broad Tumor PortalNGFR
OASIS PortalNGFR [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICNGFR  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDNGFR
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch NGFR
DgiDB (Drug Gene Interaction Database)NGFR
DoCM (Curated mutations)NGFR (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NGFR (select a term)
intoGenNGFR
NCG5 (London)NGFR
Cancer3DNGFR(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM162010   
Orphanet
MedgenNGFR
Genetic Testing Registry NGFR
NextProtP08138 [Medical]
TSGene4804
GENETestsNGFR
Huge Navigator NGFR [HugePedia]
snp3D : Map Gene to Disease4804
BioCentury BCIQNGFR
ClinGenNGFR
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4804
Chemical/Pharm GKB GenePA31615
Clinical trialNGFR
Miscellaneous
canSAR (ICR)NGFR (select the gene name)
Probes
Litterature
PubMed262 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNGFR
EVEXNGFR
GoPubMedNGFR
iHOPNGFR
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Apr 12 11:36:14 CEST 2017

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