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PTPN9 (protein tyrosine phosphatase, non-receptor type 9)

Written2016-11Barnabas Nyesiga and Anette Gjörloff Wingren
Biomedical science, Health and society, Malmö University, Malmö, Sweden nyesigabarnabas@gmail.com; anette.gjorloff-wingren@mah.se

Abstract Review on PTPN9, with data on DNA, on the protein encoded, and where the gene is implicated.

Keywords PTPN9; Endocytosis;

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)MEG2
Other aliasProtein Tyrosine Phosphatase, Non-Receptor Type 9
Protein-Tyrosine Phosphatase MEG2
PTPase MEG2
EC 3.1.3.48
Tyrosine-Protein Phosphatase Non-Receptor Type 9
PTPase-MEG2
PTPMEG2
HGNC (Hugo) PTPN9
LocusID (NCBI) 5780
Atlas_Id 41922
Location 15q24.2  [Link to chromosome band 15q24]
Location_base_pair Starts at 75467121 and ends at 75579291 bp from pter ( according to hg19-Feb_2009)  [Mapping PTPN9.png]

DNA/RNA

Note PTPN9 was originally cloned by screening libraries of the MEG-01 megakaryocyte leukemia cell line and of human umbilical vein endothelial cells (Gu 1992).
Description The PTPN9 gene was mapped to chromosome 15q24.2 based on an alignment of the PTPN9 sequence (GenBank BC010863) with the genomic sequence (GRCh37).
Transcription MEG2 mRNA detected in 12 cell lines gave an indication that the protein tyrosine phosphatase (PTP) is widely expressed. A 4-kb RNA as analysed by Northern blot analysis was found in a variety of cell lines, indicating widespread expression of the gene (Gu 1992).

Protein

Note NOTE PTPN9 has a conserved PTP catalytic domain, and an NH2-terminal lipid-binding domain homologous to Sec14p, a yeast protein with phosphatidylinositol transferase activity, which is unique among PTPs (Gu 1992). The N-terminal 254 amino acids are about 28% identical to cellular retinaldehyde binding protein-1 (RLBP1; 180090) and 24% identical to the yeast protein SEC14p. The former is a carrier protein for 11-cis-retinaldehyde or 11-cis-retinol found in the retina and pineal gland, and the latter is a phosphatidylinositol transfer protein required for protein secretion from the Golgi apparatus. The PTPN9 cDNA encodes a 593-amino acid protein that has no apparent signal or transmembrane domains but does include a C-terminal region with a catalytic domain that shows 30-40% identity with other PTPs (http://www.omim.org/entry/600768).
 
  Figure 1. Schematic diagram of recombinant PTPN9 protein (Adapted from Zhao et al. 2003).The open and solid bars indicate SEC14 lipid-binding domain and PTP catalytic domain, respectively.
Description PTPN9 is a 68-kDa, class I, cysteine-based, non-receptor PTP is widely expressed in many cell types including the brain and leukocytes (Gu 1992, Saito 2007). In these cells, most of the PTPN9 is located on the cytoplasmic face of secretory vesicles (Gjörloff-Wingren 2000, Wang 2002, Kruger 2002 and Huynh 2004). On the cytoplasmic face of the enclosing membrane of secretory vesicles, PTPN9 regulates vesicle size by promoting homotypic vesicle fusion through dephosphorylating NSF (N-ethylmaleimide-sensitive factor), a key regulator of vesicle fusion (Saito 2007). PTPN9 structural uniqueness among mammalian PTPs lies in the fact that it contains a domain in its N terminus with homology to yeast Sec14p, a phosphatidylinositol-binding protein (Sha 1998). This Sec14p homology (SEC14) domain of PTPN9 (Fig 1) is known to bind phosphoinositides (Kruger 2002, Huynh 2003, Krugmann 2002), a process that leads into enzymatic activation of the phosphatase domain (Kruger 2002, Huynh 2003). Using a series of deletion mutants, Saito et al identified the N-terminal SEC14 domain of PTPN9, residues 1-261, as the region containing the secretory vesicle targeting signal (Saito 2007). The SEC14 domain, alone or attached to a heterologous protein, was localized to intracellular vesicle membranes. In addition, two proteins, mannose 6-phosphate receptor-interacting protein PLIN3 (TIP47) and ARFIP2 Arfaptin2 altered PTPN9 localization when overexpressed, and elimination of TIP47 resulted in loss of PTPN9 function. It has been shown that the truncated form of the N-terminal SEC14 domain of PTPN9 has a significantly higher activity than the full-length enzyme (Qi 2002, Kruger 2002). By using lipid-membrane overlay and liposome binding assays, a specific binding of PTPN9 to phosphatidylserine was demonstrated (Zhao 2003). The binding was found to be mediated by the SEC14 domain. In intact cells, the SEC14 domain was found to play a prominent role in the localization of PTPN9 to the perinuclear region. Moreover, PTPN9 may play an important role through specific binding of phosphatidylserine, in regulating the signaling processes associated with phagocytosis of apoptotic cells (Zhao 2003).
Expression The enzyme is expressed in many cell types (Gu 1992, Saito 2007), including at low levels in Jurkat T cells (Gjörloff-Wingren 2000), mast cells and lymphocytes (Wang 2002, Wang 2005).
Localisation Reports have shown PTPN9 residence on internal membranes, including secretory vesicles and granules in neutrophils and lymphocytes where it regulates secretory vesicle size and fusion (Gjörloff-Wingren 2000, Wang 2002, Huynh 2003, Wang 2005). It is possible that once engulfed by phagocytes, a high level of phosphatidylserine in the outer membrane of apoptotic cells may alter the distribution of PTPN9 in phagocytes (Zhao 2003). It has been suggested that the physiological function of PTPN9 may be to regulate formation of secretory vesicles of a defined and cell type-specific size (Wang 2002). PTPN9 expression is higher in mast cells (granule size 400-600 nm) than in lymphocytes (granule size 200-300 nm) (Wang 2002).
Function It was proposed that PTPN9 promotes homotypic fusion of immature secretory vesicles, which is a major step in the formation of these vesicles from post-Golgi transport vesicles containing cargo destined for secretion (Wang 2002, Huynh 2004, Huynh 2003, Wang 2005, Mustelin 2004). Additionally, PTPN9 may represent a novel connection between dephosphorylation of tyrosine and the regulation of secretory vesicles in hematopoietic cells (Wang 2002). Moreover, the possibility of PTPN9 expression in controlling the extent of the secretory apparatus of hematopoietic cells was proposed. Huyhn et al showed that PTPN9 regulates homotypic fusion of immature secretory vesicles by dephosphorylating the key regulator of vesicle fusion, N-ethylmaleimide-sensitive factor (NSF) (Huyhn 2004). PTPN9 can also regulate embryonic development (Wang 2005) and expansion of erythroid cells (Xu 2003). Studies have further demonstrated that PTPN9 controls insulin production, beta cell growth or insulin signaling by reducing insulin receptor (INSR) dephosphorylation in type II diabetes (Cho 2006, Chen 2010). Other studies have shown that PTPN9 promotes dephosphorylation of epidermal growth factor receptor (EGFR) and the receptor tyrosine protein kinase ERBB2, thereby impairing the activation of signal transducer and activator of transcription 3 (STAT3) (Yuan 2010) and STAT5 (Yuan 2010, Furth 2011) in breast cancer cells. From their observations, it was suggested that PTPN9-mediated modulation of secretory vesicle genesis and function plays an essential role in neural tube, vascular, and bone development as well as activation may participate in the transfer of hydrophobic ligands or may be involved in Golgi-related functions (Gu 1992). PTPN9 appears to regulate a balance by promoting fusion (anterograde transport) and reducing condensation (retrograde transport), thus increasing the size of secretory vesicles (Saito 2007). In addition, it was recently shown that the transport of neurotrophin receptor TRKA ( NTRK1) to the cell surface requires PTPN9 activity (Zhang 2016). Trk A is a novel substrate of PTPN9 and is dephosphorylated at both the kinase activation domain (Tyr674/675) and the signaling effector binding site (Tyr490). The studies were performed in neurite outgrowth and cortical neurons (Zhang 2016).

Implicated in

  
Entity Breast cancer
Note ErbB family of the receptor protein-tyrosine kinase plays an important role in the progression of human cancers including breast cancer. Among the 43 human protein-tyrosine phosphatases analysed, Yuan 2010 discovered the knockdown of PTPN9 to significantly increase ERBB2 tyrosine phosphorylation in the SKBR3 breast cancer cell line. Additionally, knockdown of PTPN9 expression enhances tyrosine phosphorylation of the ErbB1/EGFR in the MDA-MB-231 breast cancer cell line. Their data suggested PTPN9 to be a negative regulator of breast cancer cells through targeting ErbB2 and EGFR and inhibiting STAT activation (Yuan 2010).
  
  
Entity Hepatocellular carcinoma
Note PTPN9 expression was down-regulated in human hepatocellular carcinoma (HCC) tumor tissues, associate with worsened overall survival in HCC patients (Hu 2016). Depletion ofPTPN9 inhibits the apoptosis and promotes the proliferation of HCC cells.
  
  
Entity Diabetes
Note PTPN9 have been identified as a modulator of insulin-dependent FOXO1 subcellular localization (Cho 2006). Ectopic expression of PTPN9 in cells to suppress insulin-induced phosphorylation of the insulin receptor, while RNAi-mediated reduction of PTPN9 transcript levels enhanced insulin action. Their findings implicated PTPN9 as a mediator of blood glucose homeostasis through antagonism of insulin signaling, and proposed modulation of PTPN9 activity to be an adequate strategy in type 2 diabetes treatment. Indeed, treatment with PTPN9 inhibitors can lead to enhanced insulin action both in vitro and in vivo (Zhang 2012).
  
  
Entity Hematopoiesis
Note Xu et al identified PTPN9 to be contained in erythroid colony-forming cells (ECFCs) from polycythemia vera (PV), a human clonal myeloproliferative disorder (Xu 2003). Increased activity of PTPN9 in PV cells to be attributed to its elevated distribution in the membrane fraction. Additionally, the findings showed that PTPN9 plays a major role in the development of erythroid cells.
  
  
Entity Immunodeficiency
Note PTPN9-/- mice were reported to be immunodeficient as they displayed severe developmental malformations, such as defective skull formation and intracranial bleeding (Wang 2005). The mice remained small and the majority of them died before birth or within the first neonatal days. Furthermore, they detected defective platelet activation and very little interleukin-2 secretion in these mice. They attributed all these abnormalities to defective PTPN9 secretion.
  

Bibliography

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Identification of the tyrosine phosphatase PTP-MEG2 as an antagonist of hepatic insulin signaling
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Signal transducer and activator of transcription 5 as a key signaling pathway in normal mammary gland developmental biology and breast cancer
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Cloning and expression of a cytosolic megakaryocyte protein-tyrosine-phosphatase with sequence homology to retinaldehyde-binding protein and yeast SEC14p
Gu M, Warshawsky I, Majerus PW
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PMID 1557404
 
Downregulated Expression of PTPN9 Contributes to Human Hepatocellular Carcinoma Growth and Progression
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Pathol Oncol Res 2016 Jul;22(3):555-65
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Control of vesicle fusion by a tyrosine phosphatase
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Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells
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J Immunol 2003 Dec 15;171(12):6661-71
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Protein-tyrosine phosphatase MEG2 is expressed by human neutrophils
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Localization to the phagosome and activation by polyphosphoinositides J Biol Chem
PMID 11711529
 
Identification of ARAP3, a novel PI3K effector regulating both Arf and Rho GTPases, by selective capture on phosphoinositide affinity matrices
Krugmann S, Anderson KE, Ridley SH, Risso N, McGregor A, Coadwell J, Davidson K, Eguinoa A, Ellson CD, Lipp P, Manifava M, Ktistakis N, Painter G, Thuring JW, Cooper MA, Lim ZY, Holmes AB, Dove SK, Michell RH, Grewal A, Nazarian A, Erdjument-Bromage H, Tempst P, Stephens LR, Hawkins PT
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Protein tyrosine phosphatases in T cell physiology
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PMID 15220004
 
Purification and characterization of protein tyrosine phosphatase PTP-MEG2
Qi Y, Zhao R, Cao H, Sui X, Krantz SB, Zhao ZJ
J Cell Biochem 2002;86(1):79-89
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Association of protein-tyrosine phosphatase MEG2 via its Sec14p homology domain with vesicle-trafficking proteins
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Sha B, Phillips SE, Bankaitis VA, Luo M
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Enlargement of secretory vesicles by protein tyrosine phosphatase PTP-MEG2 in rat basophilic leukemia mast cells and Jurkat T cells
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Tyrosine phosphatase MEG2 modulates murine development and platelet and lymphocyte activation through secretory vesicle function
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Citation

This paper should be referenced as such :
Nyesiga B, Gjörloff Wingren A
PTPN9 (protein tyrosine phosphatase, non-receptor type 9);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/PTPN9ID41922ch15q24.html


External links

Nomenclature
HGNC (Hugo)PTPN9   9661
Cards
AtlasPTPN9ID41922ch15q24
Entrez_Gene (NCBI)PTPN9  5780  protein tyrosine phosphatase, non-receptor type 9
AliasesMEG2; PTPMEG2
GeneCards (Weizmann)PTPN9
Ensembl hg19 (Hinxton)ENSG00000169410 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000169410 [Gene_View]  chr15:75467121-75579291 [Contig_View]  PTPN9 [Vega]
ICGC DataPortalENSG00000169410
TCGA cBioPortalPTPN9
AceView (NCBI)PTPN9
Genatlas (Paris)PTPN9
WikiGenes5780
SOURCE (Princeton)PTPN9
Genetics Home Reference (NIH)PTPN9
Genomic and cartography
GoldenPath hg38 (UCSC)PTPN9  -     chr15:75467121-75579291 -  15q24.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PTPN9  -     15q24.2   [Description]    (hg19-Feb_2009)
EnsemblPTPN9 - 15q24.2 [CytoView hg19]  PTPN9 - 15q24.2 [CytoView hg38]
Mapping of homologs : NCBIPTPN9 [Mapview hg19]  PTPN9 [Mapview hg38]
OMIM600768   
Gene and transcription
Genbank (Entrez)BC010863 BC071574 BT007405 DQ890986 M83738
RefSeq transcript (Entrez)NM_002833
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PTPN9
Cluster EST : UnigeneHs.445775 [ NCBI ]
CGAP (NCI)Hs.445775
Alternative Splicing GalleryENSG00000169410
Gene ExpressionPTPN9 [ NCBI-GEO ]   PTPN9 [ EBI - ARRAY_EXPRESS ]   PTPN9 [ SEEK ]   PTPN9 [ MEM ]
Gene Expression Viewer (FireBrowse)PTPN9 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5780
GTEX Portal (Tissue expression)PTPN9
Protein : pattern, domain, 3D structure
UniProt/SwissProtP43378   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP43378  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP43378
Splice isoforms : SwissVarP43378
Catalytic activity : Enzyme3.1.3.48 [ Enzyme-Expasy ]   3.1.3.483.1.3.48 [ IntEnz-EBI ]   3.1.3.48 [ BRENDA ]   3.1.3.48 [ KEGG ]   
PhosPhoSitePlusP43378
Domaine pattern : Prosite (Expaxy)CRAL_TRIO (PS50191)    TYR_PHOSPHATASE_1 (PS00383)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domains : Interpro (EBI)CRAL-TRIO_dom    CRAL/TRIO_N_dom    Prot-tyrosine_phosphatase-like    PTPase_domain    Tyr_Pase_AS    Tyr_Pase_cat    TYR_PHOSPHATASE_dom   
Domain families : Pfam (Sanger)CRAL_TRIO (PF00650)    Y_phosphatase (PF00102)   
Domain families : Pfam (NCBI)pfam00650    pfam00102   
Domain families : Smart (EMBL)CRAL_TRIO_N (SM01100)  PTPc (SM00194)  PTPc_motif (SM00404)  SEC14 (SM00516)  
Conserved Domain (NCBI)PTPN9
DMDM Disease mutations5780
Blocks (Seattle)PTPN9
PDB (SRS)2PA5    4GE2    4GE5    4GE6    4ICZ   
PDB (PDBSum)2PA5    4GE2    4GE5    4GE6    4ICZ   
PDB (IMB)2PA5    4GE2    4GE5    4GE6    4ICZ   
PDB (RSDB)2PA5    4GE2    4GE5    4GE6    4ICZ   
Structural Biology KnowledgeBase2PA5    4GE2    4GE5    4GE6    4ICZ   
SCOP (Structural Classification of Proteins)2PA5    4GE2    4GE5    4GE6    4ICZ   
CATH (Classification of proteins structures)2PA5    4GE2    4GE5    4GE6    4ICZ   
SuperfamilyP43378
Human Protein AtlasENSG00000169410
Peptide AtlasP43378
HPRD02864
IPIIPI00852804   IPI01010466   
Protein Interaction databases
DIP (DOE-UCLA)P43378
IntAct (EBI)P43378
FunCoupENSG00000169410
BioGRIDPTPN9
STRING (EMBL)PTPN9
ZODIACPTPN9
Ontologies - Pathways
QuickGOP43378
Ontology : AmiGOprotein tyrosine phosphatase activity  non-membrane spanning protein tyrosine phosphatase activity  protein binding  cytoplasm  protein dephosphorylation  peptidyl-tyrosine dephosphorylation  
Ontology : EGO-EBIprotein tyrosine phosphatase activity  non-membrane spanning protein tyrosine phosphatase activity  protein binding  cytoplasm  protein dephosphorylation  peptidyl-tyrosine dephosphorylation  
NDEx NetworkPTPN9
Atlas of Cancer Signalling NetworkPTPN9
Wikipedia pathwaysPTPN9
Orthology - Evolution
OrthoDB5780
GeneTree (enSembl)ENSG00000169410
Phylogenetic Trees/Animal Genes : TreeFamPTPN9
HOVERGENP43378
HOGENOMP43378
Homologs : HomoloGenePTPN9
Homology/Alignments : Family Browser (UCSC)PTPN9
Gene fusions - Rearrangements
Fusion : MitelmanPTPN9/AGBL1 [15q24.2/15q25.3]  
Fusion : MitelmanSIN3A/PTPN9 [15q24.2/15q24.2]  [t(15;15)(q24;q24)]  
Fusion: TCGAPTPN9 15q24.2 AGBL1 15q25.3 BRCA
Fusion: TCGASIN3A 15q24.2 PTPN9 15q24.2 LGG
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPTPN9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTPN9
dbVarPTPN9
ClinVarPTPN9
1000_GenomesPTPN9 
Exome Variant ServerPTPN9
ExAC (Exome Aggregation Consortium)PTPN9 (select the gene name)
Genetic variants : HAPMAP5780
Genomic Variants (DGV)PTPN9 [DGVbeta]
DECIPHERPTPN9 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPTPN9 
Mutations
ICGC Data PortalPTPN9 
TCGA Data PortalPTPN9 
Broad Tumor PortalPTPN9
OASIS PortalPTPN9 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPTPN9  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPTPN9
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PTPN9
DgiDB (Drug Gene Interaction Database)PTPN9
DoCM (Curated mutations)PTPN9 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PTPN9 (select a term)
intoGenPTPN9
NCG5 (London)PTPN9
Cancer3DPTPN9(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600768   
Orphanet
MedgenPTPN9
Genetic Testing Registry PTPN9
NextProtP43378 [Medical]
TSGene5780
GENETestsPTPN9
Target ValidationPTPN9
Huge Navigator PTPN9 [HugePedia]
snp3D : Map Gene to Disease5780
BioCentury BCIQPTPN9
ClinGenPTPN9
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5780
Chemical/Pharm GKB GenePA34005
Clinical trialPTPN9
Miscellaneous
canSAR (ICR)PTPN9 (select the gene name)
Probes
Litterature
PubMed29 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePTPN9
EVEXPTPN9
GoPubMedPTPN9
iHOPPTPN9
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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