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PTPRA (protein tyrosine phosphatase, receptor type, A)

Written2014-05Jian Huang, Xueping Lai, Xinmin Zheng
Department of Biochemistry, Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China (JH, XL); Department of Molecular Biology, Genetics, Cornell University, Ithaca, NY, USA (XZ)

Abstract Review on PTPRA, with data on DNA/RNA expression, on the protein encoded, and the functional importance of the gene.

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)HEPTP
HLPR
HPTPA
HPTPalpha
LRP
PTPA
PTPRL2
R-PTP-alpha
RPTPA
HGNC (Hugo) PTPRA
HGNC Alias symbLRP
HLPR
HPTPA
RPTPA
HGNC Previous namePTPRL2
 PTPA
LocusID (NCBI) 5786
Atlas_Id 41923
Location 20p13  [Link to chromosome band 20p13]
Location_base_pair Starts at 2923207 and ends at 3038669 bp from pter ( according to hg19-Feb_2009)  [Mapping PTPRA.png]
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
HOXB3 (17q21.32) / PTPRA (20p13)PTPRA (20p13) / BPIFA2 (20q11.21)PTPRA (20p13) / LAMA5 (20q13.33)
PTPRA (20p13) / N4BP1 (16q12.1)PTPRA (20p13) / PDIA4 (7q36.1)PTPRA (20p13) / PTPRA (20p13)
PTPRA (20p13) / SLC48A1 (12q13.11)PTPRA (20p13) / TADA2A (17q12)SMC6 (2p24.2) / PTPRA (20p13)

DNA/RNA

 
  Schematic depiction of human gene PTPRA (upper panel), derived alternative transcripts (middle panel) and corresponding protein isoforms (lower panel). Arrows in the upper panel indicate the three distinct transcriptional start sites within chromosome 20p13. 28 exon numbers according to transcript variant #1 (NM_002836.3) are indicated above the corresponding boxes. In the middle panel the build-up of the three different PTPRA transcripts, deduced based on cDNA deposits in public databases, is depicted. Transcript variant 1 (NM_002836.3) represents the longest transcript and encodes the longer isoform 1. Transcript variant 2 (NM_080840.2) contains an alternate 5' UTR exon which is different from transcript variant 1, and lacks coding exons one to five and exon ten, when compared to variant 1. Transcript variant 3 (NM_080841.2) contains an additional exon within the 5' UTR, and lacks an coding exon and exon one to five, when compared to variant 1. Transcript variant 2 and transcript variant 3 encode the short isoform 2. The N-terminal, the protein domain reflects the signal peptide (SP). The transmembrane spanning regions (TM) and protein tyrosine phosphatase catalytic domain (D1 and D2) are shown respectively. Isoform 2 lacks a 9 aa internal segment, because of exon ten missing, compared to Isoform 1.
Description Human PTPRA is located at Chromosome 20: 2844830-3019722 bp. Its Entrez gene ID is 5786 (NCBI) or 9664 (HGNC). PTPRA consists of 21 coding exons (protein isoform 1) or 20 coding exons (protein isoform 2). 82 organisms have orthologs with human gene PTPRA. The PTPRA gene is conserved across species including chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and C. elegans.
Transcription Three transcript variants encoding different isoforms have been found for PTPRA gene. Transcript variant 1 (NM_002836.3) represents the longest transcript and encodes the longer isoform1 including 802 aa residues. Transcript variant 2 (NM_080840.2) contains an alternate 5' UTR exon which is different from transcript variant 1, and lacks exons one to five and coding exon ten, when compared to variant 1. Transcript variant 3 (NM_080841.2) contains an additional exon within the 5' UTR, when compared to variant 2. Transcript variant 2 and transcript variant 3 encode the short isoform 2. Isoform 2 lacks a 9 aa internal segment, because exon ten missing, compared to Isoform 1. It is known that the expression of RPTPa mRNA is increased by 2 to 10-fold in 70% (10 of 14) of late-stage colon tumors compared to normal colonic mucosa (Tabiti et al., 1995). Another study demonstrated that RPTPa mRNA was increased in 29% (15 of 51) of primary breast carcinomas and correlated with its protein overexpression (Ardini et al., 2000). Recently, PTPRA mRNA splice mutants were described from Chinese colon, breast, and liver tumors (Huang et al., 2011).
Pseudogene One pseudogene (ID: PGOHUM00000236674) for PTPRA described on the website Pseudogenes.org.

Protein

Description The protein encoded by PTPRA gene is a member of the protein tyrosine phosphatase (PTP) family. This PTP contains an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. Three alternatively spliced variants of this gene are well known to encode two distinct isoforms differing only in their extracellular region. The shorter form, expressed in most tissues, has 793 aa of which 123 are extracellular. The longer form, RPTPa802, has nine extra amino acids located just before the transmembrane region and is expressed only in a few tissues, especially in brain. It is noted that extensive N- and O-linked glycosylation of RPTPa gives rise to a mature 130 kD form of the protein (Daum et al., 1994).
Expression PTPRA gene was originally isolated by PCR-based PTP identification and cloning from several groups (Sap et al., 1990; Kaplan et al., 1990; Matthews et al., 1990). The protein, RPTPa, is a widely distributed transmembrane molecule that is particularly highly expressed in the brain and kidney (Sap et al., 1990). RPTPa is highly expressed in the developing central and peripheral nervous system of mouse, especially in the dorsal root ganglia, cranial ganglia and adrenal gland (den Hertog et al., 1996). During chicken development, chicken RPTPa (ChPTPa) is expressed in pre-migratory and migrating granule cells, and in Bergmann glia and their radial processes as determined by in situ hybridization and immunostaining (Fang et al., 1996). Taken together, these studies demonstrate that RPTPa is highly expressed in the developing brain of various species (Shock et al., 1995; Yang and Friesel, 1998; den Hertog et al., 1999).
Localisation Membrane. A typical single-pass type I membrane protein.
Function Generally, RPTPa has been shown to dephosphorylate and activate Src family kinases (SFKs), and is implicated in the regulation of integrin signaling, cell adhesion and proliferation. Studies involving overexpression of RPTPa were the first to demonstrate that PTP can dephosphorylate tyrosine 527 of Src and activate c-Src in vivo and in vitro. This activation causes cellular transformation (Zheng et al., 1992). Dephosphorylation of tyrosine 527 of c-Src in RPTPa overexpressing P19 embryonal carcinoma cells activates c-Src and induces neuronal differentiation (den Hertog et al., 1993). This observation has been independent validated in studied involving RPTPa knockout mice that exhibit a dramatic decrease (50-70%) in c-Src activity in the brain (Ponniah et al., 1999; Su et al., 1999).
In addition to Src, RPTPa regulates other Src family kinases. As an example, Fyn dephosphorylation and activation is observed in cells co-expressing RPTPa and Fyn (Bhandari et al., 1998). Additionally, dephosphorylation of c-Src, Fyn and Yes, but not Lyn, was observed in A431 cells expressing RPTPa (Harder et al., 1998), indicating some degree of specificity of RPTPa. It is noteworthy that there is no evidence of gross physical abnormalities in the RPTPa-deficient mice, indicating that RPTPa is not essential for embryonic development. One explanation is that certain functions of RPTPa are compensated for by other PTPs in mice deficient in RPTPa (Pallen, 2003).
RPTPa is involved in promoting integrin signaling through activation of SFKs. An earlier study shows that c-Src activation by RPTPa can increase the association of c-Src with focal adhesion kinase (FAK), and enhance tyrosine phosphorylation of the Src/FAK substrate paxillin (Harder et al., 1998). Recently, Sun et al. described a novel molecular complex of RPTPa-BCAR3-Cas-Src that is important in integrin signaling (Sun et al., 2012). This complex forms in response to RPTPaTyr789 phosphorylation and mediates Cas localization to focal adhesions and Cas downstream signaling to promote cell migration (Sun et al., 2012). More recently, Cheng et al. identified two roles of Grb2 in integrin signaling: one as a regulator of paxillin stability and upstream promoter of FAKTyr397 phosphorylation that is required for Src-FAK complex activation and another as an essential coordinator of RPTPa and activation of the Src-FAK interaction thus enabling the phosphorylation of RPTPaTyr789 (Cheng et al., 2014).

Mutations

Note Huang et al. sequence RPTPa cDNAs from five types of Chinese human tumors and paired normal samples. They observed three sequences encoding truncated proteins, designated RPTPa245, RPTPa445, or RPTPa652, lacking the D1 domain or both the D1 and D2 domains. One mutant, RPTPa245, widely expressed in colon, breast, and liver tumors from individuals of Chinese origin, can form an RPTPa-RPTPa245 heterodimer and activate c-Src. (Huang et al., 2011).

Implicated in

Note
  
Entity Breast cancer
Note It is clear that RPTPa functions as an activator of c-Src family kinases, and thus was considered to be an oncogene. However, the first study on human breast tumors by Ardini et al. revealed an unexpected and interesting role of RPTPa. RPTPa protein levels are found significantly overexpressed in 29% of 51 samples. High RPTPa protein levels correlated with low tumor grade and positive estrogen receptor status.
Overexpression of RPTPa in MCF-7 breast cancer cells (ER+) resulted in growth inhibition while activating c-Src (Ardini et al., 2000). In a later study, Zheng reported that knockdown of RPTPa and c-Src using RNAi induced apoptosis in estrogen receptor-negative breast cancer cells, but not in immortalized noncancerous breast cells and ER-positive breast cancer cells (including MCF-7). It is noted by Zheng that correlation between ER status and c-Src/RPTPa dependence in breast cancer may be important for planning therapeutic strategy (Zheng et al., 2008). Recently, Wang J and colleagues reported that EGF-induced RPTPa phosphorylation at Ser180 and Ser204 in BT-20 and SKBR3 breast cancer cell lines results in increased c-Src kinase activity, due to a decrease in RPTPa binding with Grb2 and an increase in RPTPa binding with c-Src. These observations reveal novel aspects of integration of an EGF/PKC/RPTPa/Src pathway in breast cancer cell lines (Wang et al., 2013). Currently, Meyer et al. demonstrate that RPTPa functions as a positive mediator of tumor initiation and maintenance in both HER2/Neu-positive breast tumors (Meyer et al., 2014).
  
  
Entity Colorectal cancer
Note The first report correlation with RPTPa and colonic tumors was reported by Tabiti et al. in 1995. They quantified mRNA levels of RPTPa from 14 colon carcinomas and compared these levels to adjacent healthy colon mucosa. They observed a 2 to 10-fold increase in mRNA levels in advanced (Dukes' stage D) carcinoma. Another study from Zheng et al. reported that RNAi knockdown of RPTPa reduced c-Src kinase activity in several colon cancer cell lines (HCT-15, HCT-116 and HT-29), which suppresses anchorage-independent growth and induces apoptosis (Zheng et al., 2008). Recently, tissue-arrays containing 50 colorectal cancer specimens and 10 normal colon samples were analysed by immunohistochemistry for RPTPa expression. In normal tissue samples, RPTPa expression was restricted to smooth muscle cells. None of the normal colonocyte expressed RPTPa in measurable quantities. However, over 70% of the colon cancer samples demonstrated expression of RPTPa (Krndija et al., 2010). These data provide evidence for an oncogenic role of RPTPa in colorectal cancer.
  
  
Entity Gastric cancer
Note To date, only one study has revealed an association between RPTPa expression and gastric cancer. RPTPa expression is observed in 44% of gastric samples and was the most widely expressed of the five PTPs. Several clinicopathological features were significantly linked with the expression of RPTPa, including gross appearance, lymphovascular invasion, lymph node metastasis, liver metastasis and peritoneal dissemination. (Wu et al., 2006).
  
  
Entity Oral squamous cell carcinoma (OSCC)
Note In an earlier study, Berndt et al. evaluated RPTPa expression in 12 oral squamous cell carcinoma (OSCC) samples. Interestingly, not only the tumor cells but also the stromal fibro/myofibroblasts as well as inflammatory cells account for RPTPa expression in OSCC. In particular, immunostaining revealed a predominantly intracellular pattern of RPTPa expression, which may be due to an incompletely glycosylated form (Berndt et al., 1999) and/or to proteolytic cleavage of RPTPa in vivo (Gil-Henn et al., 2001).
  
  
Entity Diffuse large B-cell lymphoma
Cytogenetics A dup(20)(p13p13) was found in a case of diffuse large B-cell lymphoma (Morin et al., 2013).
Hybrid/Mutated Gene TMC2/PTPRA.
  

Bibliography

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Grb2 promotes integrin-induced focal adhesion kinase (FAK) autophosphorylation and directs the phosphorylation of protein tyrosine phosphatase a by the Src-FAK kinase complex.
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Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.
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Citation

This paper should be referenced as such :
J Huang, X Lai, X Zheng
PTPRA (protein tyrosine phosphatase, receptor type, A)
Atlas Genet Cytogenet Oncol Haematol. 2015;19(2):121-125.
Free journal version : [ pdf ]   [ DOI ]

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  dup(20)(p13p13) TMC2/PTPRA

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(16;20)(q12;p13) PTPRA/N4BP1

External links

Nomenclature
HGNC (Hugo)PTPRA   9664
Cards
AtlasPTPRAID41923ch20p13
Entrez_Gene (NCBI)PTPRA  5786  protein tyrosine phosphatase receptor type A
AliasesHEPTP; HLPR; HPTPA; HPTPalpha; 
LRP; PTPA; PTPRL2; R-PTP-alpha; RPTPA
GeneCards (Weizmann)PTPRA
Ensembl hg19 (Hinxton)ENSG00000132670 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000132670 [Gene_View]  ENSG00000132670 [Sequence]  chr20:2923207-3038669 [Contig_View]  PTPRA [Vega]
ICGC DataPortalENSG00000132670
TCGA cBioPortalPTPRA
AceView (NCBI)PTPRA
Genatlas (Paris)PTPRA
WikiGenes5786
SOURCE (Princeton)PTPRA
Genetics Home Reference (NIH)PTPRA
Genomic and cartography
GoldenPath hg38 (UCSC)PTPRA  -     chr20:2923207-3038669 +  20p13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PTPRA  -     20p13   [Description]    (hg19-Feb_2009)
GoldenPathPTPRA - 20p13 [CytoView hg19]  PTPRA - 20p13 [CytoView hg38]
ImmunoBaseENSG00000132670
genome Data Viewer NCBIPTPRA [Mapview hg19]  
OMIM176884   
Gene and transcription
Genbank (Entrez)AB209702 AI284972 AK090743 AK290233 AK294499
RefSeq transcript (Entrez)NM_002836 NM_080840 NM_080841
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PTPRA
Alternative Splicing GalleryENSG00000132670
Gene ExpressionPTPRA [ NCBI-GEO ]   PTPRA [ EBI - ARRAY_EXPRESS ]   PTPRA [ SEEK ]   PTPRA [ MEM ]
Gene Expression Viewer (FireBrowse)PTPRA [ Firebrowse - Broad ]
GenevisibleExpression of PTPRA in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5786
GTEX Portal (Tissue expression)PTPRA
Human Protein AtlasENSG00000132670-PTPRA [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP18433   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP18433  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP18433
Splice isoforms : SwissVarP18433
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 ]   [ MEROPS ]
PhosPhoSitePlusP18433
Domaine pattern : Prosite (Expaxy)TYR_PHOSPHATASE_1 (PS00383)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domains : Interpro (EBI)Prot-tyrosine_phosphatase-like    PTPase_domain    Tyr_Pase_AS    Tyr_Pase_cat    Tyr_Pase_rcpt_a/e-type    Tyr_Pase_rcpt_alpha    TYR_PHOSPHATASE_dom   
Domain families : Pfam (Sanger)Y_phosphatase (PF00102)   
Domain families : Pfam (NCBI)pfam00102   
Domain families : Smart (EMBL)PTPc (SM00194)  PTPc_motif (SM00404)  
Conserved Domain (NCBI)PTPRA
DMDM Disease mutations5786
Blocks (Seattle)PTPRA
SuperfamilyP18433
Human Protein Atlas [tissue]ENSG00000132670-PTPRA [tissue]
Peptide AtlasP18433
HPRD01476
IPIIPI01011765   IPI00221067   IPI00843944   IPI00304030   IPI00743698   IPI01014939   IPI01009440   IPI00647151   IPI00647541   IPI00644107   IPI00644501   
Protein Interaction databases
DIP (DOE-UCLA)P18433
IntAct (EBI)P18433
FunCoupENSG00000132670
BioGRIDPTPRA
STRING (EMBL)PTPRA
ZODIACPTPRA
Ontologies - Pathways
QuickGOP18433
Ontology : AmiGOMAPK cascade  protein tyrosine phosphatase activity  transmembrane receptor protein tyrosine phosphatase activity  protein binding  plasma membrane  integral component of plasma membrane  focal adhesion  protein dephosphorylation  axon guidance  insulin receptor signaling pathway  peptidyl-tyrosine dephosphorylation  receptor complex  modulation of chemical synaptic transmission  extracellular exosome  Schaffer collateral - CA1 synapse  integral component of synaptic membrane  
Ontology : EGO-EBIMAPK cascade  protein tyrosine phosphatase activity  transmembrane receptor protein tyrosine phosphatase activity  protein binding  plasma membrane  integral component of plasma membrane  focal adhesion  protein dephosphorylation  axon guidance  insulin receptor signaling pathway  peptidyl-tyrosine dephosphorylation  receptor complex  modulation of chemical synaptic transmission  extracellular exosome  Schaffer collateral - CA1 synapse  integral component of synaptic membrane  
REACTOMEP18433 [protein]
REACTOME PathwaysR-HSA-5673001 [pathway]   
NDEx NetworkPTPRA
Atlas of Cancer Signalling NetworkPTPRA
Wikipedia pathwaysPTPRA
Orthology - Evolution
OrthoDB5786
GeneTree (enSembl)ENSG00000132670
Phylogenetic Trees/Animal Genes : TreeFamPTPRA
HOGENOMP18433
Homologs : HomoloGenePTPRA
Homology/Alignments : Family Browser (UCSC)PTPRA
Gene fusions - Rearrangements
Fusion : MitelmanPTPRA/N4BP1 [20p13/16q12.1]  
Fusion PortalPTPRA 20p13 N4BP1 16q12.1 BRCA
Fusion PortalPTPRA 20p13 TADA2A 17q12 LUAD
Fusion : Fusion_HubABL1--PTPRA    ANKRD36--PTPRA    CHD6--PTPRA    COQ4--PTPRA    CSDE1--PTPRA    DLGAP1--PTPRA    FASTKD5--PTPRA    HM13--PTPRA    HOXB3--PTPRA    LYZ--PTPRA    MAP2--PTPRA    MTR--PTPRA    PPP1CB--PTPRA    PTPRA--AC011530.4    PTPRA--BCKDHA   
PTPRA--BPIFA2    PTPRA--CDK5RAP1    PTPRA--CLIP2    PTPRA--DEGS1    PTPRA--DNM1L    PTPRA--EXT1    PTPRA--HMGB1    PTPRA--HNRNPUL2    PTPRA--IL2RG    PTPRA--LAMA5    PTPRA--N4BP1    PTPRA--NPEPL1    PTPRA--PDIA4    PTPRA--POLDIP2    PTPRA--PPARG   
PTPRA--PRSS1    PTPRA--PTPRA    PTPRA--RAB13    PTPRA--RTFDC1    PTPRA--SEC14L1    PTPRA--SEPT9    PTPRA--SLC48A1    PTPRA--SNRPB    PTPRA--SPIN1    PTPRA--SUPT16H    PTPRA--TADA2A    PTPRA--TMA16    PTPRA--UBOX5    PTPRA--YTHDC2    RNF114--PTPRA   
SLC28A1--PTPRA    SMC6--PTPRA    TMLHE--PTPRA    TRIP11--PTPRA   
Fusion : QuiverPTPRA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPTPRA [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTPRA
dbVarPTPRA
ClinVarPTPRA
MonarchPTPRA
1000_GenomesPTPRA 
Exome Variant ServerPTPRA
GNOMAD BrowserENSG00000132670
Varsome BrowserPTPRA
Genetic variants : HAPMAP5786
Genomic Variants (DGV)PTPRA [DGVbeta]
DECIPHERPTPRA [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPTPRA 
Mutations
ICGC Data PortalPTPRA 
TCGA Data PortalPTPRA 
Broad Tumor PortalPTPRA
OASIS PortalPTPRA [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPTPRA  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPTPRA
Mutations and Diseases : HGMDPTPRA
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PTPRA
DgiDB (Drug Gene Interaction Database)PTPRA
DoCM (Curated mutations)PTPRA (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PTPRA (select a term)
intoGenPTPRA
NCG6 (London) select PTPRA
Cancer3DPTPRA(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM176884   
Orphanet
DisGeNETPTPRA
MedgenPTPRA
Genetic Testing Registry PTPRA
NextProtP18433 [Medical]
TSGene5786
GENETestsPTPRA
Target ValidationPTPRA
Huge Navigator PTPRA [HugePedia]
snp3D : Map Gene to Disease5786
BioCentury BCIQPTPRA
ClinGenPTPRA
Clinical trials, drugs, therapy
Protein Interactions : CTD5786
Pharm GKB GenePA34009
Clinical trialPTPRA
Miscellaneous
canSAR (ICR)PTPRA (select the gene name)
HarmonizomePTPRA
DataMed IndexPTPRA
Probes
Litterature
PubMed108 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePTPRA
EVEXPTPRA
GoPubMedPTPRA
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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