Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Taking over the Atlas
Dear Colleagues,
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EPHA1 (EPH receptor A1)

Identity

Other namesEPH
EPHT
EPHT1
EphA1
HGNC (Hugo) EPHA1
LocusID (NCBI) 2041
Location 7q34
Location_base_pair Starts at 143088205 and ends at 143105985 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order (cen) ZYX ->, 8bp, <- EPHA1, 34.5kb, TASR60 -> (tel)

DNA/RNA

 
  Genomic neighbourhood and organisation of EPHA1.
Description EPHA1 consists of 18 exons and 17 introns and spans 17.78kb of genomic DNA. EPHA1 is located within the human tilepath clone RP11-811J9.
Transcription 3,359 nucleotide mRNA. Two alternative splice variants, predicted to result in truncation within the extracellular domain of EphA1, have been reported.
Pseudogene None identified.

Protein

Note EphA1 was isolated originally from an erythropoietin producing hepatoma cell line, from which its name, and the name of its gene family, derives.
 
  Domain organisation of EphA1.
Description The EPHA1 gene encodes a 976 amino acid protein with a calculated molecular weight of 108,126.89 and an isoelectric point of 6.6254. Amino acids 1-25 constitute a signal peptide.
EphA1 is the founding member of what is recognised as the largest subfamily of the receptor tyrosine kinases. This is an evolutionarily ancient protein group with members being present in sponges, worms and fruit flies. The expansion in the number of Eph receptor-encoding genes along with genes encoding their ligands, the ephrins (Eph receptor interacting proteins), is proposed to have contributed to the increase in complexity of the bilaterian body plan. Fourteen Eph receptors have been identified in vertebrates. These are subdivided into either EphA (EphA1, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphA10) or EphB ( EphB1, EphB2, EphB3, EphB4, EphB6) subclasses which differ primarily in the structure of their ligand binding domains. EphA receptors also exhibit greater affinity for binding GPI-linked ephrin-A ligands while EphB receptors bind transmembrane ephrin-B ligands. While interactions are somewhat promiscuous, and some cross-class binding occurs, each Eph receptor displays distinct affinity for the different ephrin ligands. Eph-ephrin binding involves cell-cell contact. Upon binding, both Eph and ephrin proteins on respective cells dimerise, and undergo higher order clustering. This results in signalling within both the Eph- and ephrin-bearing cells (bidirectional signalling) and either subsequent adhesion or repulsion of the interacting cells. Cell-cell contact, and thus Eph-ephrin signalling, may be terminated either by enzymatic cleavage of the extracellular domain of the Eph receptor or ephrin ligand or endocytosis of Eph-ephrin complexes.
The high affinity ligands for EphA1 are ephrin-A1 and ephrin-A3. EphA1 also binds fibronectin, a non-activating ligand.
Expression Embryonic stem (ES) cells and embryoid bodies differentiated from ES cells in vitro; dynamic and regionalised expression during murine embryogenesis (including epiblast, primitive streak, paraxial mesoderm, tail bud mesoderm, distal limb bud); human lung, small intestinal, kidney, bladder, thymus, skin and colon. Murine adult epithelial tissues (including epidermis of skin and vagina, endometrium, renal collecting system). Rat normal liver, kidney, lung. Human tumours and cell lines of epithelial origin.
Localisation Membrane; single-pass type I membrane protein.
Function Not yet entirely established. Generally repulsive interaction with its high affinity ligands ephrin-A1 and ephrin-A3. Transgenic expression of EphA1 in the blastula of pre-implantation mice is lethal (Duffy et al., unpublished). EphA1 homozygous null mice exhibit kinked tails (80%) and imperforate vagina (18% of females). The apparent absence of EphA1 in fish (zebrafish, medaka, fugu) and amphibia (Xenopus) and its emergence in vertebrates with reptiles (anole lizard) and birds (chicken) hints at an association with the transition of life from an aquatic to terrestrial environment. The presence of a membrane-embedded ionogenic Glu547 residue within the transmembrane domain of EphA1 also is unique among the Eph receptors. The structural-dynamic properties of the transmembrane domain have been shown to be dependent on the ionisation state of this residue, a finding that implies that the conformational flexibility and activation of the EphA1 receptor can be regulated by such external and local factors as pH and lipid composition of the membrane, a finding which may be of particular relevance to EphA1 function in the skin and kidney.
 
Homology Phylogenetic tree for the Eph receptors. Amino acid sequences used for this compilation were EphA1 (NP_005223), EphA2 (NM_004431), EphA3 (NP_005224), EphA4 (NP_004429), EphA5 (NM_004439), EphA6 (ENSP00000374323), EphA7 (NP_004431), EphA8 (NP_065387), EphA10 (NP_001092909), EphB1 (NP_004432), EphB2 (NP_004433), EphB3 (NP_004434), EphB4 (NP_004435) and EphB6 (NP_004436).

Mutations

Germinal No germinal mutations identified to be associated with cancer so far.
Somatic Rare. A single heterozygous missense mutation E703K within the tyrosine kinase domain has been reported for a lobular breast carcinoma.

Implicated in

Entity Colorectal cancer
Note An immunohistochemical study of 20 colorectal adenomas and 111 colorectal carcinomas specimens detected EphA1 protein expression in all adenomas and reduced expression in 54% of colorectal cancers. Reduced expression of EphA1 was found more often in male patients (P=0.028) and in patients with poor differentiation (P=0.027), greater depth of wall invasion (P=0.003), lymph node metastasis (P=0.034), and advanced tumour stage (P=0.003).
Prognosis Patients with colorectal cancer in this study with reduced EphA1 expression had a poor overall survival (P=0.059). Reduced EphA1 expression in patients over 55 years or with rectal cancers and sigmoid colon cancers was associated with a poor overall survival (P=0.034 and 0.015, respectively).
  
Entity Nonmelanoma skin cancer
Note EphA1, which in human adults is expressed in the epidermis of the skin, is significantly downregulated at the protein level in basal cell and squamous cell carcinomas.
  
Entity Glioblastoma
Note EphA1 expression is significantly downregulated in human glioblastoma and glioblastoma cell lines.
  
Entity Breast cancer
Note Down regulation of EphA1 was associated with increased invasiveness in a breast cancer progression model using quantitative real time RT-PCR expression profiles of EphA1 mRNA in MCF-10A, MCF-7, and MDA-MB-231 cells, representing normal breast, non-invasive breast tumour, and invasive tumour, respectively, based on their characteristic phenotypes in Matrigel matrix.
  
Entity Prostate cancer
Note EphA1 mRNA transcript expression was found to decrease progressively in a panel of human prostate cancer cell lines representative of the transition from normal prostate to primary prostate tumour to metastatic tumour.
  
Entity Ovarian cancer
Note Overexpression of EphA1 in the presence of elevated expression of its high affinity ligand ephrin-A1 was observed with more aggressive ovarian cancer phenotypes.
  
Entity Head and neck squamous cell carcinoma (HNSCC )
Note EphA1 was reported to be highly expressed in HNSCC using an approach that cloned receptor tyrosine kinases by RT-PCR using degenerate receptor tyrosine kinase primers from seven HNSCC specimens and confirmed abundant EphA1 protein expression by immunohistochemistry in eight independent HNSCC specimens.
  

External links

Nomenclature
HGNC (Hugo)EPHA1   3385
Cards
AtlasEPHA1ID40461ch7q35
Entrez_Gene (NCBI)EPHA1  2041  EPH receptor A1
GeneCards (Weizmann)EPHA1
Ensembl hg19 (Hinxton)ENSG00000146904 [Gene_View]  chr7:143088205-143105985 [Contig_View]  EPHA1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000146904 [Gene_View]  chr7:143088205-143105985 [Contig_View]  EPHA1 [Vega]
ICGC DataPortalENSG00000146904
cBioPortalEPHA1
AceView (NCBI)EPHA1
Genatlas (Paris)EPHA1
WikiGenes2041
SOURCE (Princeton)EPHA1
Genomic and cartography
GoldenPath hg19 (UCSC)EPHA1  -     chr7:143088205-143105985 -  7q32-q36   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)EPHA1  -     7q32-q36   [Description]    (hg38-Dec_2013)
EnsemblEPHA1 - 7q32-q36 [CytoView hg19]  EPHA1 - 7q32-q36 [CytoView hg38]
Mapping of homologs : NCBIEPHA1 [Mapview hg19]  EPHA1 [Mapview hg38]
OMIM179610   
Gene and transcription
Genbank (Entrez)AA723562 AA723620 AA788809 AI057542 AK290351
RefSeq transcript (Entrez)NM_005232
RefSeq genomic (Entrez)AC_000139 NC_000007 NC_018918 NT_007933 NW_001839073 NW_004929333
Consensus coding sequences : CCDS (NCBI)EPHA1
Cluster EST : UnigeneHs.89839 [ NCBI ]
CGAP (NCI)Hs.89839
Alternative Splicing : Fast-db (Paris)GSHG0028676
Alternative Splicing GalleryENSG00000146904
Gene ExpressionEPHA1 [ NCBI-GEO ]     EPHA1 [ SEEK ]   EPHA1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP21709 (Uniprot)
NextProtP21709  [Medical]
With graphics : InterProP21709
Splice isoforms : SwissVarP21709 (Swissvar)
Catalytic activity : Enzyme2.7.10.1 [ Enzyme-Expasy ]   2.7.10.12.7.10.1 [ IntEnz-EBI ]   2.7.10.1 [ BRENDA ]   2.7.10.1 [ KEGG ]   
Domaine pattern : Prosite (Expaxy)EGF_2 (PS01186)    EPH_LBD (PS51550)    FN3 (PS50853)    PROTEIN_KINASE_ATP (PS00107)    PROTEIN_KINASE_DOM (PS50011)    PROTEIN_KINASE_TYR (PS00109)    RECEPTOR_TYR_KIN_V_1 (PS00790)    RECEPTOR_TYR_KIN_V_2 (PS00791)    SAM_DOMAIN (PS50105)   
Domains : Interpro (EBI)Eph_TM    Ephrin_rcpt_lig-bd_dom    Fibronectin_type3    Galactose-bd-like    Growth_fac_rcpt_N_dom    Ig-like_fold    Kinase-like_dom    Prot_kinase_dom    Protein_kinase_ATP_BS    SAM    SAM/pointed    SAM_type1    Ser-Thr/Tyr_kinase_cat_dom    Tyr_kinase_AS    Tyr_kinase_cat_dom    Tyr_kinase_ephrin_rcpt    Tyr_kinase_rcpt_V_CS   
Related proteins : CluSTrP21709
Domain families : Pfam (Sanger)EphA2_TM (PF14575)    Ephrin_lbd (PF01404)    fn3 (PF00041)    Pkinase_Tyr (PF07714)    SAM_1 (PF00536)   
Domain families : Pfam (NCBI)pfam14575    pfam01404    pfam00041    pfam07714    pfam00536   
Domain families : Smart (EMBL)EPH_lbd (SM00615)  FN3 (SM00060)  SAM (SM00454)  TyrKc (SM00219)  
DMDM Disease mutations2041
Blocks (Seattle)P21709
PDB (SRS)2K1K    2K1L    3HIL    3KKA   
PDB (PDBSum)2K1K    2K1L    3HIL    3KKA   
PDB (IMB)2K1K    2K1L    3HIL    3KKA   
PDB (RSDB)2K1K    2K1L    3HIL    3KKA   
Human Protein AtlasENSG00000146904
Peptide AtlasP21709
HPRD01554
IPIIPI00294250   IPI00908698   IPI00911030   
Protein Interaction databases
DIP (DOE-UCLA)P21709
IntAct (EBI)P21709
FunCoupENSG00000146904
BioGRIDEPHA1
IntegromeDBEPHA1
STRING (EMBL)EPHA1
Ontologies - Pathways
QuickGOP21709
Ontology : AmiGOangiogenesis  positive regulation of cell-matrix adhesion  protein kinase activity  transmembrane-ephrin receptor activity  ATP binding  integral component of plasma membrane  negative regulation of protein kinase activity  cell surface receptor signaling pathway  positive regulation of cell proliferation  peptidyl-tyrosine phosphorylation  protein kinase binding  positive regulation of cell migration  negative regulation of cell migration  regulation of Rac GTPase activity  activation of Rho GTPase activity  substrate adhesion-dependent cell spreading  positive regulation of angiogenesis  protein autophosphorylation  ephrin receptor signaling pathway  positive regulation of stress fiber assembly  
Ontology : EGO-EBIangiogenesis  positive regulation of cell-matrix adhesion  protein kinase activity  transmembrane-ephrin receptor activity  ATP binding  integral component of plasma membrane  negative regulation of protein kinase activity  cell surface receptor signaling pathway  positive regulation of cell proliferation  peptidyl-tyrosine phosphorylation  protein kinase binding  positive regulation of cell migration  negative regulation of cell migration  regulation of Rac GTPase activity  activation of Rho GTPase activity  substrate adhesion-dependent cell spreading  positive regulation of angiogenesis  protein autophosphorylation  ephrin receptor signaling pathway  positive regulation of stress fiber assembly  
Pathways : KEGGAxon guidance   
Protein Interaction DatabaseEPHA1
DoCM (Curated mutations)EPHA1
Wikipedia pathwaysEPHA1
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerEPHA1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)EPHA1
dbVarEPHA1
ClinVarEPHA1
1000_GenomesEPHA1 
Exome Variant ServerEPHA1
SNP (GeneSNP Utah)EPHA1
SNP : HGBaseEPHA1
Genetic variants : HAPMAPEPHA1
Genomic Variants (DGV)EPHA1 [DGVbeta]
Mutations
ICGC Data PortalENSG00000146904 
Somatic Mutations in Cancer : COSMICEPHA1 
CONAN: Copy Number AnalysisEPHA1 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)7:143088205-143105985
Mutations and Diseases : HGMDEPHA1
OMIM179610   
MedgenEPHA1
NextProtP21709 [Medical]
GENETestsEPHA1
Disease Genetic AssociationEPHA1
Huge Navigator EPHA1 [HugePedia]  EPHA1 [HugeCancerGEM]
snp3D : Map Gene to Disease2041
DGIdb (Drug Gene Interaction db)EPHA1
General knowledge
Homologs : HomoloGeneEPHA1
Homology/Alignments : Family Browser (UCSC)EPHA1
Phylogenetic Trees/Animal Genes : TreeFamEPHA1
Chemical/Protein Interactions : CTD2041
Chemical/Pharm GKB GenePA27817
Clinical trialEPHA1
Cancer Resource (Charite)ENSG00000146904
Other databases
Probes
Litterature
PubMed53 Pubmed reference(s) in Entrez
CoreMineEPHA1
GoPubMedEPHA1
iHOPEPHA1

Bibliography

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Invasiveness of breast carcinoma cells and transcript profile: Eph receptors and ephrin ligands as molecular markers of potential diagnostic and prognostic application.
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Differential gene expression of Eph receptors and ephrins in benign human tissues and cancers.
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Expression analysis of the Epha1 receptor tyrosine kinase and its high-affinity ligands Efna1 and Efna3 during early mouse development.
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Over-expression of Eph and ephrin genes in advanced ovarian cancer: ephrin gene expression correlates with shortened survival.
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Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1.
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Generation and characterization of EphA1 receptor tyrosine kinase reporter knockout mice.
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Contributor(s)

Written12-2008Brett Stringer, Nirmitha Herath, Shannon Duffy, Mark Coulthard, Andrew Boyd
Leukaemia Foundation Research Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane Qld 4006, Australia (BS, NH, SD, MC, AB); Royal Children's Hospital, Herston Qld 4006, Australia (MC); University of Queensland, St Lucia Qld 4067, Australia (AB)

Citation

This paper should be referenced as such :
Stringer, B ; Herath, N ; Duffy, S ; Coulthard, M ; Boyd, A
EPHA1 (EPH receptor A1)
Atlas Genet Cytogenet Oncol Haematol. 2009;13(11):817-820.
Free journal version : [ pdf ]   [ DOI ]
URL : http://AtlasGeneticsOncology.org/Genes/EPHA1ID40461ch7q35.html

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