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GPX3 (Glutathione peroxidase 3)

Written2014-11Yan-Ping Yu, Jianhua Luo
Department of Pathology, University of Pittsburgh / ypyu@pitt.edu; luoj@upmc.edu

Abstract Review on GPX3, with data on DNA, on the protein encoded, and where the gene is implicated.

Keywords GPX3; Glutathione peroxidase 3

(Note : for Links provided by Atlas : click)

Identity

Alias_namesglutathione peroxidase 3 (plasma)
Other aliasGPX-P
GSHPX-3
GSHPX-P
HGNC (Hugo) GPX3
LocusID (NCBI) 2878
Atlas_Id 46158
Location 5q33.1  [Link to chromosome band 5q33]
Location_base_pair Starts at 151020412 and ends at 151028993 bp from pter ( according to hg19-Feb_2009)  [Mapping GPX3.png]
Fusion genes
(updated 2016)
AARS (16q22.1) / GPX3 (5q33.1)AFAP1L2 (10q25.3) / GPX3 (5q33.1)GPX3 (5q33.1) / CHD4 (12p13.31)
GPX3 (5q33.1) / GPX3 (5q33.1)GPX3 (5q33.1) / NSMCE1 (16p12.1)GPX3 (5q33.1) / RPN2 (20q11.23)
GPX3 (5q33.1) / S100A8 (1q21.3)GPX3 (5q33.1) / SEC63 (6q21)GPX3 (5q33.1) / SQSTM1 (5q35.3)
INPP4B (4q31.21) / GPX3 (5q33.1)

DNA/RNA

 
  The human GPx3 gene is located at the forward strand of chromosome 5 in the region between 151,020,438 to 151,028,993 bps (GRCh38), comprising 5 exons and adjacent to TNIP1 gene. There are 10 to 11 variant transcripts of GPx3, but only 7 are processed as proteins, according Ensemble Genome Browser database (ENSG00000211445), of which only one with known function (NCBI database).
Transcription Human GPx3 gene is transcribed to the GPx3 transcript of 1779 bp (NM_002084), consisting of exon 1 (1-304 bp), exon 2 (305-458), exon 3 (459-576), exon 4 (577-676), and exon 5 (677-1761). The coding DNA sequence (CDS) 218..898 bp, encodes for a protein of 226 aa, comprising a leading signal peptide sequence at 218..277 bp followed by the main coding sequence for GPx3. An OPAL codon (TGA) at 434-436 bp is translated to a Selenocycteine (Chambers et al. 1986; Fu et al. 2002; Fu et al. 2002).
Pseudogene Unknown.

Protein

 
Description Plasma glutathione peroxidase 3 is a member of glutathione peroxidase family, and is the only secretary glutathione peroxidase, accounting for the all glutatione peroxidase in extracellular compartment. Structurally, intracellular GPx3 has a leading signal peptide. GPx3, similar to other selenoproteins, contains a UGA OPAL codon at codon 73, which is coded for a selenocystein residue in the presence of selenium. IMAGE_2
Expression GPx3 is a plasma glutathione peroxidase, being secreted to extracellular compartment after synthesized in cells. GPx3 mRNA is expressed in different tissues, lung, heart, breast, prostate, placenta,and kidney. But majority (almost 70%) of plasma GPx3 is thought kidney originated(Avissar et al. 1994; Tham et al. 1998). GPx3 is transported through circulation and binds to the basement membrane of epithelia of GI (Burk et al. 2011). GPx3 mRNA is detected in a variety of tissues, while most of them are not joining in the plasma GPx3(Chu et al. 1992; Maeda et al. 1997; Tham, Whitin et al. 1998), implicating the unknown function of GPx3 in other tissues or organs.
Function Glutathione peroxydase 3, as other tetrameric GPx enzymes using reduced glutatione as electron donor, catalyses the oxydation of reduced glutathione and the simultaneous reduction of a variety of hydrogen peroxide and organoperoxides. As a result, the GPx3 functions in the system to relieve oxidative stress as an antioxidant enzyme. The catalytic residues in GPx3 have been mapped to the location of U73, Q107 and W181(Ren et al. 1997). U73 codes for selenocycteine, a residue that is involved in the reduction of hydrogen peroxide in a catalytic cycle of its atom, from reduced selenolate anion (R-se) to oxidized selenic acid (R-Se-OH). Latter regenerates selenolate anion by GSH. In physiological PH, selenole forms anion, a good reducing source in the system(Ren, Huang et al. 1997). However, electron donor GSH is limited in the extracellular space, implicating a rate limiting factor in the antioxidative function of GPx3. Conserved domain analysis classifies glutathione peroxidase as thioredoxin-like-superfamily protein (Conserved domains database[gi|6006001|ref|NP_002075|]).
In recent studies, GPx3 protein expression was found in a variety of normal tissues or cells, while down-regulated in a number of cancers. Through Yeast Two-Hybrid analyses, GPx3 was found interacting with several proteins in cells. One of such proteins is a TP53 transactivated protein, PIG3, which positively regulates apoptosis and mediates UV-induced cell death. The interaction between GPx3 and PIG3 leads to apoptotic cell death. GPx3 with mutated OPAL codon retains its capabilities in promoting cell death, suggesting that GPx3 contains pro-apoptotic activity independent of its peroxidase function(Wang et al. 2012).
 
Homology Glutathion peroxidase activity of GPx3 is conserved in other seven GPx selenocysteine containing proteins. Though encoded from different genes, all contain a common UGA OPAL codon, encoding a selenocysteine residue in coding region, an active site of enzyme activity(Tosatto et al. 2008). GPx3 sequence, if excluding signal peptide, has the highest homology (84%) and identities (72%) with GPx5 encompassing 200 out of 226 aa in the coding region; while 60% homology with GPx1, GPx2 ; but low, 46-47% with GPx4,6,7,and 8.
GPx3 is expressed in other species. Human GPx3 shares sequece homology (94%) and identities (89%) with mouse GPx3 over 226 aa including signal peptide sequence; 95-96% homology and 91-92% identities with rat(NP_071970.2)and dog (NP_001157926.1) of full coding region, but is of only limited homology to GPx3 in Xenopus Laevis (NP_001085319.2)and Zebra fish (NP_001131027.1).

Mutations

Note Not known.
 
  Expression and methylation of GPx3 gene in multiple cancer cell lines(Yu et al. 2004; Yu, Yu et al. 2007; Chen, Rao et al. 2011)GERMINAL

Implicated in

Note
  
Entity Prostate cancer
Oncogenesis Silencing of GPx3 gene with hypermethylation of GPx3 promoter was first found in a microarray study of three prostate cancer cell lines, in which treated with 5-aza-2' deoxycytidine, GPx3 expression was induced in these cells originally silenced in GPx3 (Lodygin et al. 2005). GPx3 down-regulation was subsequently confirmed in several gene expression-array analyses of a large number of human prostate cancer specimens with high rate of occurrence (LaTulippe et al. 2002; Luo et al. 2002; Yu, Landsittel et al. 2004; Yu, Yu et al. 2007). Complete inactivation of GPx3 was closely correlated with the poor clinical outcome of prostate cancer. Hemizygous and homozygous deletion of GPx3 gene occurs in a subset of prostate cancer samples(39%). CpG island hypermethylation in GPx3 promoter occurs in over 90% of prostate cancer samples (Lodygin, Epanchintsev et al. 2005; Yu, Yu et al. 2007). The frequent CpG hypermethylation in GPx3 in cancer suggests that hypermethylation plays a significant role in GPx3 down-regulation in cells. Down-regulation of GPx3 increases these cell's vulnerability to oxidative damages. Conditions predisposed to prostate cancer, such as high animal fat diet in TRAM mice and loss of tumor suppressor Nkx3.1, has been found accompanied with decrease in GPx3 expression in animal (Chang et al. 2014), (Ouyang et al. 2005).
  
  
Entity Cervical cancer
Oncogenesis GPx3 is down-regulated in cervical cancer tissues when compared with normal cervical tissues, and the down-regulation is closely correlated to lymph node metastasis and prognosis in cervical cancer patients. Promoter methylation is the major cause of GPX3 down-regulation(Zhang et al. 2014).
  
  
Entity Esophageal squamous cell carcinoma(ESCC) and Barrett's adenocarcinomas (BA)
Oncogenesis Down-regulation of GPx3 expression in ESCC was revealed in a DNA micro-array study and GPx3 gene methylation was indicated by demethylation treatment of ESCC tissues with 5-aza-2'-deoxycytidine, where GPx3 expression was restored in 71.4% of tumor samples and 10.7% of adjacent normal tissues(He et al. 2011). The GPx3 gene methylation was significantly correlated with the downregulation of GPx3 mRNAs in tumors.
In Barrett's adenocarcinomas (BA), quantitative RT-PCR revealed 91% of tumor samples with reduced levels of GPx3 mRNA. Similarly, GPx3 promoter hypermethylation was detected in 88% of BA samples with the mostly bi-alleles hypermethylation(Lee et al. 2005; Peng et al. 2009).
  
  
Entity Gastric cancer
Oncogenesis Down-regulation of GPx3 expression in gastric cancer was identified in gastric cancer tissues, which displayed a high occurrence rate of 8/9 cancer cell lines, and 83% (90/108) of gastric cancer samples. Hypermethylation of GPx3 promoter in 6 out of 9 cancer cell lines and 60% of gastric cancer samples significantly contributed to the silencing of GPx3 gene(Zhang, Yang et al. 2010; Peng et al. 2012), although loss of copy number of GPx3 gene was also detected in the cancer samples. Silencing of GPx3 was correlated to the lymph node metastasis of gastric cancer and was also detected in the adjacent normal gastric tissue samples, suggestive of cancer field effects in gastric tract. In addition, a study showed that two intronic SNPs in GPx3 significantly altered gene expression, a possible link to the increasing risks of gastric cancer (Wang et al. 2010). Wound healing analyses showed that retoring GPx3 expression in cells decreased cell motility, a possible feature involved in cancer metastasis.
  
  
Entity Breast cancer
Oncogenesis Down-regulation of GPX3 expression in breast cancer was identified through immunohistochemistry (IHC) analyses of breast cancer samples by comparing with the normal tissues. The inflammatory breast cancer (IBC), with higher frequency of GPx3 promoter methylation, had GPx3 expression significantly lower than those in non-inflammatory breast cancer (non-IBC)(Mohamed et al. 2014).
  
  
Entity Ovarian carcinoma
Oncogenesis Similar to breast cancer, abberation of GPx3 expression in ovarian cancer distinguishes cancer stage and cell type of ovarian cancer ; Decreased levels of serous glutathione peroxidase 3 were associated with late stages of papillary serous ovarian cancer or disease progression(Lau et al. 2014), while clear cell subtype showed elevated GPx3 expression(Hough et al. 2001).
  
  
Entity Colorectal Carcinoma
Oncogenesis Tumor suppression of GPx3 in the inflammatory colonic tumorigenesis (colitis associated carcinoma) model was suggested in the GPx3-knockout mice as the manifestation of the increased number of tumor with higher degree of dysplasia in colon. Knockdown of GPx3 in the colon cancer cell line resulted in increase of inflammation, proliferation, DNA damage and apoptosis following the exposure to oxidative stress (Barrett et al. 2013). Genotype analyses of three SNPs in GPx3 indicates that the genetic variations in GPx3 contribute to the risk of rectal cancer (Haug et al. 2012)
  

Bibliography

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The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the 'termination' codon, TGA
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High animal fat intake enhances prostate cancer progression and reduces glutathione peroxidase 3 expression in early stages of TRAMP mice
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Prostate 2014 Sep;74(13):1266-77
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Glutathione peroxidase tagSNPs: associations with rectal cancer but not with colon cancer
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Identification of GPX3 epigenetically silenced by CpG methylation in human esophageal squamous cell carcinoma
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Dig Dis Sci 2011 Mar;56(3):681-8
PMID 20725785
 
Coordinately up-regulated genes in ovarian cancer
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Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease
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Hypermethylation and loss of expression of glutathione peroxidase-3 in Barrett's tumorigenesis
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PMID 16229808
 
Functional epigenomics identifies genes frequently silenced in prostate cancer
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Cancer Res 2005 May 15;65(10):4218-27
PMID 15899813
 
Gene expression analysis of prostate cancers
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Mol Carcinog 2002 Jan;33(1):25-35
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Analysis of an expression profile of genes in the human adipose tissue
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Gene 1997 May 6;190(2):227-35
PMID 9197538
 
Promoter hypermethylation and suppression of glutathione peroxidase 3 are associated with inflammatory breast carcinogenesis
Mohamed MM, Sabet S, Peng DF, Nouh MA, El-Shinawi M, El-Rifai W
Oxid Med Cell Longev 2014;2014:787195
PMID 24790704
 
Loss-of-function of Nkx3
Ouyang X, DeWeese TL, Nelson WG, Abate-Shen C
1 promotes increased oxidative damage in prostate carcinogenesis Cancer Res
PMID 16061659
 
Silencing of glutathione peroxidase 3 through DNA hypermethylation is associated with lymph node metastasis in gastric carcinomas
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DNA hypermethylation regulates the expression of members of the Mu-class glutathione S-transferases and glutathione peroxidases in Barrett's adenocarcinoma
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p53-induced gene 3 mediates cell death induced by glutathione peroxidase 3
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Positive ALDH1A3 and negative GPX3 expressions are biomarkers for poor prognosis of gallbladder cancer
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Citation

This paper should be referenced as such :
Yu YP, Luo J
GPX3 (Glutathione peroxidase 3);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/GPX3ID46158ch5q33.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Esophagus: Barrett's esophagus, dysplasia and adenocarcinoma


External links

Nomenclature
HGNC (Hugo)GPX3   4555
Cards
AtlasGPX3ID46158ch5q33
Entrez_Gene (NCBI)GPX3  2878  glutathione peroxidase 3
AliasesGPx-P; GSHPx-3; GSHPx-P
GeneCards (Weizmann)GPX3
Ensembl hg19 (Hinxton)ENSG00000211445 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000211445 [Gene_View]  chr5:151020412-151028993 [Contig_View]  GPX3 [Vega]
ICGC DataPortalENSG00000211445
TCGA cBioPortalGPX3
AceView (NCBI)GPX3
Genatlas (Paris)GPX3
WikiGenes2878
SOURCE (Princeton)GPX3
Genetics Home Reference (NIH)GPX3
Genomic and cartography
GoldenPath hg38 (UCSC)GPX3  -     chr5:151020412-151028993 +  5q33.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)GPX3  -     5q33.1   [Description]    (hg19-Feb_2009)
EnsemblGPX3 - 5q33.1 [CytoView hg19]  GPX3 - 5q33.1 [CytoView hg38]
Mapping of homologs : NCBIGPX3 [Mapview hg19]  GPX3 [Mapview hg38]
OMIM138321   
Gene and transcription
Genbank (Entrez)AF217787 AK310242 AL036834 BC013218 BC013601
RefSeq transcript (Entrez)NM_001329790 NM_002084
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)GPX3
Cluster EST : UnigeneHs.386793 [ NCBI ]
CGAP (NCI)Hs.386793
Alternative Splicing GalleryENSG00000211445
Gene ExpressionGPX3 [ NCBI-GEO ]   GPX3 [ EBI - ARRAY_EXPRESS ]   GPX3 [ SEEK ]   GPX3 [ MEM ]
Gene Expression Viewer (FireBrowse)GPX3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)2878
GTEX Portal (Tissue expression)GPX3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP22352   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP22352  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP22352
Splice isoforms : SwissVarP22352
Catalytic activity : Enzyme1.11.1.9 [ Enzyme-Expasy ]   1.11.1.91.11.1.9 [ IntEnz-EBI ]   1.11.1.9 [ BRENDA ]   1.11.1.9 [ KEGG ]   
PhosPhoSitePlusP22352
Domaine pattern : Prosite (Expaxy)GLUTATHIONE_PEROXID_1 (PS00460)    GLUTATHIONE_PEROXID_2 (PS00763)    GLUTATHIONE_PEROXID_3 (PS51355)   
Domains : Interpro (EBI)Glutathione_peroxidase    GPX_AS    GPX_CS    Thioredoxin-like_fold   
Domain families : Pfam (Sanger)GSHPx (PF00255)   
Domain families : Pfam (NCBI)pfam00255   
Conserved Domain (NCBI)GPX3
DMDM Disease mutations2878
Blocks (Seattle)GPX3
PDB (SRS)2R37   
PDB (PDBSum)2R37   
PDB (IMB)2R37   
PDB (RSDB)2R37   
Structural Biology KnowledgeBase2R37   
SCOP (Structural Classification of Proteins)2R37   
CATH (Classification of proteins structures)2R37   
SuperfamilyP22352
Human Protein AtlasENSG00000211445
Peptide AtlasP22352
HPRD11750
IPIIPI00026199   IPI01016046   IPI00984125   IPI00974335   IPI00976574   IPI00974138   IPI00984754   
Protein Interaction databases
DIP (DOE-UCLA)P22352
IntAct (EBI)P22352
FunCoupENSG00000211445
BioGRIDGPX3
STRING (EMBL)GPX3
ZODIACGPX3
Ontologies - Pathways
QuickGOP22352
Ontology : AmiGOresponse to reactive oxygen species  glutathione peroxidase activity  glutathione peroxidase activity  protein binding  extracellular region  extracellular space  response to lipid hydroperoxide  transcription factor binding  selenium binding  hydrogen peroxide catabolic process  protein homotetramerization  oxidation-reduction process  extracellular exosome  cellular oxidant detoxification  
Ontology : EGO-EBIresponse to reactive oxygen species  glutathione peroxidase activity  glutathione peroxidase activity  protein binding  extracellular region  extracellular space  response to lipid hydroperoxide  transcription factor binding  selenium binding  hydrogen peroxide catabolic process  protein homotetramerization  oxidation-reduction process  extracellular exosome  cellular oxidant detoxification  
Pathways : KEGGGlutathione metabolism    Arachidonic acid metabolism    Thyroid hormone synthesis   
REACTOMEP22352 [protein]
REACTOME PathwaysR-HSA-3299685 [pathway]   
NDEx NetworkGPX3
Atlas of Cancer Signalling NetworkGPX3
Wikipedia pathwaysGPX3
Orthology - Evolution
OrthoDB2878
GeneTree (enSembl)ENSG00000211445
Phylogenetic Trees/Animal Genes : TreeFamGPX3
HOVERGENP22352
HOGENOMP22352
Homologs : HomoloGeneGPX3
Homology/Alignments : Family Browser (UCSC)GPX3
Gene fusions - Rearrangements
Fusion : MitelmanGPX3/CHD4 [5q33.1/12p13.31]  
Fusion : MitelmanGPX3/SEC63 [5q33.1/6q21]  [t(5;6)(q33;q21)]  
Fusion : MitelmanGPX3/SQSTM1 [5q33.1/5q35.3]  [t(5;5)(q33;q35)]  
Fusion: TCGAGPX3 5q33.1 CHD4 12p13.31 THCA
Fusion: TCGAGPX3 5q33.1 SEC63 6q21 THCA
Fusion: TCGAGPX3 5q33.1 SQSTM1 5q35.3 THCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerGPX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)GPX3
dbVarGPX3
ClinVarGPX3
1000_GenomesGPX3 
Exome Variant ServerGPX3
ExAC (Exome Aggregation Consortium)GPX3 (select the gene name)
Genetic variants : HAPMAP2878
Genomic Variants (DGV)GPX3 [DGVbeta]
DECIPHERGPX3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisGPX3 
Mutations
ICGC Data PortalGPX3 
TCGA Data PortalGPX3 
Broad Tumor PortalGPX3
OASIS PortalGPX3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICGPX3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDGPX3
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 GPX3
DgiDB (Drug Gene Interaction Database)GPX3
DoCM (Curated mutations)GPX3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)GPX3 (select a term)
intoGenGPX3
NCG5 (London)GPX3
Cancer3DGPX3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM138321   
Orphanet
MedgenGPX3
Genetic Testing Registry GPX3
NextProtP22352 [Medical]
TSGene2878
GENETestsGPX3
Target ValidationGPX3
Huge Navigator GPX3 [HugePedia]
snp3D : Map Gene to Disease2878
BioCentury BCIQGPX3
ClinGenGPX3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD2878
Chemical/Pharm GKB GenePA28951
Clinical trialGPX3
Miscellaneous
canSAR (ICR)GPX3 (select the gene name)
Probes
Litterature
PubMed88 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineGPX3
EVEXGPX3
GoPubMedGPX3
iHOPGPX3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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