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TYMP (thymidine phosphorylase)

Identity

Other namesECGF1
hPD-ECGF
MNGIE
PDECGF
TP
HGNC (Hugo) TYMP
LocusID (NCBI) 1890
Location 22q13.33
Location_base_pair Starts at 50964181 and ends at 50968514 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

Note The TP gene encodes an angiogenic factor which promotes angiogenesis both in vitro and in vivo and is involved in nucleotide synthesis and thymidine phosphorolysis.
 
  TYMP is located on chromosome 22 of which 3 transcripts have been identified.
Description Thymidine phosphorylase is located at chromosome 22 in the region of q13.33. cDNA is approximately 1.8 kb long, consisting of 10 exons in a 4.3 kb region (Hagiwara et al., 1991; Stenman et al., 1992). TP was first cloned and sequenced in 1989 (Ishikawa et al., 1989). The nucleic acid sequence of TP is highly conserved, the human TP shares 39% sequence identity with that of E. coli (Barton et al., 1992).
Transcription The promoter region of the TP gene has no TATA box or CCAAT box, but has a high G-C content and seven copies of the SP-1 binding site upstream from the transcription start site. Exact TP gene regulation is unknown, but has been described to be (indirectly) regulated by NFkB, TNF-alpha and IFN-gamma (Waguri et al., 1997; Zhu et al., 2002; Zhu et al., 2003; Eda et al., 1993; de Bruin et al., 2004).

Protein

Note Thymidine phosphorylase was first identified as the platelet-derived endothelial cell growth factor, because it was related to endothelial cell growth (Miyazono et al., 1987; Ishikawa et al., 1989). Later on, it was found that it was identical to thymidine phosphorylase (Furukawa et al., 1992). Thymidine phosphorylase (TP) is the most correct name to refer to this protein, since it catalyzes the phopshorolysis of thymidine to thymine. TP undergoes limited post-translational modification and is not glycosylated. Covalent linkage between serine residues of TP and phosphate groups of nucleotides has been observed, which may facilitate secretion of the protein (Usuki et al., 1991). However, TP does not contain a classical secretion signal (Ishikawa et al., 1989). TP is a dimer, consisting of two identical subunits that are non-covalently associated (Desgranges et al., 1981) with its dimeric molecular mass ranging from 90 kD in Escherichia coli to 110 kD in mammals (Schwartz, 1978; Desgranges et al., 1981).
Description TP protein does not contain a known receptor binding region or a secretion signal (Ishikawa et al., 1989). It is implicated in nucleotide synthesis and degradation of thymidine. TP is also implicated in angiogenesis (reviewed in de Bruin et al., 2006; Liekens et al., 2007; Bronckaers et al., 2009).
Expression TP is highly expressed in liver tissues. Furthermore, TP is often overexpressed in tumor sites and is involved in inflammatory diseases, such as rheumatoid arthritis.
Localisation TP is expressed in the cytoplasm and the nucleus (Fox et al., 1995).
Function TP catalyzes the phosphorolysis of thymidine (TdR) to thymine and 2-deoxy-alpha-D-ribose 1-phosphate (dR-1-P). TP can also catalyze the formation of thymidine from thymine and dR-1-P. TP also catalyzes the phosphorolysis of deoxyuridine to uracil and dR-1-P. TP also has deoxyribosyl transferase activity by which the deoxyribosyl moiety is transferred from a pyrimidine nucleoside to another pyrimidine base. Subsequently a new pyrimidine nucleoside is formed.
The sugars that are formed by degradation of thymidine are thought to play a role in the induction of angiogenesis. Deoxyribose-1-P can be converted to deoxyribose-5-phosphate or degraded to deoxyribose. Deoxyribose can be secreted, and possibly attract endothelial cells to form new blood vessels (reviewed in de Bruin et al., 2006; Liekens et al., 2007; Bronckaers et al., 2009). TP in some cancer cells can also increase their invasive potential, although the exact mechanism remains unclear.
TP can also activate or inactivate several pyrimidines or pyrimidine nucleoside analogs with antiviral and antitumoral activity, such as inactivation of trifluorothymidine (TFT) (Heidelberger et al., 1964) and 5-fluoro-2'-deoxyruidine (van Laar et al., 1998), or activation of 5-fluorouracil (5-FU) (Schwartz et al., 1995) and 5-fluoro-5'-deoxyuridine (5'DFUR).
Homology The TYMP gene is conserved in chimpanzee, mouse, rat, and zebrafish.

Mutations

Note Mutations in this gene have been associated with mitochondrial neurogastrointestinal encephalomyopathy (MNGIE). Multiple alternatively spliced variants, encoding the same protein, have been identified.

Implicated in

Entity Various cancer
Note TP in tumor sites can be expressed in the cancer cells, in the most malignant cells, tumor stromal cells (such as macrophages) or in the invasive part of the tumor (van Triest et al., 1999). A high TP expression and activity have been related to a poor outcome and increased angiogenesis. The TP gene is regulated by many other factors that are implicated in cancer, such as NFkB (de Bruin et al., 2004). TP regulates the expression of IL-8, and possibly also that of other genes, although the exact mechanism of this regulation is still unclear (Brown et al., 2000; Bijnsdorp et al., 2008). The high TP activity in the tumor can selectively activate the 5FU prodrug 5'-deoxy-5-fluorouridine to 5FU. 5'deoxy-5-fluorouridine is an intermediate of the oral 5FU prodrug Capecitabine (Xeloda) (de Bruin et al., 2006). On the other hand TP can inactivate the fluoropyrimidine trifluorothymidine (TFT), which is registered as the antiviral drug Viroptic® (De Clercq, 2004). An inhibitor of TP, TPI, will prevent inactivation of TFT. TAS-102 is a combination of TFT and TPI (in a molar ratio of 1:0.5) which is developed as an anticancer drug (Temmink et al., 2007).
Disease Gastrointestinal tumors (Fox et al., 1995; Yoshikawa et al., 1999; Kimura et al., 2002; Takebayashi et al., 1996), breast cancer (Moghaddam et al., 1995), bladder cancer (O'Brien et al., 1996).
Prognosis High expression is often related to a poor prognosis, an increased microvessel density and increased metastasis.
Abnormal Protein No fusion protein has been described.
  
Entity Rheumatoid arthritis
Note Elevated levels of (circulating) PD-ECGF (TP) were found in rheumatoid arthritis patients (Asai et al., 1993). In the sera and synovial fluids of patients suffering from rheumatoid arthritis PD-ECGF (TP) was detected at high levels (Asai et al., 1993). In addition, there was a significant positive correlation between PD-ECGF (TP) levels in synovial fluid and in serum (Asai et al., 1993). The elevated PD-ECGF (TP) levels presumably arise through induction of PD-ECGF (TP) in synoviocytes, resulting from aberrant production of cytokines like TNF-alpha and IL-1 (Waguri et al., 1997).
  
Entity Atherosclerosis
Note TP is expressed in atherosclerosis. Macrophages, foam cells and giant cells from both aortic and coronary plaques expressed TP, suggesting that TP may play a role in the pathogenesis of atherosclerosis (Boyle et al., 2000).
  
Entity Psoriasis
Note Increased PD-ECGF (TP) mRNA and immunoreactivity were found in lesional psoriasis compared to the non-lesional skin (Creamer et al., 1997). In another study it was reported that the thymidine phosphorylase activity was twenty-fold higher in psoriatic lesions than in normal skin (Hammerberg et al., 1991).
  
Entity Inflammatory bowel disease
Note In inflammatory bowel disease, TP has been found to be overexpressed, predominantly in macrophages and fibroblasts of the inflamed colonic mucosa. The grade of expression augmented with an increasing grade of inflammation. In addition, TP was found in the endothelial cells of the inflamed colonic mucosa (Giatromanolaki et al., 2003; Saito et al., 2003).
  
Entity Chronic glomerulonephritis
Note TP is upregulated in chronic glomerulonephritis (a renal disease characterized by inflammation of the glomeruli) where it probably plays a critical role in the progression of interstitial fibrosis (Wang et al., 2006).
  
Entity Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE)
Note An autosomal recessive disorder involving DNA alterations (Bardosi et al., 1987). Gene mutations in the TP gene include missense, splice sites microdeletions and single nucleotide insertions (Spinazzola et al., 2002; Nishino et al., 2000). These mutations are associated with a severe reduction in TP activity. This leads to increased thymidine plasma levels, and increased deoxyuridine levels (which is also a substrate for TP).
Prognosis Not determined.
  

External links

Nomenclature
HGNC (Hugo)TYMP   3148
Cards
AtlasTYMPID40397ch22q13
Entrez_Gene (NCBI)TYMP  1890  thymidine phosphorylase
GeneCards (Weizmann)TYMP
Ensembl (Hinxton)ENSG00000025708 [Gene_View]  chr22:50964181-50968514 [Contig_View]  TYMP [Vega]
AceView (NCBI)TYMP
Genatlas (Paris)TYMP
WikiGenes1890
SOURCE (Princeton)NM_001113755 NM_001113756 NM_001257988 NM_001257989 NM_001953
Genomic and cartography
GoldenPath (UCSC)TYMP  -  22q13.33   chr22:50964181-50968514 -  22q13   [Description]    (hg19-Feb_2009)
EnsemblTYMP - 22q13 [CytoView]
Mapping of homologs : NCBITYMP [Mapview]
OMIM131222   603041   
Gene and transcription
Genbank (Entrez)AK057214 AK225269 AK298691 AK301194 AK314716
RefSeq transcript (Entrez)NM_001113755 NM_001113756 NM_001257988 NM_001257989 NM_001953
RefSeq genomic (Entrez)AC_000154 NC_000022 NC_018933 NG_011860 NG_016235 NT_011526 NW_001838756 NW_004929431
Consensus coding sequences : CCDS (NCBI)TYMP
Cluster EST : UnigeneHs.180903 [ NCBI ]
CGAP (NCI)Hs.180903
Alternative Splicing : Fast-db (Paris)GSHG0033962
Alternative Splicing GalleryENSG00000025708
Gene ExpressionTYMP [ NCBI-GEO ]     TYMP [ SEEK ]   TYMP [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP19971 (Uniprot)
NextProtP19971  [Medical]
With graphics : InterProP19971
Splice isoforms : SwissVarP19971 (Swissvar)
Catalytic activity : Enzyme2.4.2.4 [ Enzyme-Expasy ]   2.4.2.42.4.2.4 [ IntEnz-EBI ]   2.4.2.4 [ BRENDA ]   2.4.2.4 [ KEGG ]   
Domaine pattern : Prosite (Expaxy)THYMID_PHOSPHORYLASE (PS00647)   
Domains : Interpro (EBI)Glycosyl_Trfase_fam3    Glycosyl_Trfase_fam3_N_dom    PYNP_C    Pyrmidine_PPas_bac/euk    Pyrmidine_PPase    Pyrmidine_PPase_CS   
Related proteins : CluSTrP19971
Domain families : Pfam (Sanger)Glycos_trans_3N (PF02885)    Glycos_transf_3 (PF00591)    PYNP_C (PF07831)   
Domain families : Pfam (NCBI)pfam02885    pfam00591    pfam07831   
Domain families : Smart (EMBL)PYNP_C (SM00941)  
DMDM Disease mutations1890
Blocks (Seattle)P19971
PDB (SRS)1UOU    2J0F    2WK5    2WK6   
PDB (PDBSum)1UOU    2J0F    2WK5    2WK6   
PDB (IMB)1UOU    2J0F    2WK5    2WK6   
PDB (RSDB)1UOU    2J0F    2WK5    2WK6   
Human Protein AtlasENSG00000025708
Peptide AtlasP19971
HPRD08833
IPIIPI00292858   IPI00903115   IPI00910873   IPI00852987   IPI00853163   
Protein Interaction databases
DIP (DOE-UCLA)P19971
IntAct (EBI)P19971
FunCoupENSG00000025708
BioGRIDTYMP
InParanoidP19971
Interologous Interaction database P19971
IntegromeDBTYMP
STRING (EMBL)TYMP
Ontologies - Pathways
Ontology : AmiGOmitochondrial genome maintenance  angiogenesis  phosphorylase activity  platelet-derived growth factor receptor binding  cytosol  pyrimidine nucleobase metabolic process  pyrimidine nucleotide metabolic process  DNA replication  chemotaxis  growth factor activity  thymidine phosphorylase activity  pyrimidine-nucleoside phosphorylase activity  transferase activity, transferring pentosyl groups  cell differentiation  pyrimidine nucleoside salvage  small molecule metabolic process  pyrimidine nucleoside catabolic process  nucleobase-containing small molecule metabolic process  
Ontology : EGO-EBImitochondrial genome maintenance  angiogenesis  phosphorylase activity  platelet-derived growth factor receptor binding  cytosol  pyrimidine nucleobase metabolic process  pyrimidine nucleotide metabolic process  DNA replication  chemotaxis  growth factor activity  thymidine phosphorylase activity  pyrimidine-nucleoside phosphorylase activity  transferase activity, transferring pentosyl groups  cell differentiation  pyrimidine nucleoside salvage  small molecule metabolic process  pyrimidine nucleoside catabolic process  nucleobase-containing small molecule metabolic process  
Pathways : KEGGPyrimidine metabolism    Drug metabolism - other enzymes    Bladder cancer   
REACTOMETYMP
Protein Interaction DatabaseTYMP
Wikipedia pathwaysTYMP
Gene fusion - rearrangments
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)TYMP
SNP (GeneSNP Utah)TYMP
SNP : HGBaseTYMP
Genetic variants : HAPMAPTYMP
1000_GenomesTYMP 
ICGC programENSG00000025708 
Somatic Mutations in Cancer : COSMICTYMP 
CONAN: Copy Number AnalysisTYMP 
Mutations and Diseases : HGMDTYMP
OMIM131222    603041   
GENETestsTYMP
Disease Genetic AssociationTYMP
Huge Navigator TYMP [HugePedia]  TYMP [HugeCancerGEM]
Genomic VariantsTYMP  TYMP [DGVbeta]
Exome VariantTYMP
dbVarTYMP
ClinVarTYMP
snp3D : Map Gene to Disease1890
General knowledge
Homologs : HomoloGeneTYMP
Homology/Alignments : Family Browser (UCSC)TYMP
Phylogenetic Trees/Animal Genes : TreeFamTYMP
Chemical/Protein Interactions : CTD1890
Chemical/Pharm GKB GenePA162407502
Clinical trialTYMP
Cancer Resource (Charite)ENSG00000025708
Other databases
Probes
Litterature
PubMed140 Pubmed reference(s) in Entrez
CoreMineTYMP
iHOPTYMP

Bibliography

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Contributor(s)

Written03-2010Irene V Bijnsdorp, Godefridus J Peters
Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands

Citation

This paper should be referenced as such :
Bijnsdorp IV, Peters GJ . TYMP (thymidine phosphorylase). Atlas Genet Cytogenet Oncol Haematol. March 2010 .
URL : http://AtlasGeneticsOncology.org/Genes/TYMPID40397ch22q13.html

The various updated versions of this paper are referenced and archived by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/44924/1/03-2010-TYMPID40397ch22q13.pdf   [ Bibliographic record ]

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