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TNF (tumor necrosis factor (TNF superfamily, member 2))

Identity

Other namesTNFa (Tumor Necrosis Factor-a)
Cachectin
TNF superfamily member 2
DIF
HGNC (Hugo) TNF
Location 6p21.3
Location_base_pair Starts at 31651329 and ends at 31654091 bp from pter ( according to hg18-Mar_2006)  [Mapping]

DNA/RNA

Description The human TNFa gene has 4 exons spanning 2,762bp on the region of chromosome 6p21.3. The expression of TNFa gene generates a TNFa mRNA with size of 1,669nt. The 3'-UTR region of TNFa mRNA contains a cluster of "AUUUA" elements that can be seen among many mRNAs with a short half-life, (AUUAUUUAUUAUUUAUUUAUUUAUUUAUUUAUUUA). A multiple NF-kB binding elements have been identified in the promoter region of TNFa gene.

Protein

 
  The phylogenetic tree of TNF superfamily members.
Description The human TNFa protein contains 233 amino acids with a predicated molecular weight of 25.6 kDa. The TNFa is produced initially in a membrane-associated form, which is then subjected to enzymatic remove of the N-terminal 76 amino acids by TACE/ADAM17, a TNFa converting enzyme, to generate the soluble 17kDa TNFa molecule that forms homotrimer. TNFa is the first prototypic member identified in the TNF superfamily (TNFSF, Fig.1 and Table 1). The human TNF superfamily currently has 19 well-characterized members. Other members, such as TNFSF19, TNFSF21, and TNFSF22 have not been well-established. Although each member has its own receptor preference, a functional overlapping, such as induction of apoptosis and NF-kB activation, has been observed among the majority of these members. In addition, as indicated in the phylogenetic tree in Figure 1, all of these members exhibit an evolutional conservation in their amino acid sequences, many of which show characteristics of type II membrane proteins. These features of TNF superfamily suggest that the members in this family may derived from the same ancestral gene. Several members contain a C-terminal conserved domain, named the TNF-homology domain that shares 20-30% of sequence identity. Except TNFSF1 (lymphotoxin a) and TNFSF3 (lymphotoxin b) that can form either homotrimer or heterotrimer, the active form of other members in this family is homotrimer.
Expression TNFa is expressed virtually in every type of cells in response to inflammatory signals.
Localisation membrane (type II membrane protein), extracellular soluble form, blood stream, and biological fluids.
Function The most abundant cellular sources of TNFa are macrophage and monocyte. In response to inflammatory stimulation, macrophage or monocyte secretes TNFa that can induce apoptotic or necrotic cell death of certain tumor cell lines. In addition, TNFa is also capable of inducing cell proliferation and differentiation in many types of cells under certain circumstances. TNFa can be a pyrogen that causes fever by its direct action or by stimulation of interleukin 1 secretion. Sustained generation of TNFa in a variety of human diseases, especially cancer and severe infection, can cause cachexia-like syndrome. The increased expression of TNFa in adipose tissue was considered to be responsible for the development of obesity or diabetes due to the induction of insulin resistance by TNFa. All of above functional characteristics of TNFa are executed through specific members of the TNF receptor (TNFR) superfamily, mainly TNFR1, the primary receptor for soluble TNFa, and TNFR2, the predominant receptor for membrane-associated TNFa. These receptors trigger several intracellular signaling pathways, most importantly, the IkB kinase (IKK) and mitogen-activated protein kinase (MAPK) cascades, which govern gene expression through NF-kBNF-kB and AP-1 transcription factors, respectively.

Implicated in

Disease Arthritis, asthma, cancer, cardiovascular disorders, diabetes, HIV infection and AIDS, inflammatory bowel disease, lung fibrosis, obesity, septic shock, etc..
Cytogenetics Mutations or polymorphisms in the promoter or coding region of TNFa gene have been associated with asthma, celiac, septic shock susceptibility, silicosis, Psoriasis, GVHD, Leprosy, etc..
  

External links

Nomenclature
HGNC (Hugo)TNF   11892
Entrez_Gene (NCBI)TNF  7124  tumor necrosis factor (TNF superfamily, member 2)
Cards
AtlasTNFaID319
GeneCards (Weizmann)TNF
Ensembl (Hinxton)ENSG00000232810 [Gene_View]  TNF [Vega]
AceView (NCBI)TNF
Genatlas (Paris)TNF
euGene (Indiana)7124
SOURCE (Stanford)NM_000594
Gene Expression (Array Express) ENSG00000232810
Genomic and cartography
GoldenPath (UCSC)TNF  -  6p21.3   chr6:31651329-31654091 +  6p21.3   [Description]    (hg18-Mar_2006)
EnsemblTNF - 6p21.3 [CytoView]
Mapping of homologs : NCBITNF [Mapview]
OMIM157300   191160   248310   600807   611162   
Gene and transcription
Gene : Genbank (Entrez)AB451492 AF043342 AF098751 AJ227911 AJ251878
Reference sequence (RefSeq transcript) :SRSNM_000594
Reference transcript : EntrezNM_000594
RefSeq genomic : SRSAC_000049 AC_000138 NC_000006 NG_007462 NT_007592 NT_113891 NT_167244 NT_167245 NT_167246 NT_167247 NT_167248 NT_167249 NW_001838980 NW_923073
RefSeq genomic : EntrezAC_000049 AC_000138 NC_000006 NG_007462 NT_007592 NT_113891 NT_167244 NT_167245 NT_167246 NT_167247 NT_167248 NT_167249 NW_001838980 NW_923073
Consensus coding sequences : CCDS NCBITNF
Cluster EST : UnigeneHs.241570 [ SRS ] Hs.241570 [ NCBI ]
Alternative Splicing : Fast-db (Paris)5874
Protein : pattern, domain, 3D structure
Protein : UniProt/SwissProtP01375 (SRS) P01375 (Expasy) P01375 (Uniprot)
With graphics : InterProP01375
Splice isoforms : VarSplice FASTAP01375(VarSplice FASTA)
Domaine pattern : Prosite (SRS)TNF_1 (PS00251)    TNF_2 (PS50049)   
Domain pattern : Prosite (Expaxy)TNF_1 (PS00251)    TNF_2 (PS50049)   
Domains : Interpro (SRS)TNF_a/b/c    TNF_alpha    TNF_family    Tumour_necrosis_fac-like   
Domains : Interpro (EBI)TNF_a/b/c    TNF_alpha    TNF_family    Tumour_necrosis_fac-like   
Related proteins : CluSTrP01375
Domain families : Pfam SRSTNF (PF00229)   
Domain families : Pfam SangerTNF (PF00229)   
Domain families : Pfam NCBIpfam00229   
Domain families : Smart EMBLTNF (SM00207)  
Blocks (Seattle)P01375
Crystal structure of protein : PDB SRS1A8M    1TNF    2AZ5    2E7A    2TUN    2ZJC    2ZPX    3IT8    4TSV    5TSW   
Crystal structure of protein : PDBSum1A8M    1TNF    2AZ5    2E7A    2TUN    2ZJC    2ZPX    3IT8    4TSV    5TSW   
Crystal structure of protein : IMB1A8M    1TNF    2AZ5    2E7A    2TUN    2ZJC    2ZPX    3IT8    4TSV    5TSW   
Crystal structure of protein : PDB RSDB1A8M    1TNF    2AZ5    2E7A    2TUN    2ZJC    2ZPX    3IT8    4TSV    5TSW   
HPRD01855
Protein Interaction databases
DIP (DOE-UCLA)P01375
IntAct (EBI)P01375
Polymorphism : SNP, mutations, diseases
Single Nucleotide Polymorphism (SNP) : dbSNP NCBITNF
SNP : GeneSNP UtahTNF
SNP : HGBaseTNF
Genetic variants : HAPMAPTNF
Somatic Mutations in Cancer : COSMICTNF 
Mutations and Diseases : HGMDTNF
Hereditary diseases : OMIM157300    191160    248310    600807    611162   
Hereditary diseases : GENETests157300    191160    248310    600807    611162   
Diseases : Genetic AssociationTNF
General knowledge
Homologs : HomoloGeneTNF
Homology/Alignments : Family Browser UCSCTNF
Phylogenetic Trees/Animal Genes : TreeFamTNF
Chemical/Protein Interactions : CTD7124
Keywords Ontology : AmiGOprotein import into nucleus, translocation  negative regulation of transcription from RNA polymerase II promoter  activation of MAPK activity  cell activation  phagocytic cup  positive regulation of protein amino acid phosphorylation  negative regulation of L-glutamate transport  chronic inflammatory response to antigenic stimulus  negative regulation of cytokine secretion during immune response  cytokine activity  tumor necrosis factor receptor binding  extracellular region  extracellular space  plasma membrane  integral to plasma membrane  glucose metabolic process  anti-apoptosis  activation of caspase activity  transformed cell apoptosis  inflammatory response  humoral immune response  signal transduction  multicellular organismal development  negative regulation of cell proliferation  induction of apoptosis via death domain receptors  response to mechanical stimulus  response to virus  response to salt stress  organ morphogenesis  external side of plasma membrane  positive regulation of necrotic cell death  negative regulation of transcription  calcium-mediated signaling  sequestering of triglyceride  negative regulation of interleukin-6 production  positive regulation of chemokine production  positive regulation of interleukin-6 production  receptor biosynthetic process  tumor necrosis factor-mediated signaling pathway  positive regulation of heterotypic cell-cell adhesion  positive regulation of NF-kappaB import into nucleus  defense response to bacterium  identical protein binding  positive regulation of I-kappaB kinase/NF-kappaB cascade  positive regulation of gene-specific transcription  positive regulation of neuron apoptosis  negative regulation of viral genome replication  positive regulation of chemokine biosynthetic process  membrane raft  positive regulation of nitric oxide biosynthetic process  regulation of osteoclast differentiation  positive regulation of mitosis  positive regulation of transcription  positive regulation of transcription from RNA polymerase II promoter  positive regulation of translational initiation by iron  negative regulation of glucose import  positive regulation of JNK cascade  positive regulation of smooth muscle cell proliferation  positive regulation of cytokine secretion  regulation of insulin secretion  positive regulation of synaptic transmission  leukocyte tethering or rolling  negative regulation of lipid catabolic process  regulation of immunoglobulin secretion  positive regulation of membrane protein ectodomain proteolysis  positive regulation of NF-kappaB transcription factor activity  positive regulation of protein transport  response to glucocorticoid stimulus  positive regulation of hair follicle development  recycling endosome  induction of necroptosis by extracellular signals  positive regulation of vitamin D biosynthetic process  positive regulation of calcidiol 1-monooxygenase activity  
Keywords Ontology : EGO-EBIprotein import into nucleus, translocation  negative regulation of transcription from RNA polymerase II promoter  activation of MAPK activity  cell activation  phagocytic cup  positive regulation of protein amino acid phosphorylation  negative regulation of L-glutamate transport  chronic inflammatory response to antigenic stimulus  negative regulation of cytokine secretion during immune response  cytokine activity  tumor necrosis factor receptor binding  extracellular region  extracellular space  plasma membrane  integral to plasma membrane  glucose metabolic process  anti-apoptosis  activation of caspase activity  transformed cell apoptosis  inflammatory response  humoral immune response  signal transduction  multicellular organismal development  negative regulation of cell proliferation  induction of apoptosis via death domain receptors  response to mechanical stimulus  response to virus  response to salt stress  organ morphogenesis  external side of plasma membrane  positive regulation of necrotic cell death  negative regulation of transcription  calcium-mediated signaling  sequestering of triglyceride  negative regulation of interleukin-6 production  positive regulation of chemokine production  positive regulation of interleukin-6 production  receptor biosynthetic process  tumor necrosis factor-mediated signaling pathway  positive regulation of heterotypic cell-cell adhesion  positive regulation of NF-kappaB import into nucleus  defense response to bacterium  identical protein binding  positive regulation of I-kappaB kinase/NF-kappaB cascade  positive regulation of gene-specific transcription  positive regulation of neuron apoptosis  negative regulation of viral genome replication  positive regulation of chemokine biosynthetic process  membrane raft  positive regulation of nitric oxide biosynthetic process  regulation of osteoclast differentiation  positive regulation of mitosis  positive regulation of transcription  positive regulation of transcription from RNA polymerase II promoter  positive regulation of translational initiation by iron  negative regulation of glucose import  positive regulation of JNK cascade  positive regulation of smooth muscle cell proliferation  positive regulation of cytokine secretion  regulation of insulin secretion  positive regulation of synaptic transmission  leukocyte tethering or rolling  negative regulation of lipid catabolic process  regulation of immunoglobulin secretion  positive regulation of membrane protein ectodomain proteolysis  positive regulation of NF-kappaB transcription factor activity  positive regulation of protein transport  response to glucocorticoid stimulus  positive regulation of hair follicle development  recycling endosome  induction of necroptosis by extracellular signals  positive regulation of vitamin D biosynthetic process  positive regulation of calcidiol 1-monooxygenase activity  
Pathways : BIOCARTAHIV-I Nef: negative effector of Fas and TNF [Genes]    Cells and Molecules involved in local acute inflammatory response [Genes]    Acetylation and Deacetylation of RelA in The Nucleus [Genes]    Cadmium induces DNA synthesis and proliferation in macrophages [Genes]    Cytokine Network [Genes]    Free Radical Induced Apoptosis [Genes]    Adhesion and Diapedesis of Granulocytes [Genes]    Stress Induction of HSP Regulation [Genes]    IL-10 Anti-inflammatory Signaling Pathway [Genes]    Signal transduction through IL1R [Genes]    Cytokines and Inflammatory Response [Genes]    Keratinocyte Differentiation [Genes]    Msp/Ron Receptor Signaling Pathway [Genes]    NF-kB Signaling Pathway [Genes]    NFkB activation by Nontypeable Hemophilus influenzae [Genes]    Regulation of transcriptional activity by PML [Genes]    Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha) [Genes]    SODD/TNFR1 Signaling Pathway [Genes]    TNF/Stress Related Signaling [Genes]    Chaperones modulate interferon Signaling Pathway [Genes]    TNFR1 Signaling Pathway [Genes]    Visceral Fat Deposits and the Metabolic Syndrome [Genes]   
Pathways : KEGGMAPK signaling pathwayCytokine-cytokine receptor interactionApoptosisTGF-beta signaling pathwayToll-like receptor signaling pathwayHematopoietic cell lineageNatural killer cell mediated cytotoxicityT cell receptor signaling pathwayFc epsilon RI signaling pathwayAdipocytokine signaling pathwayType II diabetes mellitusType I diabetes mellitus
Other databases
Probes
Probes : ImagenesTNF Related clones (RZPD - Berlin)
Literature
PubMed499 Pubmed reference(s) in Entrez
PubGeneTNF

Bibliography

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REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written06-2004Fei Chen

Citation

This paper should be referenced as such :
Chen F . TNF (tumor necrosis factor (TNF superfamily, member 2)). Atlas Genet Cytogenet Oncol Haematol. June 2004 .
URL : http://AtlasGeneticsOncology.org/Genes/TNFaID319.html

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indexed on : Sat Feb 27 10:52:49 CET 2010

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