Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome
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Don't let the Atlas imminent demise
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CD9 (CD9 molecule)


Other names5H9
HGNC (Hugo) CD9
LocusID (NCBI) 928
Location 12p13.31
Location_base_pair Starts at 6309482 and ends at 6347437 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order The CD9 gene is located between the VWF and the ATP5J2P5 genes.


  Genomic organisation of the CD9 gene on chromosome 12.
Description The gene spans 38 kb of DNA, including a 10 kb intron separating the first two exons. CD9 encodes 8 exons, ranging from 63 to 109 base pairs. The coding sequence is highly conserved between species. The promoter contains neither TATA nor CAAT boxes, but does contain several consensus sequences for the binding of transcription factors (GATA, ETS, E2F, NF-kB, AP2) as well as three putative Sp1 binding sites.
Transcription The CD9 transcribed RNA has 1246 bases, of which 684 bases (from 112 (Met) to 795 (Val)) encode the protein.
Pseudogene None.


  Structure of the CD9 protein.
Description CD9 is a member of the transmembrane 4 superfamily, also called the tetraspanin family. As other tetraspanins, CD9 is a cell-surface protein containing four hydrophobic transmembrane domains (indicated in green) and two extracellular domains (illustrated in violet). CD9 consists of 228 amino acids and weighs 24-27 kDa. CD9 contains four small and highly conserved hydrophobic transmembrane domains (24-27 amino acids); a small N-terminal (11 amino acids) and a C-terminal cytoplasmic (7 amino acids) tails, and a very small intracellular domain (4 amino acids). The remaining part of the protein is composed of two extracellular domains (also called loops; a small one of 20 amino acids and a large one of 83 amino acids). Two disulfide bonds, generated by four well-conserved cysteine residues (C), stabilize the large extracellular domain. CD9 also contains a tetraspanin signature (amino acids 65-89) and a CCG motif (amino acids 152 to 154), but lacks other motifs found on other tetraspanins (DW, PxSc3, Gc4).
Expression CD9 is expressed by a variety of hematopoietic and epithelial cells. It is transiently expressed during development of spinal motoneurons and other fetal nervous system sites, as well as in hematopoietic development. CD9 is glycosylated (the glycosylation site is in the first extracellular loop unlike most glycosylated tetraspanins where the site is located in the second extracellular loop) and acylated. CD9 is also phosphorylated on tyrosine following B-cell activation.
CD9 is up-regulated on activated B and T lymphocytes.
Localisation In normal cells, CD9 localizes mainly in the membranes while in cancer cells the protein may also be detected throughout the cytoplasm.
Function CD9 can interact or form complexes with many other proteins, including other tetraspanins, integrins, EWI molecules, TGF-a, diphtheria toxin receptor, receptor tyrosine kinase, pregnancy specific glycoproteins, and proteins of the immune system such as MHC class II molecules and members of the Ig superfamily. Moreover, probably because of its localization in the cell membrane, CD9 is involved in platelet activation and aggregation, as well as in cell adhesion, spreading, cell motility and tumor metastasis. CD9 also regulates paranodal junction formation, and is required for gamete fusion. Furthermore, CD9 promotes muscle cell fusion and supports myotube maintenance.
Homology Although there are variations in the amino acid sequence in the extracellular loops, the CD9 protein sequence is very well conserved between species (90% between human, mice and rat). CD9 share also some homologies with other tetraspanins, particularly in the transmembrane domains.


Note Although no genomic CD9 mutation has been reported, in prostate cancer, there is mention of cDNA mutation compatible with an RNA editing mechanism. So far, CD9 has never been implicated in gene fusion that could result in a modified protein.

Implicated in

Entity Various cancers
Note Decreased expression of the CD9 protein has been associated with many types of cancer.
Disease - Expressed in 90% of non-T cell acute lymphoblastic leukemia cells and in 50% of chronic lymphocytic leukemia and acute myeloblastic leukemia.
- Expression inversely correlated with metastatic potential of melanoma.
- Expression suppresses motility and metastasis of carcinoma cells.
- Reduction of expression correlated with poor prognosis in breast, lung and colon carcinomas.

Other Solid tumors implicated (Data extracted from papers in the Atlas)

Solid Tumors AmeloblastomID5945

External links

HGNC (Hugo)CD9   1709
Entrez_Gene (NCBI)CD9  928  CD9 molecule
GeneCards (Weizmann)CD9
Ensembl hg19 (Hinxton)ENSG00000010278 [Gene_View]  chr12:6309482-6347437 [Contig_View]  CD9 [Vega]
Ensembl hg38 (Hinxton)ENSG00000010278 [Gene_View]  chr12:6309482-6347437 [Contig_View]  CD9 [Vega]
ICGC DataPortalENSG00000010278
AceView (NCBI)CD9
Genatlas (Paris)CD9
SOURCE (Princeton)CD9
Genomic and cartography
GoldenPath hg19 (UCSC)CD9  -     chr12:6309482-6347437 +  12p13   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CD9  -     12p13   [Description]    (hg38-Dec_2013)
EnsemblCD9 - 12p13 [CytoView hg19]  CD9 - 12p13 [CytoView hg38]
Mapping of homologs : NCBICD9 [Mapview hg19]  CD9 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AB079244 AI003581 AK296332 AK296894 AK298431
RefSeq transcript (Entrez)NM_001769
RefSeq genomic (Entrez)AC_000144 NC_000012 NC_018923 NT_009759 NW_001838050 NW_004929382
Consensus coding sequences : CCDS (NCBI)CD9
Cluster EST : UnigeneHs.712104 [ NCBI ]
CGAP (NCI)Hs.712104
Alternative Splicing : Fast-db (Paris)GSHG0006410
Alternative Splicing GalleryENSG00000010278
Gene ExpressionCD9 [ NCBI-GEO ]     CD9 [ SEEK ]   CD9 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP21926 (Uniprot)
NextProtP21926  [Medical]
With graphics : InterProP21926
Splice isoforms : SwissVarP21926 (Swissvar)
Domaine pattern : Prosite (Expaxy)TM4_1 (PS00421)   
Domains : Interpro (EBI)CD81_LEL    Tetraspanin    Tetraspanin/Peripherin    Tetraspanin_CS    Tetraspanin_EC2   
Related proteins : CluSTrP21926
Domain families : Pfam (Sanger)Tetraspannin (PF00335)   
Domain families : Pfam (NCBI)pfam00335   
DMDM Disease mutations928
Blocks (Seattle)P21926
Human Protein AtlasENSG00000010278
Peptide AtlasP21926
IPIIPI00215997   IPI00908644   IPI00556460   IPI00657796   IPI01012333   
Protein Interaction databases
IntAct (EBI)P21926
Ontologies - Pathways
Ontology : AmiGOplatelet degranulation  integrin binding  protein binding  extracellular space  plasma membrane  integral component of plasma membrane  cellular component movement  cell adhesion  single fertilization  fusion of sperm to egg plasma membrane  fusion of sperm to egg plasma membrane  brain development  blood coagulation  negative regulation of cell proliferation  response to water deprivation  external side of plasma membrane  oligodendrocyte development  apical plasma membrane  platelet activation  platelet activation  paranodal junction assembly  platelet alpha granule membrane  multicellular organism reproduction  extracellular vesicular exosome  
Ontology : EGO-EBIplatelet degranulation  integrin binding  protein binding  extracellular space  plasma membrane  integral component of plasma membrane  cellular component movement  cell adhesion  single fertilization  fusion of sperm to egg plasma membrane  fusion of sperm to egg plasma membrane  brain development  blood coagulation  negative regulation of cell proliferation  response to water deprivation  external side of plasma membrane  oligodendrocyte development  apical plasma membrane  platelet activation  platelet activation  paranodal junction assembly  platelet alpha granule membrane  multicellular organism reproduction  extracellular vesicular exosome  
Pathways : KEGGHematopoietic cell lineage   
REACTOMEP21926 [protein]
REACTOME PathwaysREACT_604 Hemostasis [pathway]
REACTOME PathwaysREACT_163848 Reproduction [pathway]
Protein Interaction DatabaseCD9
DoCM (Curated mutations)CD9
Wikipedia pathwaysCD9
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerCD9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CD9
Exome Variant ServerCD9
SNP (GeneSNP Utah)CD9
Genetic variants : HAPMAPCD9
Genomic Variants (DGV)CD9 [DGVbeta]
ICGC Data PortalENSG00000010278 
Somatic Mutations in Cancer : COSMICCD9 
CONAN: Copy Number AnalysisCD9 
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] 
DECIPHER (Syndromes)12:6309482-6347437
Mutations and Diseases : HGMDCD9
NextProtP21926 [Medical]
Disease Genetic AssociationCD9
Huge Navigator CD9 [HugePedia]  CD9 [HugeCancerGEM]
snp3D : Map Gene to Disease928
DGIdb (Drug Gene Interaction db)CD9
General knowledge
Homologs : HomoloGeneCD9
Homology/Alignments : Family Browser (UCSC)CD9
Phylogenetic Trees/Animal Genes : TreeFamCD9
Chemical/Protein Interactions : CTD928
Chemical/Pharm GKB GenePA26247
Clinical trialCD9
Cancer Resource (Charite)ENSG00000010278
Other databases
PubMed164 Pubmed reference(s) in Entrez


Assignment to chromosome 12 of the gene coding for the human cell surface antigen CD9(p24) using the monoclonal antibody ALB6.
Boucheix C, Nguyen-van-Cong, Perrot JY, Foubert C, Gross MS, Weil D, Laisney V, Rosenfeld C, Frezal J.
Ann Genet. 1985;28(1):19-24.
PMID 3893311
Mechanisms of the mAb ALB6(CD9) induced human platelet activation: comparison with thrombin.
Rendu F, Boucheix C, Lebret M, Bourdeau N, Benoit P, Maclouf J, Soria C, Levy-Toledano S.
Biochem Biophys Res Commun. 1987 Aug 14;146(3):1397-404.
PMID 3039999
The functional glycoprotein CD9 is variably acylated: localization of the variably acylated region to a membrane-associated peptide containing the binding site for the agonistic monoclonal antibody 50H.19.
Seehafer JG, Tang SC, Slupsky JR, Shaw AR.
Biochim Biophys Acta. 1988 Dec 2;957(3):399-410.
PMID 3058210
Molecular cloning of the CD9 antigen. A new family of cell surface proteins.
Boucheix C, Benoit P, Frachet P, Billard M, Worthington RE, Gagnon J, Uzan G.
J Biol Chem. 1991 Jan 5;266(1):117-22.
PMID 1840589
Suppression of cell motility and metastasis by transfection with human motility-related protein (MRP-1/CD9) DNA.
Ikeyama S, Koyama M, Yamaoko M, Sasada R, Miyake M.
J Exp Med. 1993 May 1;177(5):1231-7.
PMID 8478605
Organization of the human CD9 gene.
Rubinstein E, Benoit P, Billard M, Plaisance S, Prenant M, Uzan G, Boucheix C.
Genomics. 1993 Apr;16(1):132-8.
PMID 8486348
Expression of the neuroglandular antigen and analogues in melanoma. CD9 expression appears inversely related to metastatic potential of melanoma.
Si Z, Hersey P.
Int J Cancer. 1993 Apr 22;54(1):37-43.
PMID 8478146
Distribution of CD9 in the developing and mature rat nervous system.
Tole S, Patterson PH.
Dev Dyn. 1993 Jun;197(2):94-106.
PMID 8219357
Reduced motility related protein-1 (MRP-1/CD9) gene expression as a factor of poor prognosis in non-small cell lung cancer.
Higashiyama M, Taki T, Ieki Y, Adachi M, Huang CL, Koh T, Kodama K, Doi O, Miyake M.
Cancer Res. 1995 Dec 15;55(24):6040-4.
PMID 8521390
Ectopic expression of human and feline CD9 in a human B cell line confers beta 1 integrin-dependent motility on fibronectin and laminin substrates and enhanced tyrosine phosphorylation.
Shaw AR, Domanska A, Mak A, Gilchrist A, Dobler K, Visser L, Poppema S, Fliegel L, Letarte M, Willett BJ.
J Biol Chem. 1995 Oct 13;270(41):24092-9.
PMID 7592610
Transcriptional regulation of the human CD9 gene: characterization of the 5'-flanking region.
Le Naour F, Prenant M, Francastel C, Rubinstein E, Uzan G, Boucheix C.
Oncogene. 1996 Aug 1;13(3):481-6.
PMID 8760289
Motility-related protein-1 (MRP-1/CD9) reduction as a factor of poor prognosis in breast cancer.
Miyake M, Nakano K, Itoi SI, Koh T, Taki T.
Cancer Res. 1996 Mar 15;56(6):1244-9.
PMID 8640807
Differential display cloning identifies motility-related protein (MRP1/CD9) as highly expressed in primary compared to metastatic human colon carcinoma cells.
Cajot JF, Sordat I, Silvestre T, Sordat B.
Cancer Res. 1997 Jul 1;57(13):2593-7.
PMID 9205061
The tetraspanin superfamily: molecular facilitators.
Maecker HT, Todd SC, Levy S.
FASEB J. 1997 May;11(6):428-42. (REVIEW)
PMID 9194523
CD19 is linked to the integrin-associated tetraspans CD9, CD81, and CD82.
Horvath G, Serru V, Clay D, Billard M, Boucheix C, Rubinstein E.
J Biol Chem. 1998 Nov 13;273(46):30537-43.
PMID 9804823
The tetraspanin CD9 influences the adhesion, spreading, and pericellular fibronectin matrix assembly of Chinese hamster ovary cells on human plasma fibronectin.
Cook GA, Wilkinson DA, Crossno JT Jr, Raghow R, Jennings LK.
Exp Cell Res. 1999 Sep 15;251(2):356-71.
PMID 10471321
Role of transmembrane 4 superfamily (TM4SF) proteins CD9 and CD81 in muscle cell fusion and myotube maintenance.
Tachibana I, Hemler ME.
J Cell Biol. 1999 Aug 23;146(4):893-904.
PMID 10459022
Requirement of CD9 on the egg plasma membrane for fertilization.
Miyado K, Yamada G, Yamada S, Hasuwa H, Nakamura Y, Ryu F, Suzuki K, Kosai K, Inoue K, Ogura A, Okabe M, Mekada E.
Science. 2000 Jan 14;287(5451):321-4.
PMID 10634791
Structure of the tetraspanin main extracellular domain. A partially conserved fold with a structurally variable domain insertion.
Seigneuret M, Delaguillaumie A, Lagaudriere-Gesbert C, Conjeaud H.
J Biol Chem. 2001 Oct 26;276(43):40055-64. Epub 2001 Aug 1.
PMID 11483611
Tetraspanin protein CD9 is a novel paranodal component regulating paranodal junctional formation.
Ishibashi T, Ding L, Ikenaka K, Inoue Y, Miyado K, Mekada E, Baba H.
J Neurosci. 2004 Jan 7;24(1):96-102.
PMID 14715942
Structural organization and interactions of transmembrane domains in tetraspanin proteins.
Kovalenko OV, Metcalf DG, DeGrado WF, Hemler ME.
BMC Struct Biol. 2005 Jun 28;5:11.
PMID 15985154
Down-regulation of CD9 expression during prostate carcinoma progression is associated with CD9 mRNA modifications.
Wang JC, Begin LR, Berube NG, Chevalier S, Aprikian AG, Gourdeau H, Chevrette M.
Clin Cancer Res. 2007 Apr 15;13(8):2354-61. Epub 2007 Apr 3.
PMID 17406028
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Written08-2009Laure Humbert, Mario Chevrette
The Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada


This paper should be referenced as such :
Humbert, L ; Chevrette, M
CD9 (CD9 molecule)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(7):-.
Free journal version : [ pdf ]   [ DOI ]

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indexed on : Tue Feb 17 20:43:52 CET 2015

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