CCR9 (chemokine (C-C motif) receptor 9)

2009-03-01   Hisayuki Nomiyama  , Osamu Yoshie  

Department of Biochemistry, Kumamoto University Medical School, Honjo, Kumamoto 860-0811, Japan (HN); Department of Microbiology, Kinki University School of Medicine, Osaka-Sayama, Osaka 589-8511, Japan (OY)

Identity

HGNC
LOCATION
3p21.31
LOCUSID
ALIAS
CC-CKR-9,CDw199,GPR-9-6,GPR28

DNA/RNA

Note

The gene and mRNA for CCR9 are 16.6 and 2.7 kb in length, respectively.
Atlas Image
The CCR9 gene generates two distinct mRNAs.

Description

The CCR9 gene consists of three exons, the second and third exons being the coding-exons. Alternative splicing of the gene generates two distinct mRNAs, CCR9-A and CCR9-B. The CCR9-A cDNA was the first to be cloned.

Transcription

The CCR9-A mRNA is encoded by the three exons, while the CCR9-B lacks the sequence derived from the second exon of 49 bp. The CCR9 mRNAs are expressed predominantly in the thymus. Among the cell lines tested, T cell leukemia line MOLT-4 and HTLV-1+ T cells express CCR9 mRNA. The CCR9-A mRNA is expressed at ~10-fold higher levels than CCR9-B mRNA in the cells and cell lines investigated.

Pseudogene

None.

Proteins

Note

CCR9-A: 369 amino acids, 42015 Da.
CCR9-B: 357 amino acids, 40712 Da.

Description

CCR9 is a member of the seven transmembrane G protein-coupled receptor superfamily, and is the single receptor for chemokine CCL25.

Expression

CCR9 is present on thymocytes as well as on intraepithelial and lamina propria lymphocytes of the small intestine. A small subset of lymphocytes in the colon is also expressing CCR9.

Localisation

Cell membrane; Multi-pass membrane protein.

Function

CCR9 mediates chemotaxis to CCL25, which is selectively expressed in the thymus and small intestine, and plays an important role in the recruitment of T cells into gut mucosa. Dendritic cells derived from gut-associated lymphoid tissues as well as retinoic acid have been shown to induce the expression of alpha4beta7 integrin and CCR9 on T cells, resulting in their preferential homing to the gut. Although CCR9 deletion in mice has no major effects on the intrathymic T-cell development, down-regulation of CCR9 on activated CD4+CD8+ double positive thymocytes has been shown to allow the migration of maturing thymocytes from the cortex to the medulla.
The EC50 of CCL25 for CCR9-A is somewhat lower than that for CCR9-B. CCR9-A-expressing cells are therefore more responsive to CCL25 than the cells expressing CCR9-B in chemotaxis and calcium influx experiments.

Homology

CCR9 is closely related to the chemokine receptors CCR6, CCR7, and CXCR6.

Implicated in

Oncogenesis
Qiuping et al. (2003) assessed the expression of CCR9 in 21 T-ALL and 17 "T-cell chronic lymphocytic leukemia" (T-CLL) cases, and found that functionally active CCR9 was selectively and frequently expressed on T-ALL CD4+ T cells and was moderately expressed on T-CLL CD4+ T cells.
Annels et al. (2004) investigated homing receptor expression on the blast cells of 11 pediatric T-ALL patients. They found that CCR9 and CD103 (alphaE integrin) were expressed at high levels on T-ALL cells of one patient. This patient later switched to a clonally related acute myeloid leukemia during treatment, and the relapse of leukemia was confined to the gut. This study suggests a role of CCR9 in infiltration of leukemic cells into the gut.
Entity name
Adult T-cell leukemia (ATL)
Oncogenesis
ATL frequently invades the gastrointestinal tract. Nagakubo et al. (2007) examined CCR9 expression in five ATL-derived cell lines and 10 blood samples from ATL patients containing leukemic cells at high levels. Although all ATL cell lines were CCR9-positive, fresh ATL cells derived from patients were mostly negative. However, ATL cells became readily positive for CCR9 mRNA after one-day culture in parallel with the expression of Tax mRNA. This study suggests that CCR9 is inducible in ATL cells and may play a role in the high incidence of ATL cell invasion into the gastrointestinal tract.
Entity name
Melanoma metastasis to the small intestine
Oncogenesis
Letsch et al. (2004) assessed CCR9 expression in 20 melanoma cell lines. The CCR9-positive cell lines were established from metastases to small intestine (n = 3), lymph node (n = 4), and skin (n = 1). Only melanoma cell lines derived from small intestinal metastases, however, were responsive to CCL25. This study correlated functional expression of CCR9 with melanoma metastasis to the small intestine.
Amersi et al. (2008) assessed CCR9 expression in primary (n = 23) and metastatic (n = 198) melanomas, and melanoma lines derived from small intestinal metastases (n = 8). CCR9 expression was observed in 88 of 102 metastatic melanomas from the small intestine, 8 of 8 melanoma lines derived from small intestine metastasis, but none of 96 metastatic melanomas from other sites. In addition, 11 of 23 primary melanomas were CCR9-positive and 7 of these later developed small intestinal metastases. This study suggests that CCR9 has a role in melanoma metastasis to the small intestine.
Entity name
Melanoma metastasis
Oncogenesis
Seidl et al. (2007) investigated expression of eight chemokine receptors including CCR9 in 51 tissue samples of melanocytic origin. CCR9 mRNA was observed in more than half of the melanocytic lesions including lymph node metastases and visceral metastases. The authors concluded that there is no clear trend toward an association between the CCR9 expression levels and melanoma progression.
Entity name
Prostate cancer metastasis
Oncogenesis
Singh et al. (2004) investigated CCR9 expression in two prostate cancer cell lines. Both cell lines expressed CCR9. This study suggests that expression and activation of CCR9 affect prostate cancer metastasis.
Entity name
Small intestinal Crohns disease
Oncogenesis
Papadakis et al. (2001) found that CCR9+ T cells were markedly elevated in the peripheral blood of patients with Crohns disease but not those with purely colonic Crohns disease. This study suggests selective involvement of CCR9 in the pathogenesis of small bowel Crohns disease.

Article Bibliography

Pubmed IDLast YearTitleAuthors
186849452008CD46-induced immunomodulatory CD4+ T cells express the adhesion molecule and chemokine receptor pattern of intestinal T cells.Alford SK et al
182455222008Activation of CCR9/CCL25 in cutaneous melanoma mediates preferential metastasis to the small intestine.Amersi FF et al
146568932004Possible link between unique chemokine and homing receptor expression at diagnosis and relapse location in a patient with childhood T-ALL.Annels NE et al
190273302008PlexinD1 glycoprotein controls migration of positively selected thymocytes into the medulla.Choi YI et al
150865892004Chemokine receptors in melanoma: CCR9 has a potential role in metastasis to the small bowel.Hwang ST et al
154856302004Retinoic acid imprints gut-homing specificity on T cells.Iwata M et al
172912922007Generation of gut-homing T cells and their localization to the small intestinal mucosa.Johansson-Lindbom B et al
159284872005The greater chemotactic network for lymphocyte trafficking: chemokines and beyond.Kim CH et al
118255602002Chemokines and the tissue-specific migration of lymphocytes.Kunkel EJ et al
109740412000Lymphocyte CC chemokine receptor 9 and epithelial thymus-expressed chemokine (TECK) expression distinguish the small intestinal immune compartment: Epithelial expression of tissue-specific chemokines as an organizing principle in regional immunity.Kunkel EJ et al
150865542004Functional CCR9 expression is associated with small intestinal metastasis.Letsch A et al
128407632003Selective imprinting of gut-homing T cells by Peyer's patch dendritic cells.Mora JR et al
165802612006T-cell homing specificity and plasticity: new concepts and future challenges.Mora JR et al
172055122007Expression of CCR9 in HTLV-1+ T cells and ATL cells expressing Tax.Nagakubo D et al
120960272002Pivotal role of CCL25 (TECK)-CCR9 in the formation of gut cryptopatches and consequent appearance of intestinal intraepithelial T lymphocytes.Onai N et al
114875332001CCR9-positive lymphocytes and thymus-expressed chemokine distinguish small bowel from colonic Crohn's disease.Papadakis KA et al
145598392003Selectively increased expression and functions of chemokine receptor CCR9 on CD4+ T cells from patients with T-cell lineage acute lymphocytic leukemia.Qiuping Z et al
182455182008CCR9 homes metastatic melanoma cells to the small bowel.Richmond A et al
173063302007Profiles of chemokine receptors in melanocytic lesions: de novo expression of CXCR6 in melanoma.Seidl H et al
156236602004Expression and functional role of CCR9 in prostate cancer cell migration and invasion.Singh S et al
175510162007Differential homing mechanisms regulate regionalized effector CD8alphabeta+ T cell accumulation within the small intestine.Stenstad H et al
123938472002CCL25 mediates the localization of recently activated CD8alphabeta(+) lymphocytes to the small-intestinal mucosa.Svensson M et al
118844502002A role for CCR9 in T lymphocyte development and migration.Uehara S et al
151812892004Chemokine receptors and leukocyte trafficking in the mucosal immune system.Williams IR et al
116753302001Mice lacking the CCR9 CC-chemokine receptor show a mild impairment of early T- and B-cell development and a reduction in T-cell receptor gammadelta(+) gut intraepithelial lymphocytes.Wurbel MA et al
106020492000The chemokine TECK is expressed by thymic and intestinal epithelial cells and attracts double- and single-positive thymocytes expressing the TECK receptor CCR9.Wurbel MA et al
106407432000CCR9A and CCR9B: two receptors for the chemokine CCL25/TECK/Ck beta-15 that differ in their sensitivities to ligand.Yu CR et al
102297971999Cutting edge: identification of the orphan chemokine receptor GPR-9-6 as CCR9, the receptor for the chemokine TECK.Zaballos A et al
105441961999Human G protein-coupled receptor GPR-9-6/CC chemokine receptor 9 is selectively expressed on intestinal homing T lymphocytes, mucosal lymphocytes, and thymocytes and is required for thymus-expressed chemokine-mediated chemotaxis.Zabel BA et al

Other Information

Locus ID:

NCBI: 10803
MIM: 604738
HGNC: 1610
Ensembl: ENSG00000173585

Variants:

dbSNP: 10803
ClinVar: 10803
TCGA: ENSG00000173585
COSMIC: CCR9

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000173585ENST00000355983P51686
ENSG00000173585ENST00000357632P51686
ENSG00000173585ENST00000395963P51686
ENSG00000173585ENST00000422395C9JWC0

Expression (GTEx)

0
1
2
3
4
5
6
7

Pathways

PathwaySourceExternal ID
Cytokine-cytokine receptor interactionKEGGko04060
Cytokine-cytokine receptor interactionKEGGhsa04060
Chemokine signaling pathwayKEGGko04062
Chemokine signaling pathwayKEGGhsa04062
Intestinal immune network for IgA productionKEGGko04672
Intestinal immune network for IgA productionKEGGhsa04672
Signal TransductionREACTOMER-HSA-162582
Signaling by GPCRREACTOMER-HSA-372790
GPCR ligand bindingREACTOMER-HSA-500792
Class A/1 (Rhodopsin-like receptors)REACTOMER-HSA-373076
Peptide ligand-binding receptorsREACTOMER-HSA-375276
Chemokine receptors bind chemokinesREACTOMER-HSA-380108
GPCR downstream signalingREACTOMER-HSA-388396
G alpha (i) signalling eventsREACTOMER-HSA-418594

Protein levels (Protein atlas)

Not detected
Low
Medium
High

References

Pubmed IDYearTitleCitations
368221742023LncRNA15691 promotes T-ALL infiltration by upregulating CCR9 via increased MATR3 stability.1
375693262023CCR9/CXCR5 Co-Expressing CD4 T Cells Are Increased in Primary Sjögren's Syndrome and Are Enriched in PD-1/ICOS-Expressing Effector T Cells.0
368221742023LncRNA15691 promotes T-ALL infiltration by upregulating CCR9 via increased MATR3 stability.1
375693262023CCR9/CXCR5 Co-Expressing CD4 T Cells Are Increased in Primary Sjögren's Syndrome and Are Enriched in PD-1/ICOS-Expressing Effector T Cells.0
352796612022Potential for CCR9+ IL-17+ Regulatory T Cell as a Predictor of Early Necrotizing Enterocolitis.0
357203792022CCL5 Release by CCR9+ CD8 T Cells: A Potential Contributor to Immunopathology of Primary Sjögren's Syndrome.3
365054312022In patients with primary Sjögren's syndrome innate-like MAIT cells display upregulated IL-7R, IFN-γ, and IL-21 expression and have increased proportions of CCR9 and CXCR5-expressing cells.4
352796612022Potential for CCR9+ IL-17+ Regulatory T Cell as a Predictor of Early Necrotizing Enterocolitis.0
357203792022CCL5 Release by CCR9+ CD8 T Cells: A Potential Contributor to Immunopathology of Primary Sjögren's Syndrome.3
365054312022In patients with primary Sjögren's syndrome innate-like MAIT cells display upregulated IL-7R, IFN-γ, and IL-21 expression and have increased proportions of CCR9 and CXCR5-expressing cells.4
330384342021Role of CC chemokine receptor 9 in the progression of murine and human non-alcoholic steatohepatitis.13
333476172021CCL25 and CCR9 is a unique pathway that potentiates pannus formation by remodeling RA macrophages into mature osteoclasts.10
336192452021Genome and epigenome editing identify CCR9 and SLC6A20 as target genes at the 3p21.31 locus associated with severe COVID-19.28
341611592021Development of Anti-Human CC Chemokine Receptor 9 Monoclonal Antibodies for Flow Cytometry.6
348084972021LINC00853 restrains T cell acute lymphoblastic leukemia invasion and infiltration by regulating CCR9/CCL25.5

Citation

Hisayuki Nomiyama ; Osamu Yoshie

CCR9 (chemokine (C-C motif) receptor 9)

Atlas Genet Cytogenet Oncol Haematol. 2009-03-01

Online version: http://atlasgeneticsoncology.org/gene/44380/meetings/haematological-explorer/css/lib/bootstrap.min.css