PDGFRB

PDGFRB
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1GQ5, 1H9O, 1SHA, 2L6W, 2PLD, 2PLE, 3MJG
Identifiers
Aliases	PDGFRB, CD140B, IBGC4, IMF1, JTK12, PDGFR, PDGFR-1, PDGFR1, KOGS, PENTT, platelet derived growth factor receptor beta
External IDs	OMIM: 173410 MGI: 97531 HomoloGene: 1960 GeneCards: PDGFRB
Gene location (Human) Chr. Chromosome 5 (human)[1] Band 5q32 Start 150,113,839 bp[1] End 150,155,872 bp[1]
Gene location (Mouse) Chr. Chromosome 18 (mouse)[2] Band 18 E1|18 34.41 cM Start 61,178,222 bp[2] End 61,218,133 bp[2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in stromal cell of endometrium right coronary artery canal of the cervix gallbladder Achilles tendon right lung left coronary artery ascending aorta left uterine tube gastric mucosa Top expressed in external carotid artery internal carotid artery calvaria left lung lobe vas deferens body of femur dermis ascending aorta aortic valve ankle More reference expression data BioGPS More reference expression data
Gene ontology Molecular function vascular endothelial growth factor binding kinase activity platelet-derived growth factor-activated receptor activity transmembrane receptor protein tyrosine kinase activity signaling receptor binding ATP binding protein kinase activity platelet-derived growth factor binding platelet activating factor receptor activity transferase activity platelet-derived growth factor receptor binding protein binding protein tyrosine kinase activity protein kinase binding platelet-derived growth factor beta-receptor activity nucleotide binding phosphatidylinositol 3-kinase binding phosphatidylinositol-4,5-bisphosphate 3-kinase activity enzyme binding Cellular component cytoplasm membrane focal adhesion nucleus apical plasma membrane lysosome extracellular exosome integral component of membrane plasma membrane lysosomal lumen intrinsic component of plasma membrane cytoplasmic vesicle cell surface Golgi apparatus integral component of plasma membrane intracellular membrane-bounded organelle receptor complex Biological process positive regulation of MAP kinase activity positive regulation of phospholipase C activity cell migration involved in vasculogenesis cardiac myofibril assembly positive regulation of smooth muscle cell migration protein phosphorylation response to lipid positive regulation of phosphoprotein phosphatase activity positive regulation of reactive oxygen species metabolic process metanephric glomerular mesangial cell proliferation involved in metanephros development positive regulation of ERK1 and ERK2 cascade cell chemotaxis inner ear development metanephric S-shaped body morphogenesis positive regulation of mitotic nuclear division platelet-derived growth factor receptor-beta signaling pathway positive regulation of collagen biosynthetic process phosphatidylinositol metabolic process transmembrane receptor protein tyrosine kinase signaling pathway cell migration involved in coronary angiogenesis metanephric comma-shaped body morphogenesis positive regulation of chemotaxis positive regulation of DNA biosynthetic process protein autophosphorylation platelet-derived growth factor receptor signaling pathway response to toxic substance positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway regulation of actin cytoskeleton organization response to retinoic acid phosphorylation response to hyperoxia retina vasculature development in camera-type eye metanephric glomerulus morphogenesis metanephric mesenchymal cell migration wound healing cellular response to platelet-derived growth factor stimulus negative regulation of apoptotic process response to fluid shear stress response to estrogen chemotaxis metanephric mesenchyme development response to hydrogen peroxide positive regulation of smooth muscle cell proliferation response to estradiol intracellular signal transduction response to organic cyclic compound smooth muscle cell chemotaxis positive regulation of cell migration aorta morphogenesis MAPK cascade positive regulation of phosphatidylinositol 3-kinase activity metanephric glomerular capillary formation multicellular organism development positive regulation of calcium ion import glycosaminoglycan biosynthetic process positive regulation of cell population proliferation positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway positive regulation of phosphatidylinositol 3-kinase signaling peptidyl-tyrosine phosphorylation cell migration signal transduction positive regulation of Rho protein signal transduction G protein-coupled receptor signaling pathway phosphatidylinositol phosphate biosynthetic process positive regulation of hepatic stellate cell activation positive regulation of fibroblast proliferation positive regulation of apoptotic process human ageing male gonad development lung growth negative regulation of platelet-derived growth factor receptor-beta signaling pathway phosphatidylinositol-mediated signaling positive regulation of protein kinase B signaling hematopoietic progenitor cell differentiation positive regulation of MAPK cascade Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 5159 18596 Ensembl ENSG00000113721 ENSMUSG00000024620 UniProt P09619 P05622 RefSeq (mRNA) NM_002609 NM_001355016 NM_001355017 NM_001146268 NM_008809 RefSeq (protein) NP_002600 NP_001341945 NP_001341946 NP_001139740 NP_032835 Location (UCSC) Chr 5: 150.11 – 150.16 Mb Chr 18: 61.18 – 61.22 Mb PubMed search [3] [4]
Wikidata
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Platelet-derived growth factor receptor beta is a protein that in humans is encoded by the PDGFRB gene. Mutations in PDGFRB are mainly associated with the clonal eosinophilia class of malignancies.

Gene

The PDGFRB gene is located on human chromosome 5 at position q32 (designated as 5q32) and contains 25 exons. The gene is flanked by the genes for granulocyte-macrophage colony-stimulating factor and Colony stimulating factor 1 receptor (also termed macrophage-colony stimulating factor receptor), all three of which may be lost together by a single deletional mutation thereby causing development of the 5q-syndrome.^[5] Other genetic abnormalities in PDGFRB lead to various forms of potentially malignant bone marrow disorders: small deletions in and chromosome translocations causing fusions between PDGFRB and any one of at least 30 genes can cause Myeloproliferative neoplasms that commonly involve eosinophilia, eosinophil-induced organ injury, and possible progression to aggressive leukemia (see blow).^[6]

Structure

The PDGFRB gene encodes a typical receptor tyrosine kinase, which belongs to the type III tyrosine kinase receptor (RTK) family and is structurally characterized by five extracellular immunoglobulin-like domains, a single membrane-spanning helix domain, an intracellular juxtamembrane domain, a split tyrosine kinase domain and a carboxylic tail.^[7] In the absence of ligand, PDGFRβ adopts an inactive conformation in which the activation loop folds over the catalytic site, the juxtamembrane region over a loop occluding the active site and the carboxy-terminal tail over the kinase domain. Upon PDGF binding the dimerization of receptor releases the inhibitory conformations due to auto-phosphorylation of regulatory tyrosine residues in trans fashion. Tyrosine residues 857 and 751 are major phosphorylation sites for the activation of PDGFRβ.^[8]

The molecular mass of the mature, glycosylated PDGFRβ protein is approximately 180 kDa.

Modes of activation

Activation of PDGFRβ requires de-repression of the receptor's kinase activity. The ligand for PDGFRβ (PDGF) accomplishes this in the course of assembling a PDGFRβ dimer. Two of the five PDGF isoforms activate PDGFRβ (PDGF-B and PDGF-D). The activated receptor phosphorylates itself and other proteins, and thereby engages intracellular signaling pathways that trigger cellular responses such as migration and proliferation. There are also PDGF-independent modes of de-repressing the PDGFRβ's kinase activity and hence activating it. For instance, forcing PDGFRβ into close proximity of each other by overexpression or with antibodies directed against the extracellular domain. Alternatively, mutations in the kinase domain that stabilize a kinase active conformation result in constitutive activation.

Unlike PDGFRα, PDGFRβ cannot be indirectly activated. This is because PDGFRβ recruits RasGAP and thereby attenuates Ras/PI3K activity, which is required to engage a feed-forward loop that is responsible for this mode of activation.^[9][10]

Role in physiology/pathology

The phenotype of knock out mice demonstrates that PDGFRB is essential for vascular development, and that PDGFRB is responsible for activating PDGFRβ during embryogenesis. Eliminating either PDGFRB, or PDGF-B reduces the number of pericytes and vascular smooth muscle cells, and thereby compromises the integrity and/or functionality of the vasculature in multiple organs, including the brain, heart, kidney, skin and eye.^{[11][12][13][14]}

In vitro studies using cultured cells indicate that endothelial cells secrete PDGF, which recruits PDGFRβ-expressing pericytes that stabilize nascent blood vessels.^[15] Mice harboring a single activated allele of PDGFRB show a number of postnatal phenotypes including reduced differentiation of aortic vascular smooth muscle cells and brain pericytes. Similarly, differentiation of adipose from pericytes and mesenchymal cells is suppressed.^[16] Misregulation of the PDGFRβ's kinase activity (typically activation) contributes to endemic diseases such as cancer and cardiovascular disease.^[17][18][19]

PDGFRB mutations

5q- Syndrome

Human chromosome 5 deletions that remove three adjacent genes, those for granulocyte-macrophage colony-stimulating factor, PDGFRB, and Colony stimulating factor 1 receptor, cause the Chromosome 5q deletion syndrome (5q- syndrome). This syndrome is a unique type of myelodysplastic syndrome characterized by a prolonged disease course, a low rate of transformation to an aggressive form of leukemia, and an anemia which in many patients is profound, refractory to traditional therapies (e.g. iron supplements, Erythropoietin), and requiring maintenance red blood cell transfusions. The disease is treated with a chemotherapy drug, lenalidomide.^[5][20]

PDGFRB Translocations

Human chromosome translocations between the PDGFRB gene and at least any one of 30 genes on other chromosomes lead to myeloid and/or lymphoid neoplasms that are many ways similar to the neoplasm caused by the fusion of the PDGFRA (i.e. platelet derived growth factor receptor A or alpha-type-platelet derived growth factor receptor) gene with the FIP1L1 gene (see FIP1L1-PDGFRA fusion gene. The most common of these rare mutations is the translocation of PDGFRB gene with the ETV6 gene (also termed ETS variant gene 6).

PDGFRB-ETV6 translocations

The ETV6 gene codes for a transcription factor protein that in mice appears to be required for hematopoiesis and maintenance of the developing vascular network. The gene is located on human chromosome 12 at the p13 position, consists of 14 exons, and is well-known to be involved in a large number of chromosomal rearrangements associated with leukemia and congenital fibrosarcoma.^[21] Translocations between it and the PDGFRB gene, notated as t(5;12)(q33;p13), yield a PDGFRB-ETV6 fused gene that encodes a fusion protein, PDGFRB-ETV6. This chimeric protein, unlike the PDGFRB protein: a) has continuously active PDGFRB-mediated tyrosine kinase due to its forced dimerization by the PNT protein binding domain of the ETV6 protein; b) is highly stable due to its resistance to ubiquitin-Proteasome degradation; and c) therefore over-stimulates cell signaling pathways such as STAT5, NF-κB, and Extracellular signal-regulated kinases which promote cell growth and proliferation. This continuous signaling, it is presumed, leads to the development of myeloid and/or lymphoid neoplasms that commonly include increased numbers of blood born and tissue eosinophils, eosinophil-induced organ and tissue injury, and possible progression to aggressive form of leukemia.^[22]

PDGFRB-ETV6 fusion protein-induced neoplasms often present with features that would classify them as Chronic myelomonocytic leukemias, juvenile myelomonocytic leukemia, Atypical or Philadelphia chromosome negative chronic myeloid leukemias, myelodysplastic syndromes, acute myelogenous leukemias, or acute lymphoblastic leukemias. The disease is now classified by the World Health Organization as one form of clonal eosinophilia.^[23] It is critical that the PDGFRB-ETV6 fusion protein-driven disease be diagnostically distinguished from many of the just cited other diseases because of its very different treatment.

Patients with the PDGFRB-ETV6 fusion protein-driven disease are more often adult males but rarely children. They present with anemia, increases in blood eosinophils and monocytes, splenomegaly, and, less often, lymphadenopathy. Bone marrow examination may reveal cellular features similar to that seen in the aforementioned diseases. Diagnosis is may by conventional cytogenetic examination of blood or bone marrow cells to test for PDGFRB rearrangements using Fluorescence in situ hybridization or to test for the fused FDGFRB-ATV6 fluorescence in situ hybridization and/or Real-time polymerase chain reaction using appropriate nucleotide probes.^[22] These patients, unlike many patients with similarly appearing neoplasms, respond well to the tyrosine kinase inhibitor, imatinib. The drug often causes long-term complete hematological and cytogenic remissions as doses well below those used to treat chronic myelogenous leukemia. Primary or acquired drug resistance to this drug is very rare. Additional adjuvant chemotherapy may be necessary if a patient's disease is unresponsive to tyrosine kinase inhibitor therapy and/or progresses to more aggressive disease phase similar to that seen in the blast crisis of chronic myelogenous leukemia.^[22][6]

Other PDGFRB translocations

The PDGFRB gene has been found to fuse with at least 36 other genes to form fusion genes that encode chimeric proteins that are known or presumed to possess: a) continuously active PDGFRB-derived tyrosine kinase activity; b) the ability to continuously stimulate the growth and proliferation of hematological stem cells; and c) the ability to cause myeloid and lymphoid neoplasms that commonly but not always are associated with eosinophilia. In all instances, these gene fusion diseases are considered types of clonal eosinophilia with recommended treatment regimens very different than those of similar hematological malignancies. The genes fusing to PDGFRB, their chromosomal location, and the notations describing their fused genes are given in the following table.^[6][22]

Similar to PDGFRB-ETV6 translocations, these translocations are generally in-frame and encode for fusion proteins with their PDGFRB-derived tyrosine kinase being continuously active and responsible for causing the potentially malignant growth of its myeloid and/or lymphoid harboring cells. Patients are usually middle-aged men. They commonly present with anemia, eosinophilia, monocytosis, and splenomegaly and have their disease classified as chronic myelomonocytic leukemia, atypical chronic myelomonocytic leukemia, juvenile myelomonocytic leukemia, myelodysplastic syndrome, acute myelogenous leukemia, acute lymphoblastic leukemia, or T lymphoblastic lymphoma. Diagnosis relies on cytogenetic analyses to detect breakpoints in the long arm of chromosome 5 by Fluorescence in situ hybridization. These patients usually respond well to imatinib therapy.^[6][22][33]

Primary familial brain calcification

Primary familial brain calcification (see Fahr's syndrome) is a rare disease involving bilateral calcifications in the brain, predominantly in basal ganglia but also cerebellum, thalamus, and brainstem in patients presenting with diverse neurologic (e.g. movement disorders, parkinsonism, seizures, headache) features and psychiatric (e.g. cognitive impairment, mood disorders, psychotic symptoms, and obsessive-compulsive) disturbances. In a minority of cases, the disease is associated with apparent autosomal dominant loss of function mutations in PDGFRB or the gene which encodes a ligand that simulates PDGFRB, Platelet-derived growth factor, PDGFB. PDGFRB is extensively expressed in the neurons, chorioid plexus, vascular smooth muscle cells, and pericytes of the human brain, particularly the basal ganglia and the dentate nucleus. It is proposed that signal transduction through PDGFRB maintains blood–brain barrier integrity and that loss of the PDGFRB receptor or its ligand, PDGFB, disrupts the blood–brain barrier, subsequently promoting (peri)vascular calcium deposition and thereby causing the dysfunction and death of neurons.^[34][35]

Interactions

PDGFRB has been shown to interact with:

Notes

1. ^ ^{a b c} GRCh38: Ensembl release 89: ENSG00000113721 – Ensembl, May 2017
2. ^ ^{a b c} GRCm38: Ensembl release 89: ENSMUSG00000024620 – Ensembl, May 2017
3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. ^ ^{a b} "PDGFRB platelet derived growth factor receptor beta [Homo sapiens (human)] - Gene - NCBI".
6. ^ ^{a b c d} Reiter A, Gotlib J (2017). "Myeloid neoplasms with eosinophilia". Blood. 129 (6): 704–714. doi:10.1182/blood-2016-10-695973. PMID 28028030.
7. ^ Heldin CH, Lennartsson J (August 2013). "Structural and functional properties of platelet-derived growth factor and stem cell factor receptors". Cold Spring Harbor Perspectives in Biology. 5 (8): a009100. doi:10.1101/cshperspect.a009100. PMC 3721287. PMID 23906712.
8. ^ Kelly JD, Haldeman BA, Grant FJ, Murray MJ, Seifert RA, Bowen-Pope DF, et al. (May 1991). "Platelet-derived growth factor (PDGF) stimulates PDGF receptor subunit dimerization and intersubunit trans-phosphorylation". The Journal of Biological Chemistry. 266 (14): 8987–92. doi:10.1016/S0021-9258(18)31541-2. PMID 1709159.
9. ^ Lei H, Kazlauskas A (2014). "A reactive oxygen species-mediated, self-perpetuating loop persistently activates platelet-derived growth factor receptor α". Molecular and Cellular Biology. 34 (1): 110–22. doi:10.1128/MCB.00839-13. PMC 3911282. PMID 24190966.
10. ^ Lei H, Qian CX, Lei J, Haddock LJ, Mukai S, Kazlauskas A (2015). "RasGAP Promotes Autophagy and Thereby Suppresses Platelet-Derived Growth Factor Receptor-Mediated Signaling Events, Cellular Responses, and Pathology". Molecular and Cellular Biology. 35 (10): 1673–85. doi:10.1128/MCB.01248-14. PMC 4405646. PMID 25733681.
11. ^ Soriano P (1994). "Abnormal kidney development and hematological disorders in PDGF beta-receptor mutant mice". Genes & Development. 8 (16): 1888–96. doi:10.1101/gad.8.16.1888. PMID 7958864.
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13. ^ Lindahl P, Hellström M, Kalén M, Karlsson L, Pekny M, Pekna M, Soriano P, Betsholtz C (1998). "Paracrine PDGF-B/PDGF-Rbeta signaling controls mesangial cell development in kidney glomeruli". Development. 125 (17): 3313–22. doi:10.1242/dev.125.17.3313. PMID 9693135.
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19. ^ Heldin CH (2014). "Targeting the PDGF signaling pathway in the treatment of non-malignant diseases". Journal of Neuroimmune Pharmacology. 9 (2): 69–79. doi:10.1007/s11481-013-9484-2. PMID 23793451. S2CID 17343813.
20. ^ Nimer SD (2006). "Clinical management of myelodysplastic syndromes with interstitial deletion of chromosome 5q". Journal of Clinical Oncology. 24 (16): 2576–82. doi:10.1200/JCO.2005.03.6715. PMID 16735711.
21. ^ "ETV6 ETS variant 6 [Homo sapiens (human)] - Gene - NCBI".
22. ^ ^{a b c d e} Vega F, Medeiros LJ, Bueso-Ramos CE, Arboleda P, Miranda RN (2015). "Hematolymphoid neoplasms associated with rearrangements of PDGFRA, PDGFRB, and FGFR1". American Journal of Clinical Pathology. 144 (3): 377–92. doi:10.1309/AJCPMORR5Z2IKCEM. PMID 26276769.
23. ^ Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, Bloomfield CD, Cazzola M, Vardiman JW (2016). "The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia". Blood. 127 (20): 2391–405. doi:10.1182/blood-2016-03-643544. PMID 27069254.
24. ^ ^{a b} "WDR48 WD repeat domain 48 [Homo sapiens (human)] - Gene - NCBI".
25. ^ "PRKG2 protein kinase cGMP-dependent 2 [Homo sapiens (human)] - Gene - NCBI".
26. ^ "CEP85L centrosomal protein 85 like [Homo sapiens (human)] - Gene - NCBI".
27. ^ "CCDC6 coiled-coil domain containing 6 [Homo sapiens (human)] - Gene - NCBI".
28. ^ "CAPRIN1 cell cycle associated protein 1 [Homo sapiens (human)] - Gene - NCBI".
29. ^ "NIN ninein [Homo sapiens (human)] - Gene - NCBI".
30. ^ "CCDC88C coiled-coil domain containing 88C [Homo sapiens (human)] - Gene - NCBI".
31. ^ "BIN2 bridging integrator 2 [Homo sapiens (human)] - Gene - NCBI".
32. ^ "DTD1 D-tyrosyl-tRNA deacylase 1 [Homo sapiens (human)] - Gene - NCBI".
33. ^ Gotlib J (2015). "World Health Organization-defined eosinophilic disorders: 2015 update on diagnosis, risk stratification, and management". American Journal of Hematology. 90 (11): 1077–89. doi:10.1002/ajh.24196. PMID 26486351. S2CID 42668440.
34. ^ Tadic V, Westenberger A, Domingo A, Alvarez-Fischer D, Klein C, Kasten M (2015). "Primary familial brain calcification with known gene mutations: a systematic review and challenges of phenotypic characterization". JAMA Neurology. 72 (4): 460–7. doi:10.1001/jamaneurol.2014.3889. PMID 25686319.
35. ^ Batla A, Tai XY, Schottlaender L, Erro R, Balint B, Bhatia KP (2017). "Deconstructing Fahr's disease/syndrome of brain calcification in the era of new genes" (PDF). Parkinsonism & Related Disorders (Submitted manuscript). 37: 1–10. doi:10.1016/j.parkreldis.2016.12.024. PMID 28162874.
36. ^ Matsumoto T, Yokote K, Take A, Takemoto M, Asaumi S, Hashimoto Y, Matsuda M, Saito Y, Mori S (April 2000). "Differential interaction of CrkII adaptor protein with platelet-derived growth factor alpha- and beta-receptors is determined by its internal tyrosine phosphorylation". Biochem. Biophys. Res. Commun. 270 (1): 28–33. doi:10.1006/bbrc.2000.2374. PMID 10733900.
37. ^ Yamamoto M, Toya Y, Jensen RA, Ishikawa Y (March 1999). "Caveolin is an inhibitor of platelet-derived growth factor receptor signaling". Exp. Cell Res. 247 (2): 380–8. doi:10.1006/excr.1998.4379. PMID 10066366.
38. ^ ^{a b c} Braverman LE, Quilliam LA (February 1999). "Identification of Grb4/Nckbeta, a src homology 2 and 3 domain-containing adapter protein having similar binding and biological properties to Nck". J. Biol. Chem. 274 (9): 5542–9. doi:10.1074/jbc.274.9.5542. PMID 10026169.
39. ^ Arvidsson AK, Rupp E, Nånberg E, Downward J, Rönnstrand L, Wennström S, Schlessinger J, Heldin CH, Claesson-Welsh L (October 1994). "Tyr-716 in the platelet-derived growth factor beta-receptor kinase insert is involved in GRB2 binding and Ras activation". Mol. Cell. Biol. 14 (10): 6715–26. doi:10.1128/mcb.14.10.6715. PMC 359202. PMID 7935391.
40. ^ Tang J, Feng GS, Li W (October 1997). "Induced direct binding of the adapter protein Nck to the GTPase-activating protein-associated protein p62 by epidermal growth factor". Oncogene. 15 (15): 1823–32. doi:10.1038/sj.onc.1201351. PMID 9362449.
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42. ^ Chen M, She H, Davis EM, Spicer CM, Kim L, Ren R, Le Beau MM, Li W (September 1998). "Identification of Nck family genes, chromosomal localization, expression, and signaling specificity". J. Biol. Chem. 273 (39): 25171–8. doi:10.1074/jbc.273.39.25171. PMID 9737977.
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