Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CSF1R (colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog)

Identity

Other namesC-FMS
CD115
CSF-1-R
CSFR
EC 2.7.10.1
FIM2
FMS
c-fms
HGNC (Hugo) CSF1R
LocusID (NCBI) 1436
Location 5q32
Location_base_pair Starts at 149432854 and ends at 149492935 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order The human CSF1R gene is located at the distal end of the q arm of chromosome 5 with telomere to centromere orientation. Proximal flanking genes include CSF2 (GM-CSF) and IL-3 at 5q31.1. Distal flanking genes include PDGFRB at 5q31-q32.
Note CSF1R (C-FMS) is the human cellular homologue of the retroviral oncogene v-fms. The v-fms oncogene, first identified and isolated by Heisterkamp et al. in 1983, is transduced by the feline sarcoma virus Susan McDonough (SM) and HZ-5 strains, which cause fibrosarcomas in domestic cats. The v-fms oncogene is equivalent to the c-fms gene in its sequence, but has undergone genetic alterations, which constitutively activate the receptor kinase in the absence of its ligand, the colony stimulating factor-1 ( CSF1 ). Infection of mammalian cells with v-fms leads to cell transformation in vitro and in vivo.

DNA/RNA

Note The presence of an anti-sense CSF1R transcript starting within the FIRE region has been reported in mouse macrophages and B cells.
 
  A: Genomic structure of the human CSF1R gene.
B: Scheme showing the regulatory regions of the mouse Csf1r gene. The regulatory regions and transcription binding sites within are highly conserved between mouse and human. (Diagram based on Bonifer et al. Frontiers in Bioscience 2008)
Description The human CSF1R gene, on the minus strand, spans a region of 60,077 bases (Start: 149,413,051 bp from pter; End: 149,473,128 bp from pter) interrupted by introns ranging from 26kb for intron 1, to a range between 6.3kb to less than 0.1 kb for the other introns. The human CSF1R gene is composed of a total of 22 exons, of which the first exon is non-coding and where the remaining 21 exons (starting with exon 2) encode for the CSF1R protein.
The human CSF1R and mouse Csf1r genomic structures are highly conserved.
Transcription The 5' end of the human CSF1R gene has 2 alternative transcription start site regions, preceded by two alternative promoters. The transcription of CSF1R mRNA can be initiated at the two independent start sites in a tissue specific manner. The transcription of exon 1 through exon 22 occurs only in placental trophoblasts, and is driven by a trophoblast-specific promoter approximately 20kb upstream of the first exon. The transcript produced is predicted to be approximately 4kb long. In macrophages and a few other tissues (see expression section) transcription of CSF1R occurs only from exon 2 through exon 22 producing a transcript predicted to be approximately 3.9kb in length, which is translated into the CSF1R protein. The transcription this transcript is under the control of two major regulatory regions, which are highly conserved between human and mouse: the Promoter upstream of exon 2 and the fms-intronic regulatory region (FIRE). Most studies on CSF1R transcriptional regulation have focused on the mouse gene. However, most of the features of mouse Csf1r are highly conserved in human.
The mouse Csf1r promoter is TATA-less, and drives transcription from multiple sites (known as broad class transcription start sites). This promoter is not GC rich and there are no CpG islands in the vicinity. This promoter contains binding sites for various transcription factors including: PU.1, C/EBP, PAX5, and FUS/TLS - TBP. The mouse FIRE region is located in the second intron, approximately 2kb downstream from the transcription start site. It contains binding sites for a number of transcription factors including: Sp1 / Sp3, Ets, Egr-2 / Sp1, Runx1, AP-1 as well as PU.1 and C/EBP. With a few exceptions, the features described for the mouse Csfr1 regulatory regions are highly conserved in human. Specifically, the human CSF1R can be regulated in a hormone dependent fashion via a glucocorticoid response element present in the human CSF1R promoter, but not in the mouse Csf1r promoter.
Pseudogene The first CSF1R intron contains a transcriptionally inactive ribosomal protein L7 processed pseudogene that is oriented in the opposite direction of the CSF1R gene itself. This pseudogene is not functional but its sequence is highly conserved across all mammalian species.

Protein

 
  CSF1R Protein Structure. A. Schematic representation of CSF1R protein showing the CSF1-binding IG domains in the extracellular portion, and the tyrosine kinase catalytic domain in the intracellular portion. Phosphorylated tyrosines (Y) are indicated.
Description The CSF1R protein consists of 972 amino acids and has a molecular mass of approximately 108 kDa. However due to post-translational modifications, which include phosphorylation, glycosylation, and the acquisition of N-linked oligosaccharides, the proteins molecular size increases. The CSF1R protein also contains a signal peptide and a 512 amino acid N-terminal extracellular segment which contains the ligand binding domain, a hydrophobic 25 amino acid membrane spanning region, and intracellular domain 435 amino acids in length that includes all sequences necessary for tyrosine kinase activity (occurring at tyrosine (Y) Y699 and Y708, as well as Y809). The CSF1R protein contains a glycine-rich signature sequence that is characteristic of kinases, as well as an ATP binding site at lysine (K) K616. The immature intracellular glycoprotein has a molecular mass of 130 kDa after it acquires N-linked oligosaccharides of the high mannose type during co-translational glycosylation. The molecular mass of CSF1R is increased further during intracellular transport to the plasma membrane, where the glycoprotein's N-linked carbohydrates undergo modifications in the Golgi complex, resulting in an increase to 150 kDa molecular mass. There are variations in molecular mass of CSF1R across species due to the differential processing of carbohydrate chains in a species specific manner.
 
  CSF1R Protein Structure. B. Diagram of the 2.7 A Crystal Structure of the Autoinhibited Human CSF1R/ kinase Domain (as described in Walter et al. J. Mol. Biol. 2007).
Expression The major site of CSF1R expression is in macrophages. In hematopoiesis, CSF1R is upregulated during monocytic differentiation, but is downregulated during granulopoiesis. CSF1R is expressed predominantly in committed macrophage precursors (CFU-Ms), monocytes, and tissue macrophages. CSF1R mRNA can be detected granulocytes, but is not translated. CSF1R mRNA/protein expression has been reported also in non-hematopoietic cells such as trophoblasts (where is seems to derive from an alternative transcript including the non-coding exon 1), osteoclasts, smooth muscle cells, and neurons, as well as in female mammary gland epithelium during development and lactation. Expression of CSF1R mRNA/protein has also been reported in breast, ovarian, and endometrial tumors, as well as in hepatocellular carcinomas.
CSF1R expression during hematopoiesis is regulated by tissue-specific sets of transcription factors that play a key role in myeloid differentiation. CSF1R is activated in a synergistic manner by the co-expression of the macrophage-specific transcription factor Pu.1 and c-Ets-2. During B-cell lineage restriction and differentiation, the CSF1R gene is repressed by the transcription factor PAX5. It has been shown that PAX5 is required during B-cell differentiation to keep CSF1R in a silent state. It has also been shown that CSF1R can be repressed by Foxp1, a forkhead transcription factor that is in turn regulated by the Beta-2-integrin Mac-1.
Localisation CSF1R is located at the cell plasma membrane. Transport of CSF1R from the endoplasmic reticulum (the site of synthesis) to the plasma membrane occurs efficiently with detection of the receptor at the surface within 30 minutes of synthesis.
Function CSF1R is the receptor for the ligand colony stimulating factor-1 (CSF1). CSF1R is an integral transmembrane glycoprotein that exhibits ligand-induced tyrosine-specific protein kinase activity, which triggers a signaling cascade eventually affecting transcription of CSF1-responsive genes. CSF1R tyrosine phosphorylation is induced upon binding of CSF1, leading to activation of Ras / Erk and class I-A phosphatidylinositol 3-kinase signaling pathways, which in turn activate the signal transducers and activators of transcription (STATs) pathways, specifically STAT1, STAT3, and STAT5. CSF1R activation by CSF1 results in increased growth, proliferation and differentiation.
Homology Like the CSF1R gene, the CSF1R protein sequence appears to be conserved across Euteleostomi (vertebrates) including: Homo sapiens (Human), Canis lupus familiaris (Dog), Mus musculus (Mouse), Rattus norvegicus (Rat), Gallus gallus (Chicken), and Danio rerio (Zebrafish).
CSF1R is a member of the gp140 family of the type I cytokine receptor group and shares a high degree of amino acid sequence homology to platelet-derived growth factor receptor (PDGFRB), specifically in its kinase domain.

Mutations

Germinal None identified as of yet.
Somatic Chromosomal abnormalities: A partial deletion of chromosome 5 containing the CSF1R locus has been consistently observed in patients with myelodysplastic syndrome. The CSF1R locus is also affected by the acute megakaryoblastic leukemia-associated translocation t(3;5)(p21;q33) in which the CSF1R gene on chromosome 5 is fused to the RBM6 gene on chromosome 3, resulting in a fusion protein RBM6-CSF1R.
Gene mutations: CSF1R point mutations have been detected mainly in hematopoietic/lymphoid tissue and liver, where they correlate with myelodysplastic syndrome and acute myeloid leukemia (AML) and hepatocellular carcinoma, respectively. Specifically, mutations at codons 301 (exon 7) and 969 (exon 22) seem to occur with a higher frequency in both tissues. According to earlier studies these are activating mutations that would play a role in leukemogenesis. However, later studies have failed to find these mutations in AML patients. Additional mutations were discovered in AML patients at codons 245 (exon 6) and 413 (exon 9). However, their contribution to leukemogenesis is not known.
Epi-mutations: Specific fusion proteins resulting from leukemia-associated chromosomal translocations, including the AML1-MTG fusion proteins, result in transcriptional down-regulation of specific AML1 target genes such as CSF1R. AML1-MTG-induced CSF1R downregulation is epigenetic, as it is marked by specific repressive histone changes as well as DNA hypermethylation at the CSF1R regulatory regions. CSF1R epigenetic down-regulation is associated with block of myeloid differentiation and defects in cell proliferation in vitro.

Implicated in

Entity Myelodysplastic syndrome (MDS)
Disease The human CSF1R gene is consistently lost by partial deletions occurring in chromosome 5 in MDS patients. Moreover, specific deletion of the CSFS1R gene has been detected in as many as 40% of MDS patients.
  
Entity Acute Myeloid Leukemia (AML)
Disease Early studies had suggested a link between AML and the presence of CSF1R codon 301 and 969 activating mutations. While there is strong evidence that these mutations have potential transforming activity, recent studies have failed to find these mutations in AML patients. Thus the pathogenic role of CSF1R mutations in leukemogenesis is still controversial.
CSF1R might be involved in leukemia through mechanisms other than gene mutations. CSF1R downregulation has been reported in specific AML subtypes. One of the factors that may lead to CSF1R downregulation is the expression of the AML-associated fusion proteins AML1-MTG8 (AML1-ETO) and AML1-MTG16, derived from the t(8;21) and t(16;21) chromosomal translocations, respectively. Specifically, in patients with the t(8;21) translocation, which accounts for approximately 12% of all AML cases, CSF1R down-regulation is marked by epigenetic repressive changes (epi-mutations).
  
Entity t(3;5)(p21;q33) in Acute Megakaryoblastic Leukemia (AMKL)
Disease CSF1R has been reported to be affected by the chromosomal translocation t(3;5)(p21;q33) in the AMKL cell line MKPL-1. The fusion protein produced by this translocation, RBM6-CSF1R is found only in the cytoplasm and is constitutively active in the megakaryocyte lineage. The RBM6-CSF1R confers IL-3 independence to the mouse Pro-B cell line BaF3, and induced myeloproliferative disease in a murine transplant model. The AMKL subtype represents 1% or less of the cases of AML. It most often occurs in children, and is associated with Down syndrome. The prognosis for AMKL is poor.
  
Entity Breast Cancer
Disease 58% of all breast carcinomas and 85% of invasive breast carcinomas express higher levels of CSF1R compared to normal resting breast tissue. It has been demonstrated that exogenous expression of CSF1R in untransformed human mammary epithelial cells results in aberrant acinar morphogenesis, anchorage-independent growth and an invasive phenotype. Expression of CSF1R in breast tumors correlates with increased invasiveness and adverse prognostic features like high histological grade, and an advanced clinical stage of presentation of breast cancer.
  
Entity Cervical Cancer
Disease A significant increase in CSF1R expression has been reported in cervical carcinomas as compared to normal cervical tissue. The expression of CSF1R in cervical cancer is usually associated with a more aggressive and invasive disease. It has been suggested that there is an autocrine mode of regulation by CSF1 in this cancer cell type.
  

Breakpoints

Note The only breakpoint known for the CSF1R gene can be inferred by the identification of the novel fusion protein RBM6-CSF1R, in which the N-terminal portion of the RBM6 (a.a. 1-36) is fused to the C-terminal portion of CSF1R (a.a. 574-972). This fusion protein is predicated to be produced by the translocation t(3;5)(p21;q33).

External links

Nomenclature
HGNC (Hugo)CSF1R   2433
Cards
AtlasCSF1RID40161ch5q32
Entrez_Gene (NCBI)CSF1R  1436  colony stimulating factor 1 receptor
GeneCards (Weizmann)CSF1R
Ensembl (Hinxton)ENSG00000182578 [Gene_View]  chr5:149432854-149492935 [Contig_View]  CSF1R [Vega]
AceView (NCBI)CSF1R
Genatlas (Paris)CSF1R
WikiGenes1436
SOURCE (Princeton)NM_005211
Genomic and cartography
GoldenPath (UCSC)CSF1R  -  5q32   chr5:149432854-149492935 -  5q32   [Description]    (hg19-Feb_2009)
EnsemblCSF1R - 5q32 [CytoView]
Mapping of homologs : NCBICSF1R [Mapview]
OMIM164770   221820   
Gene and transcription
Genbank (Entrez)AB208819 AK294467 AK304491 BC047521 BC129939
RefSeq transcript (Entrez)NM_005211
RefSeq genomic (Entrez)AC_000137 NC_000005 NC_018916 NG_012303 NT_029289 NW_001838953 NW_004929324
Consensus coding sequences : CCDS (NCBI)CSF1R
Cluster EST : UnigeneHs.586219 [ NCBI ]
CGAP (NCI)Hs.586219
Alternative Splicing : Fast-db (Paris)GSHG0025172
Alternative Splicing GalleryENSG00000182578
Gene ExpressionCSF1R [ NCBI-GEO ]     CSF1R [ SEEK ]   CSF1R [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP07333 (Uniprot)
NextProtP07333  [Medical]
With graphics : InterProP07333
Splice isoforms : SwissVarP07333 (Swissvar)
Catalytic activity : Enzyme2.7.10.1 [ Enzyme-Expasy ]   2.7.10.12.7.10.1 [ IntEnz-EBI ]   2.7.10.1 [ BRENDA ]   2.7.10.1 [ KEGG ]   
Domaine pattern : Prosite (Expaxy)IG_LIKE (PS50835)    PROTEIN_KINASE_ATP (PS00107)    PROTEIN_KINASE_DOM (PS50011)    PROTEIN_KINASE_TYR (PS00109)    RECEPTOR_TYR_KIN_III (PS00240)   
Domains : Interpro (EBI)Ig-like_dom    Ig-like_fold    Ig_sub    Ig_sub2    Immunoglobulin    Kinase-like_dom    Prot_kinase_dom    Protein_kinase_ATP_BS    Ser-Thr/Tyr_kinase_cat_dom    Tyr_kinase_AS    Tyr_kinase_cat_dom    Tyr_kinase_CSF1/PDGF_rcpt    Tyr_kinase_rcpt_3_CS   
Related proteins : CluSTrP07333
Domain families : Pfam (Sanger)ig (PF00047)    Pkinase_Tyr (PF07714)   
Domain families : Pfam (NCBI)pfam00047    pfam07714   
Domain families : Smart (EMBL)IG (SM00409)  IGc2 (SM00408)  TyrKc (SM00219)  
DMDM Disease mutations1436
Blocks (Seattle)P07333
PDB (SRS)2I0V    2I0Y    2I1M    2OGV    3BEA    3DPK    3KRJ    3KRL    3LCD    3LCO    4DKD    4HW7   
PDB (PDBSum)2I0V    2I0Y    2I1M    2OGV    3BEA    3DPK    3KRJ    3KRL    3LCD    3LCO    4DKD    4HW7   
PDB (IMB)2I0V    2I0Y    2I1M    2OGV    3BEA    3DPK    3KRJ    3KRL    3LCD    3LCO    4DKD    4HW7   
PDB (RSDB)2I0V    2I0Y    2I1M    2OGV    3BEA    3DPK    3KRJ    3KRL    3LCD    3LCO    4DKD    4HW7   
Human Protein AtlasENSG00000182578
Peptide AtlasP07333
HPRD01269
IPIIPI00011218   IPI00922334   IPI00965831   IPI00966144   
Protein Interaction databases
DIP (DOE-UCLA)P07333
IntAct (EBI)P07333
FunCoupENSG00000182578
BioGRIDCSF1R
InParanoidP07333
Interologous Interaction database P07333
IntegromeDBCSF1R
STRING (EMBL)CSF1R
Ontologies - Pathways
Ontology : AmiGOpositive regulation of protein phosphorylation  macrophage colony-stimulating factor receptor activity  ATP binding  plasma membrane  integral to plasma membrane  inflammatory response  signal transduction  transmembrane receptor protein tyrosine kinase signaling pathway  multicellular organismal development  cell proliferation  positive regulation of cell proliferation  regulation of cell shape  cell surface  peptidyl-tyrosine phosphorylation  cytokine-mediated signaling pathway  cytokine binding  cytokine binding  hemopoiesis  monocyte differentiation  macrophage differentiation  osteoclast differentiation  positive regulation of cell migration  ruffle organization  cellular response to macrophage colony-stimulating factor stimulus  positive regulation of tyrosine phosphorylation of Stat3 protein  protein homodimerization activity  receptor complex  innate immune response  regulation of bone resorption  cell-cell junction maintenance  phosphatidylinositol metabolic process  protein autophosphorylation  phosphatidylinositol-mediated signaling  mammary gland duct morphogenesis  positive regulation of protein tyrosine kinase activity  positive regulation of ERK1 and ERK2 cascade  cellular response to cytokine stimulus  positive regulation of protein serine/threonine kinase activity  positive regulation of chemokine secretion  positive regulation of cell motility  regulation of actin cytoskeleton reorganization  
Ontology : EGO-EBIpositive regulation of protein phosphorylation  macrophage colony-stimulating factor receptor activity  ATP binding  plasma membrane  integral to plasma membrane  inflammatory response  signal transduction  transmembrane receptor protein tyrosine kinase signaling pathway  multicellular organismal development  cell proliferation  positive regulation of cell proliferation  regulation of cell shape  cell surface  peptidyl-tyrosine phosphorylation  cytokine-mediated signaling pathway  cytokine binding  cytokine binding  hemopoiesis  monocyte differentiation  macrophage differentiation  osteoclast differentiation  positive regulation of cell migration  ruffle organization  cellular response to macrophage colony-stimulating factor stimulus  positive regulation of tyrosine phosphorylation of Stat3 protein  protein homodimerization activity  receptor complex  innate immune response  regulation of bone resorption  cell-cell junction maintenance  phosphatidylinositol metabolic process  protein autophosphorylation  phosphatidylinositol-mediated signaling  mammary gland duct morphogenesis  positive regulation of protein tyrosine kinase activity  positive regulation of ERK1 and ERK2 cascade  cellular response to cytokine stimulus  positive regulation of protein serine/threonine kinase activity  positive regulation of chemokine secretion  positive regulation of cell motility  regulation of actin cytoskeleton reorganization  
Pathways : BIOCARTACBL mediated ligand-induced downregulation of EGF receptors [Genes]    METS affect on Macrophage Differentiation [Genes]   
Pathways : KEGGRas signaling pathway    Rap1 signaling pathway    Cytokine-cytokine receptor interaction    Endocytosis    PI3K-Akt signaling pathway    Osteoclast differentiation    Hematopoietic cell lineage    Pathways in cancer    Transcriptional misregulation in cancer   
REACTOMECSF1R
Protein Interaction DatabaseCSF1R
Wikipedia pathwaysCSF1R
Gene fusion - rearrangments
Rearrangement : TICdbCSF1R [5q32]  -  RBM6 [3p21.31]
Rearrangement : TICdbRBM6 [3p21.31]  -  CSF1R [5q32]
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)CSF1R
SNP (GeneSNP Utah)CSF1R
SNP : HGBaseCSF1R
Genetic variants : HAPMAPCSF1R
1000_GenomesCSF1R 
ICGC programENSG00000182578 
Somatic Mutations in Cancer : COSMICCSF1R 
CONAN: Copy Number AnalysisCSF1R 
Mutations and Diseases : HGMDCSF1R
OMIM164770    221820   
GENETestsCSF1R
Disease Genetic AssociationCSF1R
Huge Navigator CSF1R [HugePedia]  CSF1R [HugeCancerGEM]
Genomic VariantsCSF1R  CSF1R [DGVbeta]
Exome VariantCSF1R
dbVarCSF1R
ClinVarCSF1R
snp3D : Map Gene to Disease1436
General knowledge
Homologs : HomoloGeneCSF1R
Homology/Alignments : Family Browser (UCSC)CSF1R
Phylogenetic Trees/Animal Genes : TreeFamCSF1R
Chemical/Protein Interactions : CTD1436
Chemical/Pharm GKB GenePA26936
Clinical trialCSF1R
Cancer Resource (Charite)ENSG00000182578
Other databases
Probes
Litterature
PubMed137 Pubmed reference(s) in Entrez
CoreMineCSF1R
iHOPCSF1R

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Written04-2008John Adams Fischer, Stefano Rossetti, Nicoletta Sacchi
Roswell Park Cancer Institute, Department of Cancer Biology, Elm and Carlton Streets, Buffalo, NY 14263, USA

Citation

This paper should be referenced as such :
Fischer JA, Rossetti S, Sacchi N . CSF1R (colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog). Atlas Genet Cytogenet Oncol Haematol. April 2008 .
URL : http://AtlasGeneticsOncology.org/Genes/CSF1RID40161ch5q32.html

The various updated versions of this paper are referenced and archived by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/44403/1/04-2008-CSF1RID40161ch5q32.pdf   [ Bibliographic record ]

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