Atlas of Genetics and Cytogenetics in Oncology and Haematology


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FOXC1 (forkhead box C1)

Identity

Other namesARA
FKHL7
FREAC-3
FREAC3
IGDA
IHG1
IRID1
RIEG3
HGNC (Hugo) FOXC1
LocusID (NCBI) 2296
Location 6p25.3
Location_base_pair Starts at 1610681 and ends at 1614129 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

 
  Figure1: Gene sequence (grey) and transcriptional product of FOXC1. Forkhead DNA binding domain (FH Domain) contains 4 alpha helices (H1, H2, H4 and H3), 2 beta sheets (B2 and B3) and two wings (W1 and W2).
Description Orientation: Plus strand. Genomic Size: 3447 bases. Exon Count: 1. Coding Exon Count: 1. RefSeq DNA sequence: NC_000006.11- NT_007592.15 contains Fork Head domain (FHD). Basal Isoelectric point: 8.7.
Transcription Gene is transcribed into 3454 bps mRNA, containing one exon.

Protein

 
  Figure 2: Amino acid sequence of the FHD of FOXC1, spanning from 69 to 178, H3 (alpha helix) mainly contribute to binding of the domain to DNA.
Description Sequence length: 553 amino acids, mass: 56789 Dalton. It contains one Fork Head DNA binding domain, consists approximately of 110 amino acids. FHD is a conservative sequence shared by all FOX proteins. FHD, a helix-turn-helix DNA binding motif, is composed of three alpha helices and two large "wing-like" loops. FHD contains nuclear localization signals at the N- and C- termini of the forkhead box, required to translocate the protein into cell nuclei. Alpha helix no.3 is responsible for DNA specific biding (Carlsson et al., 2002).
Expression Fork head protein is expressed in all tissues and cell lines examined (Hormas et al., 1993). FOXC1 in human is expressed in cornea, eye, heart, kidney, liver, lung and muscles (Wang et al., 2001).
Localisation FOXC1 protein localizes in nucleus (Berry et al., 2002).
Function FOXC1 plays a major role in embryonic and ocular development as a transcriptional factor and transcription regulator. Function of FOXC1 is related to several hundred genes, change in expression pattern of FOXC1 may cause change in the expression pattern of hundreds of the genes (Berry et al., 2008; Huang et al., 2008).
Function of FOXC1 protein involves DNA binding and bending (Pierrou et al., 1994). Binding of the fork head proteins to their cognate sites, results in bending of the DNA at an angle of 80-90 degrees, thus, enhancing transcriptional activity of certain genes (Saleem et al., 2001). Malfunction related to various Glaucoma phenotypes including congenital glaucoma, iridogoniodysgenesis anomaly, REG3, iris hyperplasia and Peter anomaly.
During ocular development, it interacts and regulates expression of FOXO1A. The promoter region of FOXO1A contains consensus FOXC1 binding site (GTAAACAAA). FOXO1A is responsible for regulation of cellular homeostasis and cell survival during ocular development, its functioning depends on function of FOXC1. Other targets of FOXC1 in transcriptional regulation in the eye include NOTCH2, RAB3GAP and CSPG5 (Berry et al., 2008).
Function of FOXC1 protein in ocular cells is regulated by p32, a cytoplasmic protein which has a binding site at FHD of FOXC1 and can be colocalized in nucleus. It regulates FOXC1-mediated transcription activation in a dose-dependent manner but does not affect FOXC1 DNA-binding ability. Malfunction of p32 or mutation in FHD of FOXC1, effecting binding ability of p32 might result in Axenfeild-Reiger malformations (Huang et al., 2008).
FOXC1 along with FOXC2 regulates the establishment of paraxial versus intermediate mesoderm cell fates in the vertebrate embryos (Wilm et al., 2004). FOXC1 and FOXC2 are required in kidney, urinary tract and early heart development processes, especially acting upstream of the Tbx1-FGF cascade during morphogenesis of the OFT (outflow tract) (Soe and Kume, 2006; Kume et al., 2000).
Kume et al. (2001) proposed that FOXC1 and FOXC2 interact with the Notch signalling pathway and are required for prepatterning of anterior and posterior domains in the presumptive somites through a putative Notch/Delta/Mesp regulatory loop.
Savage et al. (2010) found out that expression of FOXC1 along with FOXC2 is dependent on a complex interplay from Wnt and Shh pathways during early stages of in vitro skeletal myogenesis.
Homology Fork head domain (FHD), an approximately 110 amino acid segment is a common element shared by FOX proteins. Human Forkhead-box (FOX) gene family consists of at least 43 members, including FOXA1, FOXA2, FOXA3, FOXB1, FOXC1, FOXC2, FOXD1, FOXD2, FOXD3, FOXD4, FOXD5 (FOXD4L1), FOXD6 (FOXD4L3), FOXE1, FOXE2, FOXE3, FOXF1, FOXF2, FOXG1 (FOXG1B), FOXH1, FOXI1, FOXJ1, FOXJ2, FOXJ3, FOXK1, FOXK2, FOXL1, FOXL2, FOXM1, FOXN1, FOXN2 (HTLF), FOXN3 (CHES1), FOXN4, FOXN5 (FOXR1), FOXN6 (FOXR2), FOXO1 (FOXO1A), FOXO2 (FOXO6), FOXO3 (FOXO3A), FOXO4 (MLLT7), FOXP1, FOXP2, FOXP3, FOXP4, and FOXQ1.
FOXE3-FOXD2 (1p33), FOXQ1-FOXF2-FOXC1 (6p25.3), and FOXF1-FOXC2-FOXL1 (16q24.1) loci are FOX gene clusters within the human genome. FOXC1, FOXC2, FOXE1, FOXE3, FOXL2, FOXN1, FOXP2 and FOXP3 genes are mutated in human congenital disorders (Katoh and Katoh, 2004).
The forkhead box (Fox) family of transcription factors, which originated in unicellular eukaryotes, has expanded over time through multiple duplication events, and sometimes through gene loss, to over 40 members in mammals (Hannenhalli and Kaestner, 2009) found out that Fox genes have evolved to acquire a specialized function in many key biological processes. Mutations in Fox genes have a profound effect on human disease, causing phenotypes as varied as cancer, glaucoma and language disorders.

Mutations

Germinal Deletion of distal 6p is associated with a distinctive clinical phenotype including Axenfeld-Rieger malformation, hearing loss, congenital heart disease, dental anomalies, developmental delay, and a characteristic facial appearance.
By DNA sequencing of FOXC1 in 5 families and 16 sporadic patients a 6p microdeletion resulted from a de novo 6:18 translocation was recognized. The same translocation was reported in a child with specific ocular and facial phenotype (Maclean et al., 2005). Detailed analysis confirmed deletion of the FOXC1, FOXF2 and FOXQ1 forkhead gene cluster at 6p25. It showed central nervous system (CNS) anomalies, including hydrocephalus and hypoplasia of the cerebellum, brainstem, and corpus callosum with mild to moderate developmental delay.
The mouse gene Mf1 is homolog of FOXC1. Homozygous null Mf1-lacZ mice die at birth with hydrocephalus, eye defects, and multiple skeletal abnormalities identical to those of the classic mutant, congenital hydrocephalus. Kume et al. (1998) showed that congenital hydrocephalus involves a point mutation in Mf1, generating a truncated protein lacking the DNA-binding domain. Mesenchyme cells from Mf1-lacZ embryos differentiated poorly into cartilage in micro-mass culture and did not respond to added BMP2 and TGF-beta-1. The differentiation of arachnoid cells in the mutant meninges was also abnormal.
Somatic Using genotyping and FISH as method of investigations, Lehmann et al. (2002) studied a 9-generation Scottish family segregating autosomal dominant iridogoniodysgenesis. The team found an interstitial duplication of chromosome 6p25 which encompassed the FOXC1 gene.
Nishimura et al. (2001) analyzed the coding region of the FOXC1 gene in 70 probands with congenital anterior chamber defects and detected 9 mutations, 8 of which were novel. Affected members from 2 families, one with iris-hypoplasia and the other with Peters anomaly, had 2 different partial duplications of 6p25, respectively, both encompassing the FOXC1 gene. These data suggested that both FOXC1 haploinsufficiency and increased gene dosage may cause anterior-chamber defects of the eye.
Fetterman et al. (2009) identified a heterozygous FOXC1 missense mutation outside of the forkhead domain, and in the inhibitory domain, in 2 unrelated patients with iridogoniodysgenesis. Iridogoniodysgenesis phenotype is more commonly associated with FOXC1 duplications than point mutation.
Honkanen et al. (2003) identified the F112S (a point) mutation in the FOXC1 gene in 5 affected members of a 4-generation family segregating autosomal dominant anterior segment defects, including a patient who also had Peters anomaly.
Saleem et al. (2001) investigated 5 missense mutations of the FOXC1 transcription factor found in patients with Axenfeld-Rieger malformations to determine their effects on FOXC1 structure and function. Molecular modelling of the FOXC1 fork head domain predicted that the missense mutations did not alter FOXC1 structure. Biochemical analyses indicated that whereas all mutant proteins correctly localized to the cell nucleus, the I87M mutation reduced FOXC1 protein levels. DNA-binding experiments revealed that although the S82T and S131L mutations decreased DNA binding, the F112S and I126M mutations did not. However, the F112S and I126M mutations decreased the transactivation ability of FOXC1. Saleem et al. (2003) studied an additional 5 missense mutations in the FOXC1 gene. Biological analyses indicated that all missense mutations studied caused various FOXC1 perturbations, including nuclear localization defects, reduced or abolished DNA binding capacity, and a reduction in the transactivation capacity of FOXC1.

Implicated in

Entity Breast cancer
Note Methylation status of FOXC1 promoter can be related to invasiveness of breast cancer and patient survival. Higher methylation means lower expression and more invasiveness of tumour, in advanced breast tumors as concluded by Dejeux et al. (2010) and Muggerud et al. (2010) methylation levels of FOXC1 were higher in oestrogen receptor (ER) positive vs. ER negative tumours; whereas methylation levels lower in tumours with a TP53 mutation. FOXC1 showed a significant increase in the methylation frequency in invasive tumours. Low FOXC1 gene expression in both methylated and unmethylated DCIS (ductal carcinoma in situ) and IDCs (invasive ductal carcinomas) indicates that the loss of expression of FOXC1 happens at earlier stage during the progression of breast cancer.
Prognosis Recently FOXC1 has been reported as potential prognostic biomarker with functional significance in basal like breast cancer by Ray et al. (2010) and Dejeux et al. (2010).
  
Entity Invasive carcinoma
Oncogenesis Zhou et al. (2002) showed that TGF-beta1 up regulated transcription of FOXC1 in a number of human cancer cell lines. In FOXC1 homozygous knockdown (-foxc1/-foxc1) HeLa cell line, ectopic expression of FOXC1 cDNA restored the potential of TGF-beta1 to inhibit cell growth by arresting cells in the G0/G1 phase. Which reveals the FOXC1 having a tumour suppressive function. Furthermore, screens of primary endometrial and ovarian cancers revealed that FOXC1 was deleted in 6.7% out of 11.7% transcriptional silenced primary cancers. It suggests that FOXC1 functions as a tumour suppressor through TGF-beta1 mediated signals.
Van der Heul-Nieuwenhuijsen et al. (2009) analysed a set of 12 different FOX genes, including FOXC1, by quantitative reverse transcription-polymerase chain reaction in prostate zones, prostate cancer, lymph node metastases, benign prostatic hyperplasia (BPH), xenografts and several prostate cell lines. Various members of the FOX family were differentially expressed in the zones of the normal prostate and in benign and malignant out-growths. The expression profiles of FOXF1 and FOXF2 suggest a role in epithelial to mesenchymal transition, while FOXA1 and FOXC1 expression is linked to androgen-associated growth status of cancer.
FOXC1 contribute to microvascular invasion in primary hepatocellular carcinoma, making FOXC1 a candidate predictive marker of microvascular invasion. Inhibition of FOXC1 may reduce tumour metastasis in hepatocellular carcinoma (liver cancer) (Xu et al., 2012).
  
Entity Axenfield-Reiger Syndrome (ARS) or Axenfield-Reiger syndrome type 3 (RIEG3) also known as Axenfield syndrome or Axenfield Anomaly
Note Phenotype may show posterior corneal embryotoxon, prominent Schwalbe line and iris adhesion to the Schwalbe line. It may also show hypertelorism, hypoplasia of the malar bones, congenital absence of some teeth and mental retardation. Tooth anomalies are associated with Reiger syndrome. Glaucoma may occur in almost fifty percent of the patients with Axenfield-Reiger malformations (Ito et al., 2007).
Cytogenetics As results of different studies of ARS/ RIEG3 cases:
Nishimura et al. (1998) found an 11-bp deletion upstream of the FOXC1 forkhead domain. The team also identified a C-to-T transition within the forkhead domain, causing a ser131-to-leu (S131L) amino acid substitution. The Nishimura team found a C-to-G transversion within the forkhead domain. This change resulted in an ile126-to-met (I126M) amino acid substitution. They also identified a T-to-C transition in the FOXC1 gene that resulted in a phe112-to-ser (F112S) transition within the forkhead domain.
Mirzayans et al. (2000) found that Axenfeld-Rieger syndrome (RIEG3) was associated with a 67C-T transition in the FOXC1 gene, predicted to cause a gln23-to-ter (E23X) substitution upstream of the forkhead domain.
Nishimura et al. (2001) found a 22-bp insertion from position 26 through 47 in the cDNA of theFOXC1 gene.
Mears et al. (1998) identified heterozygosity for a 245G-C transversion in the FOXC1 gene, predicted to result in a ser82-to-thr (S82T) substitution at the start of helix 1 of the forkhead domain. They also identified a 261C-G transversion in the FOXC1 gene, resulting in an ile87-to-met (I87M) substitution in helix 1 of the forkhead domain.
Ito et al. (2007) identified a heterozygous 388C-T transi-tion in the FOXC1 gene, resulting in a leu130-to-phe (L130F) substitution in helix 3, the so-called 'recognition helix' of the forkhead domain.
Weisschuh et al. (2008) identified heterozygosity for a 358C-T transition in the FOXC1 gene, resulting in a gln120-to-ter (Q120X) substitution causing truncation of part of the forkhead domain.
  
Entity Peters anomaly (PA) and Iridogoniodysgenesis anomaly (IGDA)
Note IGDA is an autosomal dominant phenotype characterized by iris hypoplasia, goniodysgenesis, and juvenile glaucoma.
Peters anomaly consists of a central corneal leukoma, absence of the posterior corneal storma and Descemet membrane, and a variable degree of iris and lenticular attachments to the central aspect of the posterior cornea (Honkanen et al., 2003).
Cytogenetics As results of different studies of PA and IGDA cases:
Lehmann et al. (2000) found by genotyping of FOXC1, with microsatellite repeat markers, the presence of a chromosomal duplication.
Nishimura et al. (2001) identified a partial duplication of chromosome 6p25, which encompassed the FOXC1 gene.
Fetterman et al. (2009) identified heterozygosity for an 889C-T transition in the FOXC1 gene, resulting in a pro297-to-ser (P297S) substitution in the inhibitory domain.
  

External links

Nomenclature
HGNC (Hugo)FOXC1   3800
Cards
AtlasFOXC1ID40624ch6p25
Entrez_Gene (NCBI)FOXC1  2296  forkhead box C1
GeneCards (Weizmann)FOXC1
Ensembl (Hinxton)ENSG00000054598 [Gene_View]  chr6:1610681-1614129 [Contig_View]  FOXC1 [Vega]
AceView (NCBI)FOXC1
Genatlas (Paris)FOXC1
WikiGenes2296
SOURCE (Princeton)NM_001453
Genomic and cartography
GoldenPath (UCSC)FOXC1  -  6p25.3   chr6:1610681-1614129 +  6p25   [Description]    (hg19-Feb_2009)
EnsemblFOXC1 - 6p25 [CytoView]
Mapping of homologs : NCBIFOXC1 [Mapview]
OMIM601090   601631   602482   
Gene and transcription
Genbank (Entrez)AK021858 BC134421 BC169306 BC169307 L12143
RefSeq transcript (Entrez)NM_001453
RefSeq genomic (Entrez)AC_000138 NC_000006 NC_018917 NG_009368 NT_007592 NW_001838972 NW_004929326
Consensus coding sequences : CCDS (NCBI)FOXC1
Cluster EST : UnigeneHs.348883 [ NCBI ]
CGAP (NCI)Hs.348883
Alternative Splicing : Fast-db (Paris)GSHG0025364
Alternative Splicing GalleryENSG00000054598
Gene ExpressionFOXC1 [ NCBI-GEO ]     FOXC1 [ SEEK ]   FOXC1 [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ12948 (Uniprot)
NextProtQ12948  [Medical]
With graphics : InterProQ12948
Splice isoforms : SwissVarQ12948 (Swissvar)
Domaine pattern : Prosite (Expaxy)FORK_HEAD_1 (PS00657)    FORK_HEAD_2 (PS00658)    FORK_HEAD_3 (PS50039)   
Domains : Interpro (EBI)TF_fork_head    TF_fork_head_CS    WHTH_DNA-bd_dom   
Related proteins : CluSTrQ12948
Domain families : Pfam (Sanger)Fork_head (PF00250)   
Domain families : Pfam (NCBI)pfam00250   
Domain families : Smart (EMBL)FH (SM00339)  
DMDM Disease mutations2296
Blocks (Seattle)Q12948
Human Protein AtlasENSG00000054598
Peptide AtlasQ12948
HPRD03054
IPIIPI01015662   IPI00290377   
Protein Interaction databases
DIP (DOE-UCLA)Q12948
IntAct (EBI)Q12948
FunCoupENSG00000054598
BioGRIDFOXC1
InParanoidQ12948
Interologous Interaction database Q12948
IntegromeDBFOXC1
STRING (EMBL)FOXC1
Ontologies - Pathways
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  skeletal system development  ossification  ovarian follicle development  eye development  ureteric bud development  in utero embryonic development  somitogenesis  kidney development  lymph vessel development  blood vessel remodeling  DNA binding  double-stranded DNA binding  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  protein binding  nucleus  nucleus  transcription factor complex  nuclear heterochromatin  nucleolus  cytoplasm  regulation of transcription, DNA-dependent  Notch signaling pathway  pattern specification process  brain development  heart development  transcription factor binding  DNA binding, bending  germ cell migration  embryo development  tissue development  neural crest cell development  collagen fibril organization  glycosaminoglycan metabolic process  chromatin DNA binding  lacrimal gland development  embryonic heart tube development  odontogenesis of dentin-containing tooth  camera-type eye development  negative regulation of apoptotic process  sequence-specific DNA binding  transcription regulatory region DNA binding  positive regulation of transcription, DNA-dependent  positive regulation of transcription, DNA-dependent  negative regulation of mitotic cell cycle  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  regulation of organ growth  vascular endothelial growth factor receptor signaling pathway  paraxial mesoderm formation  artery morphogenesis  regulation of blood vessel size  regulation of sequence-specific DNA binding transcription factor activity  ventricular cardiac muscle tissue morphogenesis  cardiac muscle cell proliferation  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  skeletal system development  ossification  ovarian follicle development  eye development  ureteric bud development  in utero embryonic development  somitogenesis  kidney development  lymph vessel development  blood vessel remodeling  DNA binding  double-stranded DNA binding  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  protein binding  nucleus  nucleus  transcription factor complex  nuclear heterochromatin  nucleolus  cytoplasm  regulation of transcription, DNA-dependent  Notch signaling pathway  pattern specification process  brain development  heart development  transcription factor binding  DNA binding, bending  germ cell migration  embryo development  tissue development  neural crest cell development  collagen fibril organization  glycosaminoglycan metabolic process  chromatin DNA binding  lacrimal gland development  embryonic heart tube development  odontogenesis of dentin-containing tooth  camera-type eye development  negative regulation of apoptotic process  sequence-specific DNA binding  transcription regulatory region DNA binding  positive regulation of transcription, DNA-dependent  positive regulation of transcription, DNA-dependent  negative regulation of mitotic cell cycle  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  regulation of organ growth  vascular endothelial growth factor receptor signaling pathway  paraxial mesoderm formation  artery morphogenesis  regulation of blood vessel size  regulation of sequence-specific DNA binding transcription factor activity  ventricular cardiac muscle tissue morphogenesis  cardiac muscle cell proliferation  
REACTOMEFOXC1
Protein Interaction DatabaseFOXC1
Wikipedia pathwaysFOXC1
Gene fusion - rearrangments
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)FOXC1
SNP (GeneSNP Utah)FOXC1
SNP : HGBaseFOXC1
Genetic variants : HAPMAPFOXC1
1000_GenomesFOXC1 
ICGC programENSG00000054598 
Somatic Mutations in Cancer : COSMICFOXC1 
CONAN: Copy Number AnalysisFOXC1 
Mutations and Diseases : HGMDFOXC1
OMIM601090    601631    602482   
GENETestsFOXC1
Disease Genetic AssociationFOXC1
Huge Navigator FOXC1 [HugePedia]  FOXC1 [HugeCancerGEM]
Genomic VariantsFOXC1  FOXC1 [DGVbeta]
Exome VariantFOXC1
dbVarFOXC1
ClinVarFOXC1
snp3D : Map Gene to Disease2296
General knowledge
Homologs : HomoloGeneFOXC1
Homology/Alignments : Family Browser (UCSC)FOXC1
Phylogenetic Trees/Animal Genes : TreeFamFOXC1
Chemical/Protein Interactions : CTD2296
Chemical/Pharm GKB GenePA28217
Clinical trialFOXC1
Cancer Resource (Charite)ENSG00000054598
Other databases
Probes
Litterature
PubMed97 Pubmed reference(s) in Entrez
CoreMineFOXC1
iHOPFOXC1

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Written11-2012Shakila Jabeen, Vessela N Kristensen
Department of Clinical Molecular Biology and Laboratory Sciences (EpiGen), Division of Medicine, Akershus University Hospital, Lorenskog, Norway

Citation

This paper should be referenced as such :
Jabeen S, Kristensen VN . FOXC1 (forkhead box C1). Atlas Genet Cytogenet Oncol Haematol. November 2012 .
URL : http://AtlasGeneticsOncology.org/Genes/FOXC1ID40624ch6p25.html

The various updated versions of this paper are referenced and archived by INIST as such :

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