Forkhead Gene Research Articles

Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies

BackgroundMembers of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP.ResultsApplication of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters.ConclusionConsideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.

Expression of the forkhead transcription factor FOXP1 is associated with that of estrogen receptorβ in primary invasive breast carcinomas

We previously identified a correlation between estrogen receptor alpha (ERalpha) and the candidate tumour suppressor gene Forkhead Box P1 (FOXP1), whose nuclear protein expression in breast tumours was associated with improved patient survival. However, the expression pattern of FOXP1 in normal breast tissue is more reminiscent of the second receptor, ERbeta, which has an emerging role as a tumour suppressor in breast cancer and critically may underlie the ability of some ERalpha-negative tumours to respond to tamoxifen. In a series of 283 breast cancers, in which ERalpha-positive tumours were treated with tamoxifen, the nuclear expression of ERbeta correlated significantly with ERalpha (p = 0.004), low-tumour grade (p = 0.008) and nuclear FOXP1 (p = 0.01). High-grade tumours exhibited significantly more cytoplasmic ERbeta than the low-grade tumours (p = 0.006). Regression analysis demonstrated that FOXP1 expression was most closely related to nuclear ERbeta (p = 0.021). Neither, nuclear or cytoplasmic ERbeta expression demonstrated prognostic significance. FOXP1 is not estrogen regulated and silencing FOXP1 expression, using siRNA, did not affect ERalpha, ERbeta or progesterone receptor expression, suggesting ER and FOXP1 co-expression may reflect a common regulatory mechanism.

Variation in numbers of CD4+CD25highFOXP3+T cells with normal immuno-regulatory properties in long-term graft outcome

Chronic rejection (CR) is a major cause of long-term graft loss that would be avoided by the induction of tolerance. We previously showed that renal transplant patients with CR have lower numbers of peripheral CD4(+)CD25(high) T cells than operationally tolerant patients, patients with stable graft function and healthy volunteers (HV). We explored here the profile of CD4(+)CD25(high) blood T cells in these patients focusing on their expression of the regulatory T cells (Treg) gene Forkhead Box P3 (FOXP3) and their suppressive function. We show that CR is associated with a decreased number of CD4(+)CD25(high)FOXP3(+)T cells with normal regulatory profile, whereas graft acceptance is associated with CD4(+)CD25(high)FOXP3(+)T cell numbers similar to HVs. These data suggest that Treg numbers, rather than their intrinsic suppressive capacity, may contribute to determining the long-term fate of renal transplants.

Immunoprecipitation mapping of TRX-associated chromosome elements in the fork head gene promoter in Drosophila melanogaster salivary gland cells

Using the method of immunoprecipitation of the in vivo crosslinked and sheared by sonication chromatin, mapping of potential trithorax-associated regulatory elements within the extended (9 kb) promoter region of the fork head gene (fkh) in the Drosophila melanogaster salivary gland cells was performed. Relative homogeneity of the salivary gland cells, along with the parallel use of the antibodies to different domains of the same trithorax protein (TRX), and the introduction of cross-hybridization steps for additional specific enrichment of initial DNA libraries, provided improvement of the method effectiveness and identification of one major and two less expressed potential TRX-binding sites.

A W148R mutation in the human FOXD4 gene segregating with dilated cardiomyopathy, obsessive-compulsive disorder, and suicidality

The forkhead/winged helix box (FOX) gene family comprises at least 43 different genes encoding transcriptional factors with a highly conserved DNA-binding domain. To date, mutations in members of the FOX gene family have been causally linked to a variety of different human diseases. We describe a three-generation Albanian pedigree in which a complex phenotype consisting of dilated cardiomyopathy, obsessive-compulsive disorder, and suicidality is segregated with a missense mutation (W148R) in the human FOXD4 gene. This mutation disrupts an extremely highly conserved tryptophan residue in the forkhead domain of FOXD4, possibly resulting in reduced DNA binding capacity and altered transcriptional activity. Our present findings widen the spectrum of diseases associated with genetic aberrations in the forkhead gene family.

Expression of the forkhead transcription factor FoxN4 in progenitor cells in the developing Xenopus laevis retina and brain

Forkhead proteins are involved in gene regulation in a large variety of developmental situations. Several forkhead gene products are expressed in the developing eye and brain. Here we characterize the expression of FoxN4 during Xenopus development. We report that FoxN4 is expressed in the eye from the earliest stages of specification through retinal maturation. FoxN4 is also expressed in the pallium, optic tectum, isthmus, reticular formation, and in cells lining the ventricle of the tadpole brain.

Rhabdomyosarcomas in adults and children: an update.

Abstract Context.—Rhabdomyosarcomas comprise a relatively common diagnostic entity among childhood cancers and a relatively rare one among adult tumors. They may possess a variety of histologies that generally differ among age groups. These lesions appear to be separate biologic entities as well as morphologic categories, with embryonal tumors having genetic lesions related to loss of heterozygosity and aberrant parental imprinting, alveolar tumors containing genetic fusions between PAX and forkhead genes, and pleomorphic tumors showing an accumulation of genetic lesions similar to other adult high-grade sarcomas. Objective.—To present guidelines for diagnosis of rhabdomyosarcoma and recent finding concerning the biology and classification of these lesions. Data Sources.—Review of recent and older published literature and distillation of the authors' experience. Conclusions.—Infants and young children tend to have embryonal rhabdomyosarcomas, adolescents and young adults tend to have alveolar rhabdomyosar...

Rhabdomyosarcomas in Adults and Children: An Update

Rhabdomyosarcomas comprise a relatively common diagnostic entity among childhood cancers and a relatively rare one among adult tumors. They may possess a variety of histologies that generally differ among age groups. These lesions appear to be separate biologic entities as well as morphologic categories, with embryonal tumors having genetic lesions related to loss of heterozygosity and aberrant parental imprinting, alveolar tumors containing genetic fusions between PAX and forkhead genes, and pleomorphic tumors showing an accumulation of genetic lesions similar to other adult high-grade sarcomas. To present guidelines for diagnosis of rhabdomyosarcoma and recent finding concerning the biology and classification of these lesions. Review of recent and older published literature and distillation of the authors' experience. Infants and young children tend to have embryonal rhabdomyosarcomas, adolescents and young adults tend to have alveolar rhabdomyosarcomas, and older adults tend to have pleomorphic rhabdomyosarcomas, although there is some overlap. Newer rare entities, including spindle cell rhabdomyosarcoma and sclerosing rhabdomyosarcoma, have been described in children and adults. Fusion-positive tumors have a distinct molecular signature with downstream activation of a number of myogenic and tumorigenic factors. Genetic testing may be successfully used for diagnosis and may guide therapy in future clinical trials. Differential diagnosis has become simpler than in previous years, because of use of myogenic factors in immunohistochemistry, but classification based solely on histologic features remains challenging.

In control of biology: of mice, men and Foxes.

Forkhead proteins comprise a highly conserved family of transcription factors, named after the original forkhead gene in Drosophila. To date, over 100 forkhead genes have been identified in a large variety of species, all sharing the evolutionary conserved 'forkhead' DNA-binding domain, and the cloning and characterization of forkhead genes have continued in recent years. Forkhead transcription factors regulate the expression of countless genes downstream of important signalling pathways in most, if not all, tissues and cell types. Recent work has provided novel insights into the mechanisms that contribute to their functional diversity, including functional protein domains and interactions of forkheads with other transcription factors. Studies using loss- and gain-of-function models have elucidated the role of forkhead factors in developmental biology and cellular functions such as metabolism, cell division and cell survival. The importance of forkhead transcription factors is underlined by the developmental defects observed in mutant model organisms, and multiple human disorders and cancers which can be attributed to mutations within members of the forkhead gene family. This review provides a comprehensive overview of current knowledge on forkhead transcription factors, from structural organization and regulatory mechanisms to cellular and developmental functions in mice and humans. Finally, we will discuss how novel insights gained from involvement of 'Foxes' in the mechanisms underlying human pathology may create new opportunities for treatment strategies.

Foxg1 is required for morphogenesis and histogenesis of the mammalian inner ear

The forkhead genes are involved in patterning, morphogenesis, cell fate determination, and proliferation. Several Fox genes (Foxi1, Foxg1) are expressed in the developing otocyst of both zebrafish and mammals. We show that Foxg1 is expressed in most cell types of the inner ear of the adult mouse and that Foxg1 mutants have both morphological and histological defects in the inner ear. These mice have a shortened cochlea with multiple rows of hair cells and supporting cells. Additionally, they demonstrate striking abnormalities in cochlear and vestibular innervation, including loss of all crista neurons and numerous fibers that overshoot the organ of Corti. Closer examination shows that some anterior crista fibers exist in late embryos. Tracing these fibers shows that they do not project to the brain but, instead, to the cochlea. Finally, these mice completely lack a horizontal crista, although a horizontal canal forms but comes off the anterior ampulla. Anterior and posterior cristae, ampullae, and canals are reduced to varying degrees, particularly in combination with Fgf10 heterozygosity. Compounding Fgf10 heterozygotic effects suggest an additive effect of Fgf10 on Foxg1, possibly mediated through bone morphogenetic protein regulation. We show that sensory epithelia formation and canal development are linked in the anterior and posterior canal systems. Much of the Foxg1 phenotype can be explained by the participation of the protein binding domain in the delta/notch/hes signaling pathway. Additional Foxg1 effects may be mediated by the forkhead DNA binding domain.

The mouse forkhead gene Foxc1 is required for primordial germ cell migration and antral follicle development

Foxc1 encodes a forkhead/winged helix transcription factor expressed in many embryonic tissues. Previous studies have investigated defects in the urogenital system of Foxc1 null mutants, but the mechanisms underlying the abnormal development of the gonad have not been explored. From earliest stages, the mutant ovaries are smaller than normal, with fewer germ cells and disorganized somatic issue. No bursa membrane is formed, and the oviduct remains uncoiled. Although germ cells are specified correctly, many of them do not migrate to the gonadal ridge, remaining trapped in the hindgut. Consequently, the number initially reaching the gonad is less than 25% of normal. Once in the ovary, germ cells proliferate normally, but the supporting somatic cells are not organized correctly. Since mutant embryos die at birth, further development was followed in ovaries grafted underneath the kidney capsule of ovariectomized females. Transplanted ovaries display normal folliculogenesis up to preantral stages. However, no follicles develop beyond early antral stages. Mutant follicles are often polyovulatory and have disrupted theca and granulosa cell layers. We conclude that alongside its previously known roles in kidney, cardiovascular and eye development, Foxc1 has essential functions during at least two stages of gonad development—germ cell migration and folliculogenesis.

Identification of forkhead transcription factors in cortical and dopaminergic areas of the adult murine brain

The murine forkhead family of transcription factors consists of over 30 members, the vast majority of which is important in embryonic development. Implicated in processes such as proliferation, differentiation and survival, forkhead factors show highly restricted expression patterns. In search for forkhead genes expressed in specific neural systems, we identified multiple family members. We performed a detailed expression analysis for Foxj2, Foxk1 and the murine orthologue of the human ILF1 gene, which show a remarkable preference for complex cortical structures. In addition, a comprehensive examination of forkhead gene expression in dopamine neurons of the ventral tegmental area and substantia nigra pars compacta, revealed Ilf1 as a novel transcriptional regulator in midbrain dopamine neurons. These forkhead transcription factors may play a role in maintenance and survival of developing and adult neurons.

Blepharophimosis and bilateral Duane syndrome associated with a FOXL2 mutation

This case describes the novel coexistence of sporadic blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) and bilateral type I Duane syndrome in a female infant, with a FOXL2 mutation. Mutational analysis of FOXL2 demonstrated a 30-nucleotide duplication (c.672(-)701dup30) within the polyalanine tract of FOXL2. The association of BPES and Duane syndrome represents a novel phenotype which may suggest a greater pleiotropic effect of FOXL2 in development. During the period of the 4-8th week of embryonic development, the cranial nerves, their nuclei and the corresponding innervation to the extraocular muscles develop, the extraocular muscles undergo development and differentiation. This coincides with the period of time that FOXL2 is expressed strongly in the developing eyelids and the surrounding tissues. Forkhead genes are transcription factors and likely to be involved in signal transduction pathways. This case expands the spectrum of FOXL2 mutations associated with BPES.

Genomic inventory and expression of Sox and Fox genes in the cnidarian Nematostella vectensis

The Sox and Forkhead (Fox) gene families are comprised of transcription factors that play important roles in a variety of developmental processes, including germ layer specification, gastrulation, cell fate determination, and morphogenesis. Both the Sox and Fox gene families are divided into subgroups based on the amino acid sequence of their respective DNA-binding domains, the high-mobility group (HMG) box (Sox genes) or Forkhead domain (Fox genes). Utilizing the draft genome sequence of the cnidarian Nematostella vectensis, we examined the genomic complement of Sox and Fox genes in this organism to gain insight into the nature of these gene families in a basal metazoan. We identified 14 Sox genes and 15 Fox genes in Nematostella and conducted a Bayesian phylogenetic analysis comparing HMG box and Forkhead domain sequences from Nematostella with diverse taxa. We found that the majority of bilaterian Sox groups have clear Nematostella orthologs, while only a minority of Fox groups are represented, suggesting that the evolutionary pressures driving the diversification of these gene families may be distinct from one another. In addition, we examined the expression of a subset of these genes during development in Nematostella and found that some of these genes are expressed in patterns consistent with roles in germ layer specification and the regulation of cellular behaviors important for gastrulation. The diversity of expression patterns among members of these gene families in Nematostella reinforces the notion that despite their relatively simple morphology, cnidarians possess much of the molecular complexity observed in bilaterian taxa.

Lack of the Central Nervous System- and Neural Crest-Expressed Forkhead Gene Foxs1 Affects Motor Function and Body Weight

To gain insight into the expression pattern and functional importance of the forkhead transcription factor Foxs1, we constructed a Foxs1-beta-galactosidase reporter gene "knock-in" (Foxs1beta-gal/beta-gal) mouse, in which the wild-type (wt) Foxs1 allele has been inactivated and replaced by a beta-galactosidase reporter gene. Staining for beta-galactosidase activity reveals an expression pattern encompassing neural crest-derived cells, e.g., cranial and dorsal root ganglia as well as several other cell populations in the central nervous system (CNS), most prominently the internal granule layer of cerebellum. Other sites of expression include the lachrymal gland, outer nuclear layer of retina, enteric ganglion neurons, and a subset of thalamic and hypothalamic nuclei. In the CNS, blood vessel-associated smooth muscle cells and pericytes stain positive for Foxs1. Foxs1beta-gal/beta-gal mice perform significantly better (P < 0.01) on a rotating rod than do wt littermates. We have also noted a lower body weight gain (P < 0.05) in Foxs1beta-gal/lbeta-gal males on a high-fat diet, and we speculate that dorsomedial hypothalamic neurons, expressing Foxs1, could play a role in regulating body weight via regulation of sympathetic outflow. In support of this, we observed increased levels of uncoupling protein 1 mRNA in Foxs1beta-gal/beta-gal mice. This points toward a role for Foxs1 in the integration and processing of neuronal signals of importance for energy turnover and motor function.

Characterisation of two novel fork-head gene homologues of Schizosaccharomyces pombe: Their involvement in cell cycle and sexual differentiation

The fork-head type transcription factors are a class of regulators that function in a broad spectrum of cellular and developmental processes in many species ranging from yeasts to human. Previous data on yeast fork-head genes suggested roles for these regulators in the control of cell division, sexual differentiation and development. The genome of Schizosaccharomyces pombe has four genes that code for proteins containing fork-head domains (FKH), two of which have been characterised. Here we describe the remaining two genes, fhl1 and fkh2, that code for proteins containing fork-head-associated domains (FHA) besides their FKHs. Neither of them is essential for viability, although the deletion of either fhl1 (putative homologue of Saccharomyces cerevisiae FHL1) or fkh2 (similar to FKH1 and FKH2 of S. cerevisiae) reduced the growth rate and caused an extension of cell length due to delayed G2-to-M transition. Occasionally, multiseptate cells were also produced, indicating the involvement of fhl1 and fkh2 in efficient septum cleavage. The fkh2Δ cells were slightly more sensitive than the wild-type cells to certain environmental stresses, showed reduced fertility and occasional deficiencies in meiosis II, indicating that fkh2 might also act in stress response and sexual differentiation.

Winged-helix transcription factors and pancreatic development

The forkhead gene family, named after the founding gene member in Drosophila, is characterized by a unique DNA-binding domain. This so-called forkhead box encodes a winged-helix DNA-binding motif, the name of which describes the structure of the domain when bound to DNA. The three Fox (forkhead box) group A genes, Foxa1, Foxa2 and Foxa3, are expressed in embryonic endoderm, the germ layer that gives rise to the digestive system, and contribute to the specification of the pancreas and the regulation of glucose homoeostasis. Deletion of the Foxa2 gene in pancreatic beta-cells in mice results in a phenotype resembling PHHI (persistent hyperinsulinaemic hypoglycaemia of infancy). Molecular analyses have demonstrated that Foxa2 is an important regulator of the genes encoding Sur1, Kir6.2 and Schad (short chain L-3-hydroxyacyl-CoA dehydrogenase), mutation of which causes PHHI in humans. Foxa1 was shown to be an essential activator of glucagon gene expression in vivo. An additional winged-helix protein, Foxo1, contributes to pancreatic beta-cell function by regulating the Pdx1 gene, which is required for pancreatic development in cooperation with Foxa2.

Forkhead transcription factors in immunology

The forkhead (Fox) gene family comprises a diverse group of "winged-helix" transcription factors that play important roles in development, metabolism, cancer and aging. Recently, several forkhead genes have been demonstrated to play critical roles in lymphocyte development and effector function, including Foxp3 in the development of regulatory T cells, Foxj1 and Foxo3a in the regulation of CD4+ T cell tolerance, and Foxn1 in thymic development. Roles for other forkhead genes have also been proposed, including Foxp1 in macrophage differentiation, Foxq1 in natural killer cell effector function and Foxd2 in T cell activation. Thus, forkhead genes promise insight into the mechanisms of immunoregulation in several immune cell lineages, and their dysregulation likely contributes to the pathogenesis of several immunological disorders, suggesting that their study will lead to the development of novel therapeutic agents.

Axenfeld-Rieger malformation and distinctive facial features: Clues to a recognizable 6p25 microdeletion syndrome

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. We report the case of a child where recognition of the specific ocular and facial phenotype, led to identification of a 6p microdeletion arising from a de novo 6:18 translocation. Detailed analysis confirmed deletion of the FOXC1 forkhead gene cluster at 6p25. CNS anomalies included hydrocephalus and hypoplasia of the cerebellum, brainstem, and corpus callosum with mild to moderate developmental delay. Unlike previous reports, hearing was normal.

Subtelomeric deletions of chromosome 6p: Molecular and cytogenetic characterization of three new cases with phenotypic overlap with Ritscher?Schinzel (3C) syndrome

We have identified six children in three families with subtelomeric deletions of 6p25 and a recognizable phenotype consisting of ptosis, posterior embryotoxon, optic nerve abnormalities, mild glaucoma, Dandy-Walker malformation, hydrocephalus, atrial septal defect, patent ductus arteriosus, and mild mental retardation. There is considerable clinical overlap between these children and individuals with the Ritscher-Schinzel (or cranio-cerebello-cardiac (3C)) syndrome (OMIM #220210). Clinical features of 3C syndrome include craniofacial anomalies (macrocephaly, prominent forehead and occiput, foramina parietalia, hypertelorism, down-slanting palpebral fissures, ocular colobomas, depressed nasal bridge, narrow or cleft palate, and low-set ears), cerebellar malformations (variable manifestations of a Dandy-Walker malformation with moderate mental retardation), and cardiac defects (primarily septal defects). Since the original report, over 25 patients with 3C syndrome have been reported. Recessive inheritance has been postulated based on recurrence in siblings born to unaffected parents and parental consanguinity in two familial cases. Molecular and cytogenetic mapping of the 6p deletions in these three families with subtelomeric deletions of chromosome 6p have defined a 1.3 Mb minimally deleted critical region. To determine if 6p deletions are common in 3C syndrome, we analyzed seven unrelated individuals with 3C syndrome for deletions of this region. Three forkhead genes (FOXF1 and FOXQ1 from within the critical region, and FOXC1 proximal to this region) were evaluated as potential candidate disease genes for this disorder. No deletions or disease-causing mutations were identified.