Fibroblast Growth Factor Gene Family Research Articles

Genome-wide identification and evolutionary analysis of the FGF gene family in buffalo

Fibroblast growth factors (FGFs) are important polypeptide growth factors that play a critical role in many developmental processes, including differentiation, cell proliferation, and migration in mammals. This study employs in silico analyses to characterize the FGF gene family in buffalo, investigating their genome-wide identification, physicochemical properties, and evolutionary patterns. For this purpose, genomic and proteomic sequences of buffalo, cattle, goat, and sheep were retrieved from NCBI database. We identified a total of 22 FGF genes in buffalo. Physicochemical properties observed through ProtParam tool showed notable features of these proteins including in-vitro instability, thermostability, hydrophilicity, and basic nature. Phylogenetic analysis grouped 22 identified genes into nine sub-families based on evolutionary relationships. Additionally, analysis of gene structure, motif patterns, and conserved domains using TBtools revealed the remarkable conservation of this gene family across selected species throughout the course of evolution. Comparative amino acid analysis performed through ClustalW demonstrated significant conservation between buffalo and cattle FGF proteins. Mutational analysis showed three non-synonymous mutations at positions R103 > G, P7 > L, and E98 > Q in FGF4, FGF6, and FGF19, respectively in buffalo. Duplication events revealed only one segmental duplication (FGF10/FGF22) in buffalo and two in cattle (FGF10/FGF22 and FGF13/FGF13-like) with Ka/Ks values <1 indicating purifying selection pressure for these duplications. Comparison of protein structures of buffalo, goat, and sheep exhibited more similarities in respective structures. In conclusion, our study highlights the conservation of the FGF gene family in buffalo during evolution. Furthermore, the identified non-synonymous mutations may have implications for the selection of animals with better performance. Communicated by Ramaswamy H. Sarma

Genome-Wide Identification and Characterization of Bovine Fibroblast Growth Factor (FGF) Gene and Its Expression during Adipocyte Differentiation.

Fibroblast growth factor (FGF) family genes are a class of polypeptide factors with similar structures that play an important role in regulating cell proliferation and differentiation, nutritional metabolism, and neural activity. In previous studies, the FGF gene has been widely studied and analyzed in many species. However, the systematic study of the FGF gene in cattle has not been reported. In this study, 22 FGF genes distributed on 15 chromosomes were identified in the Bos taurus genome and clustered into seven subfamilies according to phylogenetic analysis and conservative domains. Collinear analysis showed that the bovine FGF gene family was homologous to Bos grunniens, Bos indicus, Hybrid-Bos taurus, Bubalus bubalis, and Hybrid-Bos indicus, and tandem replication and fragment replication were the key driving forces for the expansion of the gene family. Tissue expression profiling showed that bovine FGF genes were commonly expressed in different tissues, with FGF1, FGF5, FGF10, FGF12, FGF16, FGF17, and FGF20 being highly expressed in adipose tissue. In addition, real-time fluorescence quantitative PCR (qRT-PCR) detection showed that some FGF genes were differentially expressed before and after adipocyte differentiation, indicating their diverse role in the formation of lipid droplets. This study made a comprehensive exploration of the bovine FGF family and laid a foundation for further study on the potential function in the regulation of bovine adipogenic differentiation.

Systematic analysis of expression profiles and prognostic significance of the FGF gene family in pancreatic adenocarcinoma.

Pancreatic adenocarcinoma (PAAD) is a malignant tumor with one of the highest associated mortality rates worldwide, and a 5-year survival rate of <5%. Fibroblast growth factors (FGFs) serve important roles in numerous cellular functions, and dysregulation of FGFs contributes to various cancer types. However, there are few reports on the function of FGFs in PAAD. The Assistant for Clinical Bioinformatics database, Gene Expression Profiling Interactive Analysis, Kaplan-Meier plotter and Tumor Immune Estimation Resource were utilized to perform the protein-protein interaction network, functional enrichment, univariate Cox regression, least absolute shrinkage and selection operator (LASSO) Cox, differential expression, prognostic value and immune cell infiltration analyses of FGFs in patients with PAAD. Immunohistochemistry (IHC) was used to verify the predictive value of the model. A total of 22 FGF genes were identified. Based on the results of LASSO Cox regression analysis, a total of six genes, including FGF2, FGF8, FGF9, FGF13, FGF17 and FGF22, were selected for the establishment of the prognostic gene signature. High transcriptional levels of FGF17 and FGF22 were significantly associated with long overall survival. The expression of FGFs was associated with the infiltration of various immune cells. According to univariate and multivariate analyses, FGF2 and FGF8 may be useful independent prognostic biomarkers for the prognosis of patients with PAAD. IHC demonstrated that FGF2 and FGF8 were more highly expressed in PAAD tissues compared with that in normal tissues. The present findings offer a novel understanding for the selection of FGF prognostic biomarkers in PAAD.

365P The analysis of FGFR-gene family alterations in glioma

Fibroblast growth factor (FGFR) alterations are implicated across a range of solid tumors, promoting oncogenesis as a result of amplification, mutations, and structural variations. The FGFR gene family consists of four highly conserved transmembrane tyrosine kinase receptors (FGFR1–4). FGFR signaling influences angiogenesis and tumor cell migration, differentiation, proliferation, and survival. Recently, the cIMPACT-NOW released update 4 and update research, which considered FGFR alterations as a marker in brain tumor classification and prognosis.

FGF gene family characterization provides insights into its adaptive evolution in Carnivora.

Fibroblast growth factors (FGFs) encoded by the FGF gene family can regulate development and physiology in animals. However, their evolutionary characteristics in Carnivora are largely unknown. In this study, we identified 660 sequences of three types of FGF genes from 30 unannotated genomes of Carnivora animals (before 7th May 2020), and the FGF genes from 52 Carnivora species were analyzed through the method of comparative genomics. Phylogenetic and selective pressure analyses were carried out based on the FGF genes of these 52 Carnivora species. The phylogenetic analysis results demonstrated that the FGF gene family was divided into 10 subfamilies and that FGF5 formed one clade rather than belonging to the subfamilies of FGF4 and FGF6. The evolutionary analysis results showed that the FGF genes were prominently subjected to purifying selection and were highly conserved in the process of Carnivora evolution. We also carried out phylogenetic comparative analyses, which indicated that the habitat was one of the factors that shaped the evolution of Carnivora FGF genes. The FGF1 and FGF6 genes were positively selected in the Carnivora animals, and positive selection signals were detected for the FGF19 gene in semiaquatic Carnivora animals. In summary, we clarified the phylogenetic and evolutionary characteristics of Carnivora FGF genes and provided valuable data for future studies on evolutionary characterization of Carnivora animals.

Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans

Cetacean body structure and physiology exhibit dramatic adaptations to their aquatic environment. Fibroblast growth factors (FGFs) are a family of essential factors that regulate animal development and physiology; however, their role in cetacean evolution is not clearly understood. Here, we sequenced the fin whale genome and analysed FGFs from 8 cetaceans. FGF22, a hair follicle-enriched gene, exhibited pseudogenization, indicating that the function of this gene is no longer necessary in cetaceans that have lost most of their body hair. An evolutionary analysis revealed signatures of positive selection for FGF3 and FGF11, genes related to ear and tooth development and hypoxia, respectively. We found a D203G substitution in cetacean FGF9, which was predicted to affect FGF9 homodimerization, suggesting that this gene plays a role in the acquisition of rigid flippers for efficient manoeuvring. Cetaceans utilize low bone density as a buoyancy control mechanism, but the underlying genes are not known. We found that the expression of FGF23, a gene associated with reduced bone density, is greatly increased in the cetacean liver under hypoxic conditions, thus implicating FGF23 in low bone density in cetaceans. Altogether, our results provide novel insights into the roles of FGFs in cetacean adaptation to the aquatic environment.

Genome-wide identification, phylogeny, and expression of fibroblast growth genes in common carp

Fibroblast growth factors (FGFs) are a large family of polypeptide growth factors, which are found in organisms ranging from nematodes to humans. In vertebrates, a number of FGFs have been shown to play important roles in developing embryos and adult organisms. Among the vertebrate species, FGFs are highly conserved in both gene structure and amino-acid sequence. However, studies on teleost FGFs are mainly limited to model species, hence we investigated FGFs in the common carp genome.We identified 35 FGFs in the common carp genome. Phylogenetic analysis revealed that most of the FGFs are highly conserved, though recent gene duplication and gene losses do exist. By examining the copy number of FGFs in several vertebrate genomes, we found that eight FGFs in common carp have undergone gene duplications, including FGF6a, FGF6b, FGF7, FGF8b, FGF10a, FGF11b, FGF13a, and FGF18b. The expression patterns of all FGFs were examined in various tissues, including the blood, brain, gill, heart, intestine, muscle, skin, spleen and kidney, showing that most of the FGFs were ubiquitously expressed, indicating their critical role in common carp.To some extent, examination of gene families with detailed phylogenetic or orthology analysis verified the authenticity and accuracy of assembly and annotation of the recently published common carp whole genome sequences. Gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp FGF gene family provides an important genomic resource for future biochemical, physiological, and phylogenetic studies on FGFs in teleosts.

FGF Signaling Emerged Concomitantly with the Origin of Eumetazoans

Complex metazoan bodies require cell-to-cell communication for development, a process often mediated by signaling molecules binding to specific receptors. Relatively few signaling pathways have been recruited during evolution to build multicellular animals from unicellular zygotes. Of these few signaling pathways, one of particular importance is the receptor tyrosine kinase (RTK) pathway. In metazoans, fibroblast growth factors (FGFs) bind to receptors in the RTK family, but the origin of the FGF gene family has so far remained a mystery. Here we show that extant bona fide FGFs most likely originated from proteins bearing an FGF-like domain that arose in a choanoflagellate/metazoan ancestor. We found orthologous genes closely related to FGF in choanoflagellates as well as in many metazoans such as sponges, acoels, protostomes, or nonvertebrate deuterostomes. We also show that these genes have a common evolutionary history with Retinitis Pigmentosa 1 (RP1). Even if some metazoan signaling pathways emerged long before multicellularity, we show that FGFs, like their receptors, originated in a eumetazoan ancestor.

187 EXPRESSION AND REGULATION OF THE FIBROBLAST GROWTH FACTOR GENE FAMILY DURING MOUSE FOLLICULAR DEVELOPMENT

Recent studies have shown the critical roles of fibroblast growth factors (FGFs), including FGF8 produced by oocytes, in regulating follicular development. However, the expression and regulation of the FGF gene family, which consists of 22 ligands and 4 receptors, in the mouse ovary have not been well understood. The aim of the present study was to assess the expression and regulation of FGF ligands and receptors in the mouse ovary. Transcript levels of FGF ligands and receptors in immature (3-week-old) and adult (7- to 8-week-old) ovaries as well as other tissues of B6/DBA2F1 mice were analysed with RT-PCR. Furthermore, expression levels of FGF receptors in cumulus cells (CC) and mural granulosa cells (MG) before and after equine chorionic gonadotropin (eCG) treatment were determined with RT-quantitative PCR. Among 21 FGF ligands examined, 12 and 9 transcripts were detectable in immature and adult ovaries, respectively. More FGF ligands were detected in ovary, testis, heart, and brain compared to other tissues, including liver and spleen. Transcripts of all 4 FGF receptors (Fgfr1–4) were detectable in both immature and adult ovaries. Expression levels of Fgfr1 and Fgfr2 were significantly higher in MG compared with CC before and after the eCG treatment. Levels of Fgfr4 were comparable between MG and CC before the eCG treatment, but became significantly different with higher expression levels in MG after the eCG treatment. Fgfr3 transcripts were barely detectable in CC and MG. Overall levels of Fgfr1 in granulosa cells (CC and MG) were downregulated by eCG treatment, whereas those of Fgfr2 and Fgfr4 were upregulated. In summary, many FGF ligands are expressed, at least in mRNA levels, in mouse ovaries. Moreover, the expression levels of Fgfr transcripts in granulosa cells are dynamically regulated during follicular development.

Evolution of the FGF Gene Family.

Fibroblast Growth Factors (FGFs) are small proteins generally secreted, acting through binding to transmembrane tyrosine kinase receptors (FGFRs). Activation of FGFRs triggers several cytoplasmic cascades leading to the modification of cell behavior. FGFs play critical roles in a variety of developmental and physiological processes. Since their discovery in mammals, FGFs have been found in many metazoans and some arthropod viruses. Efforts have been previously made to decipher the evolutionary history of this family but conclusions were limited due to a poor taxonomic coverage. We took advantage of the availability of many new sequences from diverse metazoan lineages to further explore the possible evolutionary scenarios explaining the diversity of the FGF gene family. Our analyses, based on phylogenetics and synteny conservation approaches, allow us to propose a new classification of FGF genes into eight subfamilies, and to draw hypotheses for the evolutionary events leading to the present diversity of this gene family.

Extending the family table: Insights from beyond vertebrates into the regulation of embryonic development by FGFs

Since the discovery of fibroblast growth factors (FGFs) much focus has been placed on elucidating the roles for each vertebrate FGF ligand, receptor, and regulating molecules in the context of vertebrate development, human disorders and cancer. Studies in human, mouse, frog, chick, and zebrafish have made great contributions to our understanding of the role of FGFs in specific processes. However, in recent years, as more genomes are sequenced, information is becoming available from many non-vertebrate models and a more complete picture of the FGF superfamily as a whole is emerging. In some cases, less redundancy in these FGF signaling systems may allow for more mechanistic insights. Studies in sea anemones have highlighted how ancient FGF signaling is and helped provide insight into the evolution of the FGF gene family. Work in nematodes has shown that different splice forms can be used for functional specificity in invertebrate FGF signaling. Comparing FGFs between urochordates and vertebrates as well as between different insect species reveals important clues into the process of gene loss, duplication and subfunctionalization of FGFs throughout evolution. Finally, comparing all members of the FGF ligand superfamily reveals variability in many properties, which may point to a feature of FGFs as being highly adaptable with regards to protein structure and signaling mechanism. Further studies on FGF signaling outside of vertebrates is likely to continue to complement work in vertebrates by contributing additional insights to the FGF field and providing unexpected information that could be used for medical applications.

Fibroblast growth factor homologous factors: Evolution, structure, and function

Fibroblast growth factor homologous factors (FHFs) bear strong sequence and structural similarity to fibroblast growth factors (FGFs). However, the biochemical and functional properties of FHFs are largely, if not totally, unrelated to those of FGFs. Whereas FGFs function through binding to the extracellular domains of FGF receptors (FGFRs), FHFs bind to intracellular domains of voltage-gated sodium channels (VGSCs) and to a neuronal MAP kinase scaffold protein, islet-brain-2 (IB2). These findings demonstrate the remarkable functional adaptability during evolution of the FGF gene family. FHF gene mutations in mice result in a range of neurological abnormalities, and at least one of these anomalies, cerebellar ataxia, is linked to FHF mutations in humans. This article reviews the sequences and structure of FHFs, along with our still limited understanding of FHF function.

Characterization of the baculovirus Bombyx mori nucleopolyhedrovirus gene homologous to the mammalian FGF gene family.

We characterized a gene of the baculovirus Bombyx mori nucleopolyhedrovirus (BmNPV) homologous to the mammalian fibroblast growth factor (FGF) family. We termed it vfgf, and examined its transcription and the properties of the gene product (vFGF). RT-PCR analysis showed that vfgf is one of the baculovirus early genes, although there are no consensus sequences of the baculovirus early gene promoters. 5'-RACE analysis revealed that its transcription started at 10 nucleotides upstream of the translation start codon. vFGF has a hydrophobic amino terminus (approximately 16 amino acids), which is a typical signal sequence. As expected, vFGF was efficiently secreted from BmNPV-infected BmN cells. Because possible glycosylation sites are found at positions 44 (Asn) and 171 (Asn), we examined whether BmNPV vFGF is glycosylated or not. Cleavage of recombinant vFGF with PNGase F revealed that BmNPV vFGF was glycosylated. We also found that secretion of vFGF is completely blocked by the treatment of Tunicamycin, which blocks N-linked glycosylation. This is the first report to characterize a virus-encoded FGF.

Notch Activation Suppresses Fibroblast Growth Factor-dependent Cellular Transformation

Aberrant activations of the Notch and fibroblast growth factor receptor (FGFR) signaling pathways have been correlated with neoplastic growth in humans and other mammals. Here we report that the suppression of Notch signaling in NIH 3T3 cells by the expression of either the extracellular domain of the Notch ligand Jagged1 or dominant-negative forms of Notch1 and Notch2 results in the appearance of an exaggerated fibroblast growth factor (FGF)-dependent transformed phenotype characterized by anchorage-independent growth in soft agar. Anchorage-independent growth exhibited by Notch-repressed NIH 3T3 cells may result from prolonged FGFR stimulation caused by both an increase in the expression of prototypic and oncogenic FGF gene family members and the nonclassical export of FGF1 into the extracellular compartment. Interestingly, FGF exerts a negative effect on Notch by suppressing CSL (CBF-1/RBP-Jk/KBF2 in mammals, Su(H) in Drosophila and Xenopus, and Lag-2 in Caenorhabditis elegans)-dependent transcription, and the ectopic expression of constitutively active forms of Notch1 or Notch2 abrogates FGF1 release and the phenotypic effects of FGFR stimulation. These data suggest that communication between the Notch and FGFR pathways may represent an important reciprocal autoregulatory mechanism for the regulation of normal cell growth.

Minimal expression of the proto-oncogene int-2 encoded protein in a series of colorectal carcinomas.

Int-2 (fibroblast growth factor-3) is a gene that belongs to the fibroblast growth factor gene family. It has been implicated in the carcinogenesis of several types of cancer, including esophageal squamous cell carcinoma, breast, head, and neck and lung carcinomas; but no firm data on its biological activity regarding neoplasms arising from the glandular epithelia of the gastrointestinal tract exists. In the present immunohistochemical study, we investigated the presence of int-2 encoded protein in a panel of 80 cases of colon carcinoma of various stages, grades and sizes. A sheep antihuman int-2 antibody was applied to paraffin-embedded tissue sections from the tumor samples. The percentage of int-2 immunostaining in the positively stained specimens was evaluated by image analysis. Int-2 was positively detected in only four tumors (i.e. 5% of the cases examined). All immunopositive cases were moderately differentiated tumors; the adjacent mucosa did not express int-2 protein. The relevant patients were male. These findings suggest that the role of int-2 in colorectal carcinogenesis is probably a limited one.

Roles of fibroblast growth factor 2 during innervation of the avian inner ear.

The importance of individual members of the fibroblast growth factor gene family during innervation of the vertebrate inner ear is not clearly defined. Here we address the role of fibroblast growth factor 2 (FGF-2 or basic FGF) during development of the chicken inner ear. We found that FGF-2 stimulated survival of isolated cochlear and vestibular neurons during distinct phases of inner ear innervation. The potential neurotrophic role of FGF-2 was confirmed by its expression in the corresponding sensory epithelia and the detection of one of its high-affinity receptors in inner ear neurons. Finally, we have analysed the potential of the amplicon system based on defective herpes simplex virus type 1 (HSV-1) vectors to express FGF-2 in cochlear neurons. Overexpression of FGF-2 in cochlear neurons resulted in neuronal differentiation demonstrating the presence of biologically active growth factor. This study underlines the potential of FGF-2 to control innervation and development of sensory epithelia in the avian inner ear. Furthermore, amplicon vectors may provide a useful tool to analyse gene function in isolated neurons of the vertebrate inner ear.

Fusions to members of fibroblast growth factor gene family to study nuclear translocation and nonclassic exocytosis

Publisher Summary The fibroblast growth factor (FGF) gene family includes at least 19 genes encoding proteins that regulate proliferation, differentiation, motility, and survival of cells of neuroectodermal and mesodermal origin. This chapter describes the fusions to members of FGF gene family to study nuclear translocation and nonclassic exocytosis. The two most abundantly expressed representatives of the family are the prototypes FGF-1 and FGF-2, which are involved in the regulation of a wide variety of developmental, pathological, and regenerative processes in mammalian organisms, including humans. Among these processes are mesodermal induction, limb formation, angiogenesis, skeletal muscle growth and regeneration, the growth and metastasis of certain types of solid tumors, atherosclerosis, and restenosis. The chapter discusses the types of protein chimeras used for the study of fibroblast growth. The protein fusion approach to the study of FGF translocations is not limited to the use of reporter genes. Known nuclear localization signal (NLS) sequences from other proteins have been used for fusion with the FGFs to direct their nuclear translocation. A comparative study of FGF-1 and FGF-2 nuclear localization and release includes the shuffling of homologous regions/domains between these two proteins.

Fibroblast Growth Factor Prototype Release and Fibroblast Growth Factor Receptor Signaling

A Brief Introduction to the Fibroblast Growth Factor Gene Family The fibroblast growth factor (FGF) family of genes presently comprise 18 members, including the two prototypes, FGF-1 (acidic) and FGF-2 (basic). Although the FGF prototypes are well described as mediators of a variety of diverse biological responses, such as mesoderm induction, neurogenesis, and angiogenesis in vivo, space constraints prevent a discussion of these activities. Likewise, while although many of the members of the FGF gene family, most notably FGF-1, FGF-2, and FGF-3, are involved in intracellular trafficking between the cytosol and nucleus, it is also not possible to discuss these data and their potential significance. Since this review will focus upon recent advances in FGF receptor signaling and the identification of the pathway for FGF-1 export/release, it is recommended that the reader consult the following citations for this information.1-5

An upstream NF-Y-binding site is required for transcriptional activation from the hst promoter in F9 embryonal carcinoma cells.

Expression of hst (k-FGF, FGF-4), a member of the fibroblast growth factor gene family, is restricted to early stages of developing embryos and to embryonal carcinoma cells. In F9, which is a prototype of embryonal carcinoma cells expressing hst, the expression of hst gene is positively regulated by a downstream octamer motif that functions as an enhancer. We have investigated, by chloramphenicol acetyltransferase (CAT) reporter fusion gene analysis in F9, the cis-acting regulatory element within the hst promoter region that interacts with this enhancer. Electrophoretic mobility shift assay and methylation interference analysis showed that the hst promoter contains, in a segment termed Y, the sequence 5'-CTGATTGGCA-3', which closely resembles the consensus binding motif for the CCAAT-binding factor NF-Y. Deletions or mutations in this element substantially reduced expression of hst-CAT constructs. The nuclear factor binding to the Y segment of the hst promoter was indistinguishable from NF-Y, as inferred from interactions with specific anti-NF-Y monoclonal and polyclonal antibodies. We conclude that the expression of the hst gene in F9 is positively regulated by the coordinated interaction between an NF-Y-binding site and an octamer motif.

Expression of Fibroblast Growth Factor Gene Family and Its Receptor Gene Family in the Human Upper Gastrointestinal Tract

All of 13 human esophageal cancer cell lines contained mRNAs for both basic fibroblast growth factor (bFGF) and its receptor, FGFR1/N- sam protein, while they did not have mRNAs for keratinocyte growth factor (KGF) despite the presence of mRNAs for the KGF receptor gene, K- sam. The results indicate that in human esophageal cancer, bFGF plays roles in an autocrine manner, while KGF acts as a paracrine mediator. In contrast, only one of seven human gastric cancer cell lines contained bFGF mRNAs, while three out of the seven had mRNAs for FGFR1/N- sam protein. The KGF gene was not expressed in any of the gastric cancer cell lines, while K- sam mRNAs were detected in six out of the seven. The results demonstrate that in most human gastric cancers, bFGF does not act as an autocrine mediator, while KGF acts as a paracrine factor. The mRNAs for the other four members of the fibroblast growth factor (FGF) family, including acidic FGF, int-2 protein, hst-1 protein, FGF5 protein and FGF6/ hst-2 protein could not be detected in the esophageal and gastric cancer cell lines.