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Yin H, Staples SCR, Pickering JG. The fundamentals of fibroblast growth factor 9. Differentiation 2023:S0301-4681(23)00070-1. [PMID: 37783652 DOI: 10.1016/j.diff.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 10/04/2023]
Abstract
Fibroblast growth factor 9 (FGF9) was first identified during a screen for factors acting on cells of the central nervous system (CNS). Research over the subsequent two decades has revealed this protein to be a critically important and elegantly regulated growth factor. A hallmark control feature is reciprocal compartmentalization, particularly during development, with epithelium as a dominant source and mesenchyme a prime target. This mesenchyme selectivity is accomplished by the high affinity of FGF9 to the IIIc isoforms of FGFR1, 2, and 3. FGF9 is expressed widely in the embryo, including the developing heart and lungs, and more selectively in the adult, including the CNS and kidneys. Global Fgf9-null mice die shortly after birth due to respiratory failure from hypoplastic lungs. As well, their hearts are dilated and poorly vascularized, the skeleton is small, the intestine is shortened, and male-to-female sex reversal can be found. Conditional Fgf9-null mice have revealed CNS phenotypes, including ataxia and epilepsy. In humans, FGF9 variants have been found to underlie multiple synostoses syndrome 3, a syndrome characterized by multiple joint fusions. Aberrant FGF9 signaling has also been implicated in differences of sex development and cancer, whereas vascular stabilizing effects of FGF9 could benefit chronic diseases. This primer reviews the attributes of this vital growth factor.
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Affiliation(s)
- Hao Yin
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Sabrina C R Staples
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Canada; Department of Medical Biophysics, Western University, London, Canada
| | - J Geoffrey Pickering
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Canada; Department of Medical Biophysics, Western University, London, Canada; Department of Biochemistry, Western University, London, Canada; Department of Medicine, Western University, London, Canada; London Health Sciences Centre, London, Canada.
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Wei Q, Dong Y, Sun G, Wang X, Wu X, Gao X, Sha W, Yang G, Zhang H. FGF gene family characterization provides insights into its adaptive evolution in Carnivora. Ecol Evol 2021; 11:9837-9847. [PMID: 34306666 PMCID: PMC8293770 DOI: 10.1002/ece3.7814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 12/31/2022] Open
Abstract
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.
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Affiliation(s)
- Qinguo Wei
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Yuehuan Dong
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Guolei Sun
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Xibao Wang
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Xiaoyang Wu
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Xiaodong Gao
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Honghai Zhang
- College of Life SciencesQufu Normal UniversityQufuChina
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Nam K, Lee KW, Chung O, Yim HS, Cha SS, Lee SW, Jun J, Cho YS, Bhak J, Magalhães JPD, Lee JH, Jeong JY. Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans. Sci Rep 2017; 7:40233. [PMID: 28074842 PMCID: PMC5225608 DOI: 10.1038/srep40233] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/02/2016] [Indexed: 11/23/2022] Open
Abstract
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.
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Affiliation(s)
- Kiwoong Nam
- INRA, UMR 1333 Diversité, Génomes &Interactions Microorganismes-Insectes, 2 place E. Bataillon, 34095 Montpellier, France.,Université Montpellier, 2 place E. Bataillon, 34095 Montpellier, France
| | - Kyeong Won Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Haeanro 787, Ansan 15627, Republic of Korea
| | - Oksung Chung
- Personal Genomics Institute, Genome Research Foundation, Osong 28160, Republic of Korea
| | - Hyung-Soon Yim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Haeanro 787, Ansan 15627, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 306-350, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sae-Won Lee
- Biomedical Research Institute and IRICT, Seoul National University Hospital, Seoul 110-744, Republic of Korea
| | - JeHoon Jun
- Personal Genomics Institute, Genome Research Foundation, Osong 28160, Republic of Korea
| | - Yun Sung Cho
- Personal Genomics Institute, Genome Research Foundation, Osong 28160, Republic of Korea.,The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan 44919, Republic of Korea
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Osong 28160, Republic of Korea.,The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan 44919, Republic of Korea.,Geromics, Ulsan 44919, Republic of Korea
| | - João Pedro de Magalhães
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Haeanro 787, Ansan 15627, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 306-350, Republic of Korea
| | - Jae-Yeon Jeong
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Haeanro 787, Ansan 15627, Republic of Korea.,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 306-350, Republic of Korea
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Cong S, Ma XT, Li YX, Wang JF. Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study. J Chem Inf Model 2013; 53:1350-7. [DOI: 10.1021/ci400003p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shan Cong
- Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Center for Systems Biomedicine,
Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiao-Tu Ma
- Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Center for Systems Biomedicine,
Shanghai Jiao Tong University, Shanghai 200240, China
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Liu Y, Liu BY, Hao P, Li X, Li YX, Wang JF. π-π Stacking mediated drug-drug interactions in human CYP2E1. Proteins 2013; 81:945-54. [PMID: 23349037 DOI: 10.1002/prot.24260] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/11/2013] [Indexed: 11/07/2022]
Abstract
Because of having many low molecular mass substrates, CYP2E1 is of particular interests to the pharmaceutical industry. Many evidences showed that this enzyme can adopt multiple substrates to significantly reduce the oxidation rate of the substrates. The detailed mechanism for this observation is still unclear. In the current study, we employed GPU-accelerated molecular dynamics simulations to study the multiple-binding mode of human CYP2E1, with an aim of offering a mechanistic explanation for the unexplained multiple-substrate binding. Our results showed that Thr303 and Phe478 were key factors for the substrate recognition and multiple-substrate binding. The former can form a significant hydrogen bond to recognize and position the substrate in the productive binding orientation in the active site. The latter acted as a mediator for the substrate communications via π-π stacking interactions. In the multiple-binding mode, the aforementioned π-π stacking interactions formed by the aromatic rings of both substrates and Phe478 drove the first substrate far away from the catalytic center, orienting in an additional binding position and going against the substrate metabolism. All these findings could give atomic insights into the detailed mechanism for the multiple-substrate binding in human CYP2E1, providing useful information for the drug metabolism mechanism and personalized use of clinical drugs.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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Scaffold-based pan-agonist design for the PPARα, PPARβ and PPARγ receptors. PLoS One 2012; 7:e48453. [PMID: 23119024 PMCID: PMC3485212 DOI: 10.1371/journal.pone.0048453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/26/2012] [Indexed: 12/25/2022] Open
Abstract
As important members of nuclear receptor superfamily, Peroxisome proliferator-activated receptors (PPAR) play essential roles in regulating cellular differentiation, development, metabolism, and tumorigenesis of higher organisms. The PPAR receptors have 3 identified subtypes: PPARα, PPARβ and PPARγ, all of which have been treated as attractive targets for developing drugs to treat type 2 diabetes. Due to the undesirable side-effects, many PPAR agonists including PPARα/γ and PPARβ/γ dual agonists are stopped by US FDA in the clinical trials. An alternative strategy is to design novel pan-agonist that can simultaneously activate PPARα, PPARβ and PPARγ. Under such an idea, in the current study we adopted the core hopping algorithm and glide docking procedure to generate 7 novel compounds based on a typical PPAR pan-agonist LY465608. It was observed by the docking procedures and molecular dynamics simulations that the compounds generated by the core hopping and glide docking not only possessed the similar functions as the original LY465608 compound to activate PPARα, PPARβ and PPARγ receptors, but also had more favorable conformation for binding to the PPAR receptors. The additional absorption, distribution, metabolism and excretion (ADME) predictions showed that the 7 compounds (especially Cpd#1) hold high potential to be novel lead compounds for the PPAR pan-agonist. Our findings can provide a new strategy or useful insights for designing the effective pan-agonists against the type 2 diabetes.
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