1
|
Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Lopez-Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson WA, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae. BMC Biol 2024; 22:141. [PMID: 38926709 PMCID: PMC11209984 DOI: 10.1186/s12915-024-01935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. RESULTS We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. CONCLUSIONS Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Collapse
Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany.
| | - Peter T Euclide
- Department of Forestry and Natural Resources | Illinois-Indiana Sea Grant, Purdue University, West Lafayette, USA
| | - Christophe Klopp
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Cédric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Margot Zahm
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | | | | | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Carole Confolent
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ming Wen
- INRAE, LPGP, 35000, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | | | | | | | | | - Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Tuwima 10, 10-748, Olsztyn, Poland
| | - Wesley A Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, 17109 Point Lena Loop Road, Auke Bay LaboratoriesJuneau, AK, 99801, USA
| | | | | | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
| | | |
Collapse
|
2
|
Gao J, Yang Y, Xiang X, Zheng H, Yi X, Wang F, Liang Z, Chen D, Shi W, Wang L, Wu D, Feng S, Huang Q, Li X, Shu W, Chen R, Zhong N, Wang Z. Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease. Respir Res 2024; 25:165. [PMID: 38622589 DOI: 10.1186/s12931-024-02805-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10-5), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10-8). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.
Collapse
Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Yuqiong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xiaopeng Xiang
- The Hong Kong Polytechnic University, Hong Kong, Hung Hom Kowloon, China
| | - Huimin Zheng
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Fengyan Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhenyu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Dandan Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Weijuan Shi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Lingwei Wang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Di Wu
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengchuan Feng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Qiaoyun Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xueping Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China.
| | - Rongchang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
| | - Zhang Wang
- Institute of Ecological Sciences, Biomedical Research Center, School of Life Sciences, State Key Laboratory of Respiratory Disease, South China Normal University, Guangzhou, Guangdong Province, China.
| |
Collapse
|
3
|
Bear RM, Caspary T. Uncovering cilia function in glial development. Ann Hum Genet 2024; 88:27-44. [PMID: 37427745 PMCID: PMC10776815 DOI: 10.1111/ahg.12519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
Primary cilia play critical roles in regulating signaling pathways that underlie several developmental processes. In the nervous system, cilia are known to regulate signals that guide neuron development. Cilia dysregulation is implicated in neurological diseases, and the underlying mechanisms remain poorly understood. Cilia research has predominantly focused on neurons and has overlooked the diverse population of glial cells in the brain. Glial cells play essential roles during neurodevelopment, and their dysfunction contributes to neurological disease; however, the relationship between cilia function and glial development is understudied. Here we review the state of the field and highlight the glial cell types where cilia are found and the ciliary functions that are linked to glial development. This work uncovers the importance of cilia in glial development and raises outstanding questions for the field. We are poised to make progress in understanding the function of glial cilia in human development and their contribution to neurological diseases.
Collapse
Affiliation(s)
- Rachel M. Bear
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta GA 30322
- Graduate Program in Neuroscience
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta GA 30322
| |
Collapse
|
4
|
Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson W, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566804. [PMID: 38014084 PMCID: PMC10680665 DOI: 10.1101/2023.11.13.566804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Collapse
Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Peter T Euclide
- Department of Forestry and Natural Resources | Illinois-Indiana Sea Grant, Purdue University, West Lafayette, Indiana, USA
| | - Christophe Klopp
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Cedric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Margot Zahm
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Carole Confolent
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ming Wen
- INRAE, LPGP, 35000, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | | | - Thomas Lecocq
- University of Lorraine, INRAE, UR AFPA, Nancy, France
| | | | | | - Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Tuwima 10, 10-748, Olsztyn, Poland
| | - Wes Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories, 17109 Point Lena Loop Road, Juneau, AK, 99801, USA
| | | | | | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | | |
Collapse
|
5
|
Bocquet B, Borday C, Erkilic N, Mamaeva D, Donval A, Masson C, Parain K, Kaminska K, Quinodoz M, Perea-Romero I, Garcia-Garcia G, Jimenez-Medina C, Boukhaddaoui H, Coget A, Leboucq N, Calzetti G, Gandolfi S, Percesepe A, Barili V, Uliana V, Delsante M, Bozzetti F, Scholl HP, Corton M, Ayuso C, Millan JM, Rivolta C, Meunier I, Perron M, Kalatzis V. TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa. JCI Insight 2023; 8:e169426. [PMID: 37768732 PMCID: PMC10721274 DOI: 10.1172/jci.insight.169426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell-derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.
Collapse
Affiliation(s)
- Béatrice Bocquet
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Caroline Borday
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Nejla Erkilic
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Daria Mamaeva
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Alicia Donval
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Christel Masson
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karine Parain
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Garcia-Garcia
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carla Jimenez-Medina
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Hassan Boukhaddaoui
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Arthur Coget
- Department of Neuroradiology and
- Institute for Human Functional Imaging (I2FH), University of Montpellier, CHU, Montpellier, France
| | | | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Medicine and Surgery
| | | | | | | | | | | | - Francesca Bozzetti
- Neuroradiology Unit, Diagnostic Department, University Hospital of Parma, Parma, Italy
| | - Hendrik P.N. Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marta Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M. Millan
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Muriel Perron
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| |
Collapse
|
6
|
Harris SC, Chong K, Chitayat D, Gilmore KL, Jorge AAL, Freire BL, Lerario A, Shannon P, Cope H, Gallentine WB, Guyader GL, Bilan F, Létard P, Davis EE, Vora NL. Diagnosis of TBC1D32-associated conditions: Expanding the phenotypic spectrum of a complex ciliopathy. Am J Med Genet A 2023; 191:1282-1292. [PMID: 36826837 PMCID: PMC10204718 DOI: 10.1002/ajmg.a.63150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/25/2023] [Accepted: 02/03/2023] [Indexed: 02/25/2023]
Abstract
Exome sequencing is a powerful tool in prenatal and postnatal genetics and can help identify novel candidate genes critical to human development. We describe seven unpublished probands with rare likely pathogenic variants or variants of uncertain significance that segregate with recessive disease in TBC1D32, including four fetal probands in three unrelated pedigrees and three pediatric probands in unrelated pedigrees. We also report clinical comparisons with seven previously published patients. Index probands were identified through an ongoing prenatal exome sequencing study and through an online data sharing platform (Gene Matcher™). A literature review was also completed. TBC1D32 is involved in the development and function of cilia and is expressed in the developing hypothalamus and pituitary gland. We provide additional data to expand the phenotype correlated with TBC1D32 variants, including a severe prenatal phenotype associated with life-limiting congenital anomalies.
Collapse
Affiliation(s)
- Sarah C. Harris
- Department of Obstetrics and Gynecology, Prisma Health, University of South Carolina Greenville, Greenville, South Carolina, USA
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Kelly L. Gilmore
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Alexander A. L. Jorge
- Unidade de Endocrinologia Genética (LIM25) e Laboratório de Endocrinologia Celular e Molecular, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Bruna L. Freire
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, São Paulo, Brazil
| | - Antonio Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Heidi Cope
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - William B. Gallentine
- Department of Neurology and Pediatrics, Stanford University, Lucile Packard Children’s Hospital, Palo Alto, California, USA
| | | | - Frederic Bilan
- Service de génétique clinique, CHU de Poitiers, Poitiers, France
- Laboratoire de Neurosciences Expérimentales et Cliniques, INSERM U1084, Université de Poitiers, Poitiers, France
| | - Pascaline Létard
- Service de génétique clinique, CHU de Poitiers, Poitiers, France
| | - Erica E. Davis
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Neeta L. Vora
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| |
Collapse
|
7
|
Lim S, Du Y, Lee Y, Panda SK, Tong D, Khalid Jawed M. Fabrication, control, and modeling of robots inspired by flagella and cilia. BIOINSPIRATION & BIOMIMETICS 2022; 18:011003. [PMID: 36533860 DOI: 10.1088/1748-3190/aca63d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Flagella and cilia are slender structures that serve important functionalities in the microscopic world through their locomotion induced by fluid and structure interaction. With recent developments in microscopy, fabrication, biology, and modeling capability, robots inspired by the locomotion of these organelles in low Reynolds number flow have been manufactured and tested on the micro-and macro-scale, ranging from medicalin vivomicrobots, microfluidics to macro prototypes. We present a collection of modeling theories, control principles, and fabrication methods for flagellated and ciliary robots.
Collapse
Affiliation(s)
- Sangmin Lim
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Yayun Du
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Yongkyu Lee
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Shivam Kumar Panda
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Dezhong Tong
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - M Khalid Jawed
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| |
Collapse
|
8
|
Sun S, Miller M, Wang Y, Tyc KM, Cao X, Scott RT, Tao X, Bromberg Y, Schindler K, Xing J. Predicting embryonic aneuploidy rate in IVF patients using whole-exome sequencing. Hum Genet 2022; 141:1615-1627. [PMID: 35347416 PMCID: PMC10095970 DOI: 10.1007/s00439-022-02450-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/16/2022] [Indexed: 01/13/2023]
Abstract
Infertility is a major reproductive health issue that affects about 12% of women of reproductive age in the United States. Aneuploidy in eggs accounts for a significant proportion of early miscarriage and in vitro fertilization failure. Recent studies have shown that genetic variants in several genes affect chromosome segregation fidelity and predispose women to a higher incidence of egg aneuploidy. However, the exact genetic causes of aneuploid egg production remain unclear, making it difficult to diagnose infertility based on individual genetic variants in mother's genome. In this study, we evaluated machine learning-based classifiers for predicting the embryonic aneuploidy risk in female IVF patients using whole-exome sequencing data. Using two exome datasets, we obtained an area under the receiver operating curve of 0.77 and 0.68, respectively. High precision could be traded off for high specificity in classifying patients by selecting different prediction score cutoffs. For example, a strict prediction score cutoff of 0.7 identified 29% of patients as high-risk with 94% precision. In addition, we identified MCM5, FGGY, and DDX60L as potential aneuploidy risk genes that contribute the most to the predictive power of the model. These candidate genes and their molecular interaction partners are enriched for meiotic-related gene ontology categories and pathways, such as microtubule organizing center and DNA recombination. In summary, we demonstrate that sequencing data can be mined to predict patients' aneuploidy risk thus improving clinical diagnosis. The candidate genes and pathways we identified are promising targets for future aneuploidy studies.
Collapse
Affiliation(s)
- Siqi Sun
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Maximilian Miller
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Katarzyna M Tyc
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Current address: Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Xiaolong Cao
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Richard T Scott
- Reproductive Medicine Associates of New Jersey, Basking Ridge, NJ, USA
| | - Xin Tao
- Foundation for Embryonic Competence, Basking Ridge, NJ, USA
| | - Yana Bromberg
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Karen Schindler
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| |
Collapse
|
9
|
Primary Cilia Influence Progenitor Function during Cortical Development. Cells 2022; 11:cells11182895. [PMID: 36139475 PMCID: PMC9496791 DOI: 10.3390/cells11182895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Corticogenesis is an intricate process controlled temporally and spatially by many intrinsic and extrinsic factors. Alterations during this important process can lead to severe cortical malformations. Apical neuronal progenitors are essential cells able to self-amplify and also generate basal progenitors and/or neurons. Apical radial glia (aRG) are neuronal progenitors with a unique morphology. They have a long basal process acting as a support for neuronal migration to the cortical plate and a short apical process directed towards the ventricle from which protrudes a primary cilium. This antenna-like structure allows aRG to sense cues from the embryonic cerebrospinal fluid (eCSF) helping to maintain cell shape and to influence several key functions of aRG such as proliferation and differentiation. Centrosomes, major microtubule organising centres, are crucial for cilia formation. In this review, we focus on how primary cilia influence aRG function during cortical development and pathologies which may arise due to defects in this structure. Reporting and cataloguing a number of ciliary mutant models, we discuss the importance of primary cilia for aRG function and cortical development.
Collapse
|
10
|
Mechanisms of Regulation in Intraflagellar Transport. Cells 2022; 11:cells11172737. [PMID: 36078145 PMCID: PMC9454703 DOI: 10.3390/cells11172737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Cilia are eukaryotic organelles essential for movement, signaling or sensing. Primary cilia act as antennae to sense a cell’s environment and are involved in a wide range of signaling pathways essential for development. Motile cilia drive cell locomotion or liquid flow around the cell. Proper functioning of both types of cilia requires a highly orchestrated bi-directional transport system, intraflagellar transport (IFT), which is driven by motor proteins, kinesin-2 and IFT dynein. In this review, we explore how IFT is regulated in cilia, focusing from three different perspectives on the issue. First, we reflect on how the motor track, the microtubule-based axoneme, affects IFT. Second, we focus on the motor proteins, considering the role motor action, cooperation and motor-train interaction plays in the regulation of IFT. Third, we discuss the role of kinases in the regulation of the motor proteins. Our goal is to provide mechanistic insights in IFT regulation in cilia and to suggest directions of future research.
Collapse
|
11
|
Satoda Y, Noguchi T, Fujii T, Taniguchi A, Katoh Y, Nakayama K. BROMI/TBC1D32 together with CCRK/CDK20 and FAM149B1/JBTS36 contributes to intraflagellar transport turnaround involving ICK/CILK1. Mol Biol Cell 2022; 33:ar79. [PMID: 35609210 PMCID: PMC9582636 DOI: 10.1091/mbc.e22-03-0089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Primary cilia are antenna-like organelles that contain specific proteins, and are crucial for tissue morphogenesis. Anterograde and retrograde trafficking of ciliary proteins are mediated by the intraflagellar transport (IFT) machinery. BROMI/TBC1D32 interacts with CCRK/CDK20, which phosphorylates and activates the intestinal cell kinase (ICK)/CILK1 kinase, to regulate the change in direction of the IFT machinery at the ciliary tip. Mutations in BROMI, CCRK, and ICK in humans cause ciliopathies, and mice defective in these genes are also known to demonstrate ciliopathy phenotypes. We show here that BROMI interacts not only with CCRK but also with CFAP20, an evolutionarily conserved ciliary protein, and with FAM149B1/ Joubert syndrome (JBTS)36, a protein in which mutations cause JBTS. In addition, we show that FAM149B1 interacts directly with CCRK as well as with BROMI. Ciliary defects observed in CCRK-knockout (KO), BROMI-KO, and FAM149B1-KO cells, including abnormally long cilia and accumulation of the IFT machinery and ICK at the ciliary tip, resembled one another, and BROMI mutants that are defective in binding to CCRK and CFAP20 were unable to rescue the ciliary defects of BROMI-KO cells. These data indicate that CCRK, BROMI, FAM149B1, and probably CFAP20 altogether regulate the IFT turnaround process under the control of ICK.
Collapse
Affiliation(s)
- Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Taiju Fujii
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Aoi Taniguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
12
|
Yin F, Wei Z, Chen F, Xin C, Chen Q. Molecular targets of primary cilia defects in cancer (Review). Int J Oncol 2022; 61:98. [DOI: 10.3892/ijo.2022.5388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/20/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Fengying Yin
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Zihao Wei
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Fangman Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Chuan Xin
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Qianming Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| |
Collapse
|
13
|
Fairfield CJ, Drake TM, Pius R, Bretherick AD, Campbell A, Clark DW, Fallowfield JA, Hayward C, Henderson NC, Iakovliev A, Joshi PK, Mills NL, Porteous DJ, Ramachandran P, Semple RK, Shaw CA, Sudlow CLW, Timmers PRHJ, Wilson JF, Wigmore SJ, Spiliopoulou A, Harrison EM. Genome-wide analysis identifies gallstone-susceptibility loci including genes regulating gastrointestinal motility. Hepatology 2022; 75:1081-1094. [PMID: 34651315 DOI: 10.1002/hep.32199] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS Genome-wide association studies (GWAS) have identified several risk loci for gallstone disease. As with most polygenic traits, it is likely that many genetic determinants are undiscovered. The aim of this study was to identify genetic variants that represent new targets for gallstone research and treatment. APPROACH AND RESULTS We performed a GWAS of 28,627 gallstone cases and 348,373 controls in the UK Biobank, replicated findings in a Scottish cohort (1089 cases, 5228 controls), and conducted a GWA meta-analysis (43,639 cases, 506,798 controls) with the FinnGen cohort. We assessed pathway enrichment using gene-based then gene-set analysis and tissue expression of identified genes in Genotype-Tissue Expression project data. We constructed a polygenic risk score (PRS) and evaluated phenotypic traits associated with the score. Seventy-five risk loci were identified (p < 5 × 10-8 ), of which 46 were new. Pathway enrichment revealed associations with lipid homeostasis, glucuronidation, phospholipid metabolism, and gastrointestinal motility. Anoctamin 1 (ANO1) and transmembrane Protein 147 (TMEM147), both in novel, replicated loci, are expressed in the gallbladder and gastrointestinal tract. Both regulate gastrointestinal motility. The gallstone risk allele rs7599-A leads to suppression of hepatic TMEM147 expression, suggesting that the protein protects against gallstone formation. The highest decile of the PRS demonstrated a 6-fold increased odds of gallstones compared with the lowest decile. The PRS was strongly associated with increased body mass index, serum liver enzymes, and C-reactive protein concentrations, and decreased lipoprotein cholesterol concentrations. CONCLUSIONS This GWAS demonstrates the polygenic nature of gallstone risk and identifies 46 novel susceptibility loci. We implicate genes influencing gastrointestinal motility in the pathogenesis of gallstones.
Collapse
Affiliation(s)
- Cameron J Fairfield
- Center for Medical InformaticsUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Thomas M Drake
- Center for Medical InformaticsUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Riinu Pius
- Center for Medical InformaticsUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Andrew D Bretherick
- MRC Human Genetics UnitInstitute of Genetics and CancerUniversity of EdinburghEdinburghScotland
| | - Archie Campbell
- Center for Medical InformaticsUsher InstituteUniversity of EdinburghEdinburghScotland
- Center for Genomic and Experimental MedicineInstitute of Genetics and CancerUniversity of EdinburghEdinburghScotland
- Health Data Research UKUniversity of EdinburghEdinburghScotland
| | - David W Clark
- Center for Global Health ResearchUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Jonathan A Fallowfield
- Centre for Inflammation ResearchQueen's Medical Research InstituteUniversity of EdinburghEdinburghScotland
| | - Caroline Hayward
- MRC Human Genetics UnitInstitute of Genetics and CancerUniversity of EdinburghEdinburghScotland
| | - Neil C Henderson
- Centre for Inflammation ResearchQueen's Medical Research InstituteUniversity of EdinburghEdinburghScotland
| | - Andrii Iakovliev
- Center for Population Health SciencesUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Peter K Joshi
- Center for Global Health ResearchUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Nicholas L Mills
- Center for Cardiovascular ScienceQueen's Medical Research InstituteUniversity of EdinburghEdinburghScotland
| | - David J Porteous
- Center for Genomic and Experimental MedicineInstitute of Genetics and CancerUniversity of EdinburghEdinburghScotland
| | - Prakash Ramachandran
- Centre for Inflammation ResearchQueen's Medical Research InstituteUniversity of EdinburghEdinburghScotland
| | - Robert K Semple
- Center for Cardiovascular ScienceQueen's Medical Research InstituteUniversity of EdinburghEdinburghScotland
| | - Catherine A Shaw
- Center for Medical InformaticsUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Cathie L W Sudlow
- Center for Medical InformaticsUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Paul R H J Timmers
- MRC Human Genetics UnitInstitute of Genetics and CancerUniversity of EdinburghEdinburghScotland
- Center for Global Health ResearchUsher InstituteUniversity of EdinburghEdinburghScotland
| | - James F Wilson
- MRC Human Genetics UnitInstitute of Genetics and CancerUniversity of EdinburghEdinburghScotland
- Center for Global Health ResearchUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Stephen J Wigmore
- Department of Clinical SurgeryDivision of Health SciencesUniversity of EdinburghEdinburghScotland
| | - Athina Spiliopoulou
- Center for Population Health SciencesUsher InstituteUniversity of EdinburghEdinburghScotland
| | - Ewen M Harrison
- Center for Medical InformaticsUsher InstituteUniversity of EdinburghEdinburghScotland
| |
Collapse
|
14
|
Cheng JY, Stern AJ, Racimo F, Nielsen R. Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components. Mol Biol Evol 2022; 39:msab294. [PMID: 34626111 PMCID: PMC8763095 DOI: 10.1093/molbev/msab294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
One of the most powerful and commonly used approaches for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this article, we present a new maximum likelihood method for finding regions under positive selection. It is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. Using simulated data, we compare our method to related approaches, and show that it is orders of magnitude faster than the state-of-the-art, while retaining similar or higher power for most simulation scenarios. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin, and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, such as immunity, fat distribution, food intake, vision, and hair development.
Collapse
Affiliation(s)
- Jade Yu Cheng
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Aaron J Stern
- Graduate Group in Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
15
|
Maurya AK, Sengupta P. xbx-4, a homolog of the Joubert syndrome gene FAM149B1, acts via the CCRK and RCK kinase cascade to regulate cilia morphology. Curr Biol 2021; 31:5642-5649.e5. [PMID: 34731674 DOI: 10.1016/j.cub.2021.10.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/23/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022]
Abstract
Primary cilia are microtubule (MT)-based organelles that mediate sensory functions in multiple cell types. Disruption of cilia structure or function leads to a diverse collection of diseases termed ciliopathies.1-3 The highly conserved CCRK and RCK kinases (ICK/MOK/MAK) negatively regulate cilia length and structure in Chlamydomonas, C. elegans, and mammalian cells.4-10 How the activity of this kinase cascade is tuned to precisely regulate cilia architecture is unclear. Mutations in the Domain of Unknown Function 3719 (DUF3719)-containing protein FAM149B1 have recently been shown to elongate cilia via unknown mechanisms and result in the ciliopathy Joubert syndrome.11 Here we identify XBX-4, a DUF3719-containing protein related to human FAM149B1, as a regulator of the DYF-18 CCRK and DYF-5 MAK kinase pathway in C. elegans. As in dyf-18 and dyf-5 mutants,10 sensory neuron cilia are elongated in xbx-4 mutants and exhibit stabilized axonemal MTs. XBX-4 promotes DYF-18 CCRK function to regulate localization and function of DYF-5 MAK. We find that Joubert syndrome-associated mutations in the XBX-4 DUF3719 domain also elongate cilia in C. elegans. Our results identify a new metazoan-specific regulator of this highly conserved kinase pathway and suggest that FAM149B1 may similarly act via the CCRK/RCK kinase pathway to regulate ciliary homeostasis in humans.
Collapse
Affiliation(s)
- Ashish K Maurya
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| | - Piali Sengupta
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| |
Collapse
|
16
|
Noguchi T, Nakamura K, Satoda Y, Katoh Y, Nakayama K. CCRK/CDK20 regulates ciliary retrograde protein trafficking via interacting with BROMI/TBC1D32. PLoS One 2021; 16:e0258497. [PMID: 34624068 PMCID: PMC8500422 DOI: 10.1371/journal.pone.0258497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/28/2021] [Indexed: 01/02/2023] Open
Abstract
CCRK/CDK20 was reported to interact with BROMI/TBC1D32 and regulate ciliary Hedgehog signaling. In various organisms, mutations in the orthologs of CCRK and those of the kinase ICK/CILK1, which is phosphorylated by CCRK, are known to result in cilia elongation. Furthermore, we recently showed that ICK regulates retrograde ciliary protein trafficking and/or the turnaround event at the ciliary tips, and that its mutations result in the elimination of intraflagellar transport (IFT) proteins that have overaccumulated at the bulged ciliary tips as extracellular vesicles, in addition to cilia elongation. However, how these proteins cooperate to regulate ciliary protein trafficking has remained unclear. We here show that the phenotypes of CCRK-knockout (KO) cells closely resemble those of ICK-KO cells; namely, the overaccumulation of IFT proteins at the bulged ciliary tips, which appear to be eliminated as extracellular vesicles, and the enrichment of GPR161 and Smoothened on the ciliary membrane. The abnormal phenotypes of CCRK-KO cells were rescued by the exogenous expression of wild-type CCRK but not its kinase-dead mutant or a mutant defective in BROMI binding. These results together indicate that CCRK regulates the turnaround process at the ciliary tips in concert with BROMI and probably via activating ICK.
Collapse
Affiliation(s)
- Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kentaro Nakamura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| |
Collapse
|
17
|
Abraham SP, Nita A, Krejci P, Bosakova M. Cilia kinases in skeletal development and homeostasis. Dev Dyn 2021; 251:577-608. [PMID: 34582081 DOI: 10.1002/dvdy.426] [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: 07/07/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 11/08/2022] Open
Abstract
Primary cilia are dynamic compartments that regulate multiple aspects of cellular signaling. The production, maintenance, and function of cilia involve more than 1000 genes in mammals, and their mutations disrupt the ciliary signaling which manifests in a plethora of pathological conditions-the ciliopathies. Skeletal ciliopathies are genetic disorders affecting the development and homeostasis of the skeleton, and encompass a broad spectrum of pathologies ranging from isolated polydactyly to lethal syndromic dysplasias. The recent advances in forward genetics allowed for the identification of novel regulators of skeletogenesis, and revealed a growing list of ciliary proteins that are critical for signaling pathways implicated in bone physiology. Among these, a group of protein kinases involved in cilia assembly, maintenance, signaling, and disassembly has emerged. In this review, we summarize the functions of cilia kinases in skeletal development and disease, and discuss the available and upcoming treatment options.
Collapse
Affiliation(s)
- Sara P Abraham
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Alexandru Nita
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Institute of Animal Physiology and Genetics of the CAS, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Michaela Bosakova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Institute of Animal Physiology and Genetics of the CAS, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| |
Collapse
|
18
|
Li M, Zhang J, Zhou H, Xiang R. Primary Cilia-Related Pathways Moderate the Development and Therapy Resistance of Glioblastoma. Front Oncol 2021; 11:718995. [PMID: 34513696 PMCID: PMC8426355 DOI: 10.3389/fonc.2021.718995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
As microtubule-based structures, primary cilia are typically present on the cells during the G0 or G1-S/G2 phase of the cell cycle and are closely related to the development of the central nervous system. The presence or absence of this special organelle may regulate the central nervous system tumorigenesis (e.g., glioblastoma) and several degenerative diseases. Additionally, the development of primary cilia can be regulated by several pathways. Conversely, primary cilia are able to regulate a few signaling transduction pathways. Therefore, development of the central nervous system tumors in conjunction with abnormal cilia can be regulated by up- or downregulation of the pathways related to cilia and ciliogenesis. Here, we review some pathways related to ciliogenesis and tumorigenesis, aiming to provide a potential target for developing new therapies at genetic and molecular levels.
Collapse
Affiliation(s)
- Minghao Li
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiaxun Zhang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Haonan Zhou
- School of Life Sciences, Central South University, Changsha, China
| | - Rong Xiang
- School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| |
Collapse
|
19
|
Lee H, Ko HW. Cell cycle-related kinase is a crucial regulator for ciliogenesis and Hedgehog signaling in embryonic mouse lung development. BMB Rep 2021. [PMID: 32317081 PMCID: PMC7396919 DOI: 10.5483/bmbrep.2020.53.7.295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cell cycle-related kinase (CCRK) has a conserved role in ciliogenesis, and Ccrk defects in mice lead to developmental defects, including exencephaly, preaxial polydactyly, skeletal abnormalities, retinal degeneration, and polycystic kidney. Here, we found that Ccrk is highly expressed in mouse trachea and bronchioles. Ccrk mutants exhibited pulmonary hypoplasia and abnormal branching morphogenesis in respiratory organ development. Furthermore, we demonstrated that Ccrk mutant lungs exhibit not only impaired branching morphogenesis but also a significant sacculation deficiency in alveoli associated with reduced epithelial progenitor cell proliferation. In pseudoglandular stages, Ccrk mutant lungs showed a downregulation of Hedgehog (Hh) signaling and defects in cilia morphology and frequency during progenitor-cell proliferation. Interestingly, we observed that activation of the Hh signaling pathway by small-molecule smoothened agonist (SAG) partially rescued bud morphology during branch bifurcation in explants from Ccrk mutant lungs. Therefore, CCRK properly regulates respiratory airway architecture in part through Hh-signal transduction and ciliogenesis.
Collapse
Affiliation(s)
- Hankyu Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Korea
| | - Hyuk Wan Ko
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| |
Collapse
|
20
|
Yamada Y, Schaap P. The proppin Bcas3 and its interactor KinkyA localize to the early phagophore and regulate autophagy. Autophagy 2021; 17:640-655. [PMID: 32116088 PMCID: PMC8032249 DOI: 10.1080/15548627.2020.1725403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 11/11/2022] Open
Abstract
To resolve the signaling mechanisms that mediate the starvation-induced processes of Dictyostelium sporulation and encystation, we performed insertional mutagenesis on cells harboring an mRFP-tagged spore gene. We isolated a mutant in kinkyA (knkA), a gene without known function, which formed fruiting bodies with a kinked stalk and lacking viable spores. Immunoprecipitation of lysates of KnkA-YFP-transformed knkA- cells yielded a mammalian BCAS3 homolog as a KnkA interactor. bcas3- phenocopied knkA- and Bcas3 colocalized with KnkA to puncta. Bcas3 shares sequence similarity with proppins (beta-propellors that bind phosphoinositides). Mutation of 2 Bcas3 residues that are essential for PtdIns3P binding in proppins prevented Bcas3 binding to PtdIns3P as well as punctate Bcas3 and KnkA localization. KnkA puncta also colocalized with small but not large vesicles that contain the autophagy protein Atg8 and were contiguous with the endoplasmic reticulum. knkA- and bcas3- cells showed a pronounced decrease of RFP-GFP-Atg8 in neutral early autophagosomes, indicating that KnkA and Bcas3 are required for macroautophagy/autophagy. Knockouts in atg7, atg5 or atg9 substantiated this finding by showing similar sporulation defects as knkA- and bcas3-. Defective Dictyostelium sporulation is evidently a useful diagnostic tool for the discovery of novel autophagy genes.Abbreviations: Atg: Autophagy-related; BCAS3: BCAS3 microtubule associated cell migration factor; cAMP: 3',5'-cyclic adenosine monophosphate; ER: endoplasmic reticulum; GFP: green fluorescent protein; PAS: phagophore assembly site; PRKA/PKA: protein kinase cAMP-dependent; Proppin: beta-propellers that bind phosphoinositides; PtdIns3P: phosphatidylinositol 3-phosphate; REMI: restriction enzyme-mediated insertional mutagenesis; RFP: red fluorescent protein; RT-qPCR: reverse transcriptase - quantitative polymerase chain reaction; WIPI: WD repeat domain, phosphoinositide interacting; YFP: yellow fluorescent protein.
Collapse
Affiliation(s)
- Yoko Yamada
- School of Life Sciences, University of Dundee, Dundee, UK
- Department of Biology, Faculty of Science, Toho University, Funabashi, Japan
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, UK
| |
Collapse
|
21
|
Abstract
Ciliogenesis describes the assembly of cilia in interphase cells. Several hundred proteins have been linked to ciliogenesis, which proceeds through a highly coordinated multistage process at the distal end of centrioles requiring membranes. In this short review, we focus on recently reported insights into the biogenesis of the primary cilium membrane and its association with other ciliogenic processes in the intracellular ciliogenesis pathway.
Collapse
Affiliation(s)
- Saurabh Shakya
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Laboratory of Cellular and Developmental Signaling, Frederick, MD 21702, USA
| | - Christopher J Westlake
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Laboratory of Cellular and Developmental Signaling, Frederick, MD 21702, USA
| |
Collapse
|
22
|
Moon KH, Ma JH, Min H, Koo H, Kim H, Ko HW, Bok J. Dysregulation of sonic hedgehog signaling causes hearing loss in ciliopathy mouse models. eLife 2020; 9:56551. [PMID: 33382037 PMCID: PMC7806262 DOI: 10.7554/elife.56551] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 12/31/2020] [Indexed: 12/11/2022] Open
Abstract
Defective primary cilia cause a range of diseases known as ciliopathies, including hearing loss. The etiology of hearing loss in ciliopathies, however, remains unclear. We analyzed cochleae from three ciliopathy mouse models exhibiting different ciliogenesis defects: Intraflagellar transport 88 (Ift88), Tbc1d32 (a.k.a. bromi), and Cilk1 (a.k.a. Ick) mutants. These mutants showed multiple developmental defects including shortened cochlear duct and abnormal apical patterning of the organ of Corti. Although ciliogenic defects in cochlear hair cells such as misalignment of the kinocilium are often associated with the planar cell polarity pathway, our results showed that inner ear defects in these mutants are primarily due to loss of sonic hedgehog signaling. Furthermore, an inner ear-specific deletion of Cilk1 elicits low-frequency hearing loss attributable to cellular changes in apical cochlear identity that is dedicated to low-frequency sound detection. This type of hearing loss may account for hearing deficits in some patients with ciliopathies.
Collapse
Affiliation(s)
- Kyeong-Hye Moon
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.,BK21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Hyun Ma
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyehyun Min
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Heiyeun Koo
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.,BK21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - HongKyung Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyuk Wan Ko
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.,BK21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
23
|
Homma Y, Hiragi S, Fukuda M. Rab family of small GTPases: an updated view on their regulation and functions. FEBS J 2020; 288:36-55. [PMID: 32542850 PMCID: PMC7818423 DOI: 10.1111/febs.15453] [Citation(s) in RCA: 210] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022]
Abstract
The Rab family of small GTPases regulates intracellular membrane trafficking by orchestrating the biogenesis, transport, tethering, and fusion of membrane‐bound organelles and vesicles. Like other small GTPases, Rabs cycle between two states, an active (GTP‐loaded) state and an inactive (GDP‐loaded) state, and their cycling is catalyzed by guanine nucleotide exchange factors (GEFs) and GTPase‐activating proteins (GAPs). Because an active form of each Rab localizes on a specific organelle (or vesicle) and recruits various effector proteins to facilitate each step of membrane trafficking, knowing when and where Rabs are activated and what effectors Rabs recruit is crucial to understand their functions. Since the discovery of Rabs, they have been regarded as one of the central hubs for membrane trafficking, and numerous biochemical and genetic studies have revealed the mechanisms of Rab functions in recent years. The results of these studies have included the identification and characterization of novel GEFs, GAPs, and effectors, as well as post‐translational modifications, for example, phosphorylation, of Rabs. Rab functions beyond the simple effector‐recruiting model are also emerging. Furthermore, the recently developed CRISPR/Cas technology has enabled acceleration of knockout analyses in both animals and cultured cells and revealed previously unknown physiological roles of many Rabs. In this review article, we provide the most up‐to‐date and comprehensive lists of GEFs, GAPs, effectors, and knockout phenotypes of mammalian Rabs and discuss recent findings in regard to their regulation and functions.
Collapse
Affiliation(s)
- Yuta Homma
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Shu Hiragi
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| |
Collapse
|
24
|
Hietamäki J, Gregory LC, Ayoub S, Iivonen AP, Vaaralahti K, Liu X, Brandstack N, Buckton AJ, Laine T, Känsäkoski J, Hero M, Miettinen PJ, Varjosalo M, Wakeling E, Dattani MT, Raivio T. Loss-of-Function Variants in TBC1D32 Underlie Syndromic Hypopituitarism. J Clin Endocrinol Metab 2020; 105:dgaa078. [PMID: 32060556 PMCID: PMC7138537 DOI: 10.1210/clinem/dgaa078] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
Abstract
CONTEXT Congenital pituitary hormone deficiencies with syndromic phenotypes and/or familial occurrence suggest genetic hypopituitarism; however, in many such patients the underlying molecular basis of the disease remains unknown. OBJECTIVE To describe patients with syndromic hypopituitarism due to biallelic loss-of-function variants in TBC1D32, a gene implicated in Sonic Hedgehog (Shh) signaling. SETTING Referral center. PATIENTS A Finnish family of 2 siblings with panhypopituitarism, absent anterior pituitary, and mild craniofacial dysmorphism, and a Pakistani family with a proband with growth hormone deficiency, anterior pituitary hypoplasia, and developmental delay. INTERVENTIONS The patients were investigated by whole genome sequencing. Expression profiling of TBC1D32 in human fetal brain was performed through in situ hybridization. Stable and dynamic protein-protein interaction partners of TBC1D32 were investigated in HEK cells followed by mass spectrometry analyses. MAIN OUTCOME MEASURES Genetic and phenotypic features of patients with biallelic loss-of-function mutations in TBC1D32. RESULTS The Finnish patients harboured compound heterozygous loss-of-function variants (c.1165_1166dup p.(Gln390Phefs*32) and c.2151del p.(Lys717Asnfs*29)) in TBC1D32; the Pakistani proband carried a known pathogenic homozygous TBC1D32 splice-site variant c.1372 + 1G > A p.(Arg411_Gly458del), as did a fetus with a cleft lip and partial intestinal malrotation from a terminated pregnancy within the same pedigree. TBC1D32 was expressed in the developing hypothalamus, Rathke's pouch, and areas of the hindbrain. TBC1D32 interacted with proteins implicated in cilium assembly, Shh signaling, and brain development. CONCLUSIONS Biallelic TBC1D32 variants underlie syndromic hypopituitarism, and the underlying mechanism may be via disrupted Shh signaling.
Collapse
Affiliation(s)
- Johanna Hietamäki
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Louise C Gregory
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sandy Ayoub
- North West Thames Regional Genetic Service, London North West University Healthcare NHS Trust, Harrow, UK
| | - Anna-Pauliina Iivonen
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kirsi Vaaralahti
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology & HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nina Brandstack
- Department of Radiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Andrew J Buckton
- London North Genomic Laboratory Hub, Great Ormond Street Hospital NHS Trust, London, UK
| | - Tiina Laine
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Johanna Känsäkoski
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Hero
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Päivi J Miettinen
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology & HiLIFE, University of Helsinki, Helsinki, Finland
| | - Emma Wakeling
- North West Thames Regional Genetic Service, London North West University Healthcare NHS Trust, Harrow, UK
| | - Mehul T Dattani
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular Basis of Rare Diseases Section, Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Endocrinology, Great Ormond Street Hospital for Children, London, UK
| | - Taneli Raivio
- Pediatric Research Center, Helsinki University Hospital, New Children’s Hospital, Pediatric Research Center, Helsinki, Finland
- Department of Physiology, Medicum Unit, and Translational Stem Cell Biology and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
25
|
Claudin-7b and Claudin-h are required for controlling cilia morphogenesis in the zebrafish kidney. Mech Dev 2019; 161:103595. [PMID: 31887432 DOI: 10.1016/j.mod.2019.103595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/08/2019] [Accepted: 12/23/2019] [Indexed: 11/22/2022]
Abstract
Claudins are a family of proteins which are the most important components of the tight junctions. The location of Claudins on the renal tubule epithelial determines its paracellular transport characteristics, but whether Claudins have other functions in kidneys remains still unclear. Here, we showed that the transcripts encoding two Claudin family proteins, claudin-7b (cldn-7b) and claudin-h (cldn-h), were expressed in the transporting cells in the zebrafish pronephros. By knocking down of cldn-7b and cldn-h in zebrafish, we showed that these claudins morphants exhibited cystic kidneys accompanied with body curvature. Further analysis showed that down regulation of cldn-7b or cldn-h led to multiple defects in apico-basolateral polarity, cilia morphology and ciliary function in kidney. Moreover, the ciliary defect was confirmed by depletion of Cldn-7b or Cldn-h using CRISPR/Cas9 system. We also showed that both cldn-7b and cldn-h were genetically interacted with a well-known ciliary gene, arl13b. Deletion of arl13b led to curly cilia in the pronephros that phenocopied with cldn-7b and cldn-h morphants. Taken together, our data suggested that the tight junction protein, Cldn-7b and Cldn-h, regulate kidney development and function by affecting cilia morphology.
Collapse
|
26
|
Che L, Song JY, Lou Y, Li GY. Analysis from the perspective of cilia: the protective effect of PARP inhibitors on visual function during light-induced damage. Int Ophthalmol 2019; 40:1017-1027. [PMID: 31802371 DOI: 10.1007/s10792-019-01245-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/23/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE To analyze the protective effect of PARP inhibitors on light-damaged retina and explore its possible mechanism from the perspective of ciliopathy. METHODS A systematic review of the literature was performed to investigate the protection of PARP inhibition on light-damaged cilia. PubMed database was retrieved to find the relevant studies and 119 literatures were involved in the review. RESULTS In retina, the outer segment of photoreceptor is regarded as a special type of primary cilium, so various retinal diseases actually belong to a type of ciliopathy. The retina is the only central nervous tissue exposed to light, but poly (ADP-ribose) polymerase (PARP), as a nuclear enzyme repairing DNA breaks, is overactivated during the light-induced DNA damage, and is involved in the cell death cascade. Studies show that both ATR and phosphorylated Akt colocalize with cilium and play an important role in regulating ciliary function. PARP may function at ATR or PI3K/Akt signal to exert protective effect on cilia. CONCLUSION PARP inhibitors may protect the cilia/OS of photoreceptor during light-induced damage, which the possible mechanism may be involved in the activation of ATR and PI3K/Akt signal.
Collapse
Affiliation(s)
- Lin Che
- Department of Ophthalmology, Second Hospital of Jilin University, Changchun, 130041, China
| | - Jing-Yao Song
- Department of Ophthalmology, Second Hospital of Jilin University, Changchun, 130041, China
| | - Yan Lou
- Department of Nephropathy, Second Hospital of Jilin University, Changchun, 130041, China
| | - Guang-Yu Li
- Department of Ophthalmology, Second Hospital of Jilin University, Changchun, 130041, China.
| |
Collapse
|
27
|
Oh YS, Wang EJ, Gailey CD, Brautigan DL, Allen BL, Fu Z. Ciliopathy-Associated Protein Kinase ICK Requires Its Non-Catalytic Carboxyl-Terminal Domain for Regulation of Ciliogenesis. Cells 2019; 8:E677. [PMID: 31277411 PMCID: PMC6678984 DOI: 10.3390/cells8070677] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 01/08/2023] Open
Abstract
Loss-of-function mutations in the human ICK (intestinal cell kinase) gene cause dysfunctional primary cilia and perinatal lethality which are associated with human ciliopathies. The enzyme that we herein call CAPK (ciliopathy-associated protein kinase) is a serine/threonine protein kinase that has a highly conserved MAPK-like N-terminal catalytic domain and an unstructured C-terminal domain (CTD) whose functions are completely unknown. In this study, we demonstrate that truncation of the CTD impairs the ability of CAPK to interact with and phosphorylate its substrate, kinesin family member 3A (KIF3A). We also find that deletion of the CTD of CAPK compromises both localization to the primary cilium and negative regulation of ciliogenesis. Thus, CAPK substrate recognition, ciliary targeting, and ciliary function depend on the non-catalytic CTD of the protein which is predicted to be intrinsically disordered.
Collapse
Affiliation(s)
- Yoon Seon Oh
- Department of Pharmacology, University of Virginia Medical School, Charlottesville, VA 22908, USA
| | - Eric J Wang
- Department of Pharmacology, University of Virginia Medical School, Charlottesville, VA 22908, USA
| | - Casey D Gailey
- Department of Pharmacology, University of Virginia Medical School, Charlottesville, VA 22908, USA
| | - David L Brautigan
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Medical School, Charlottesville, VA 22908, USA
- Center for Cell Signaling, University of Virginia Medical School, Charlottesville, VA 22908, USA
| | - Benjamin L Allen
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zheng Fu
- Department of Pharmacology, University of Virginia Medical School, Charlottesville, VA 22908, USA.
- Center for Cell Signaling, University of Virginia Medical School, Charlottesville, VA 22908, USA.
| |
Collapse
|
28
|
Shaheen R, Jiang N, Alzahrani F, Ewida N, Al-Sheddi T, Alobeid E, Musaev D, Stanley V, Hashem M, Ibrahim N, Abdulwahab F, Alshenqiti A, Sonmez FM, Saqati N, Alzaidan H, Al-Qattan MM, Al-Mohanna F, Gleeson JG, Alkuraya FS. Bi-allelic Mutations in FAM149B1 Cause Abnormal Primary Cilium and a Range of Ciliopathy Phenotypes in Humans. Am J Hum Genet 2019; 104:731-737. [PMID: 30905400 PMCID: PMC6451727 DOI: 10.1016/j.ajhg.2019.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 02/14/2019] [Indexed: 11/30/2022] Open
Abstract
Ciliopathies are clinical disorders of the primary cilium with widely recognized phenotypic and genetic heterogeneity. In two Arab consanguineous families, we mapped a ciliopathy phenotype that most closely matches Joubert syndrome (hypotonia, developmental delay, typical facies, oculomotor apraxia, polydactyly, and subtle posterior fossa abnormalities) to a single locus in which a founder homozygous truncating variant in FAM149B1 was identified by exome sequencing. We subsequently identified a third Arab consanguineous multiplex family in which the phenotype of Joubert syndrome/oral-facial-digital syndrome (OFD VI) was found to co-segregate with the same founder variant in FAM149B1. Independently, autozygosity mapping and exome sequencing in a consanguineous Turkish family with Joubert syndrome highlighted a different homozygous truncating variant in the same gene. FAM149B1 encodes a protein of unknown function. Mutant fibroblasts were found to have normal ciliogenesis potential. However, distinct cilia-related abnormalities were observed in these cells: abnormal accumulation IFT complex at the distal tips of the cilia, which assumed bulbous appearance, increased length of the primary cilium, and dysregulated SHH signaling. We conclude that FAM149B1 is required for normal ciliary biology and that its deficiency results in a range of ciliopathy phenotypes in humans along the spectrum of Joubert syndrome.
Collapse
Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Nan Jiang
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Tarfa Al-Sheddi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Damir Musaev
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Abduljabbar Alshenqiti
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 1211, Saudi Arabia
| | - Fatma Mujgan Sonmez
- Karadeniz Technical University, Faculty of Medicine, Department of Child Neurology, Retired Lecturer, Trabzon 61080, Turkey
| | - Nadia Saqati
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 1211, Saudi Arabia
| | - Hamad Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 1211, Saudi Arabia
| | | | - Futwan Al-Mohanna
- Department of Cell Biology, King Faisal Specialist Hospital and Research Center, PO Box 245, Riyadh 11211, Saudi Arabia
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, PO Box 3354, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12371, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
| |
Collapse
|
29
|
Wang Y, Ren Y, Pan J. Regulation of flagellar assembly and length in
Chlamydomonas
by LF4, a MAPK‐related kinase. FASEB J 2019; 33:6431-6441. [DOI: 10.1096/fj.201802375rr] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yingrui Wang
- Ministry of Education (MOE) Key Laboratory for Protein ScienceTsinghua‐Peking Center for Life SciencesSchool of Life SciencesTsinghua University Beijing China
| | - Yahui Ren
- Ministry of Education (MOE) Key Laboratory for Protein ScienceTsinghua‐Peking Center for Life SciencesSchool of Life SciencesTsinghua University Beijing China
| | - Junmin Pan
- Ministry of Education (MOE) Key Laboratory for Protein ScienceTsinghua‐Peking Center for Life SciencesSchool of Life SciencesTsinghua University Beijing China
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and Technology Qingdao China
| |
Collapse
|
30
|
Peng P, Zheng Y, Lv J. TBC1D32-RET: A Novel RET Oncogenic Fusion in Lung Adenocarcinoma. J Thorac Oncol 2019; 14:e7-e9. [DOI: 10.1016/j.jtho.2018.08.2029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 01/26/2023]
|
31
|
Yoon J, Comerci CJ, Weiss LE, Milenkovic L, Stearns T, Moerner WE. Revealing Nanoscale Morphology of the Primary Cilium Using Super-Resolution Fluorescence Microscopy. Biophys J 2018; 116:319-329. [PMID: 30598282 PMCID: PMC6349968 DOI: 10.1016/j.bpj.2018.11.3136] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/20/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
Super-resolution (SR) microscopy has been used to observe structural details beyond the diffraction limit of ∼250 nm in a variety of biological and materials systems. By combining this imaging technique with both computer-vision algorithms and topological methods, we reveal and quantify the nanoscale morphology of the primary cilium, a tiny tubular cellular structure (∼2-6 μm long and 200-300 nm in diameter). The cilium in mammalian cells protrudes out of the plasma membrane and is important in many signaling processes related to cellular differentiation and disease. After tagging individual ciliary transmembrane proteins, specifically Smoothened, with single fluorescent labels in fixed cells, we use three-dimensional (3D) single-molecule SR microscopy to determine their positions with a precision of 10-25 nm. We gain a dense, pointillistic reconstruction of the surfaces of many cilia, revealing large heterogeneity in membrane shape. A Poisson surface reconstruction algorithm generates a fine surface mesh, allowing us to characterize the presence of deformations by quantifying the surface curvature. Upon impairment of intracellular cargo transport machinery by genetic knockout or small-molecule treatment of cells, our quantitative curvature analysis shows significant morphological differences not visible by conventional fluorescence microscopy techniques. Furthermore, using a complementary SR technique, two-color, two-dimensional stimulated emission depletion microscopy, we find that the cytoskeleton in the cilium, the axoneme, also exhibits abnormal morphology in the mutant cells, similar to our 3D results on the Smoothened-measured ciliary surface. Our work combines 3D SR microscopy and computational tools to quantitatively characterize morphological changes of the primary cilium under different treatments and uses stimulated emission depletion to discover correlated changes in the underlying structure. This approach can be useful for studying other biological or nanoscale structures of interest.
Collapse
Affiliation(s)
- Joshua Yoon
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California
| | - Colin J Comerci
- Biophysics Program, Stanford University, Stanford, California
| | - Lucien E Weiss
- Department of Chemistry, Stanford University, Stanford, California
| | | | - Tim Stearns
- Department of Biology, Stanford University, Stanford, California
| | - W E Moerner
- Department of Applied Physics, Stanford University, Stanford, California; Department of Chemistry, Stanford University, Stanford, California.
| |
Collapse
|
32
|
Mok MT, Zhou J, Tang W, Zeng X, Oliver AW, Ward SE, Cheng AS. CCRK is a novel signalling hub exploitable in cancer immunotherapy. Pharmacol Ther 2018; 186:138-151. [PMID: 29360538 DOI: 10.1016/j.pharmthera.2018.01.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyclin-dependent kinase 20 (CDK20), or more commonly referred to as cell cycle-related kinase (CCRK), is the latest member of CDK family with strong linkage to human cancers. Accumulating studies have reported the consistent overexpression of CCRK in cancers arising from brain, colon, liver, lung and ovary. Such aberrant up-regulation of CCRK is clinically significant as it correlates with tumor staging, shorter patient survival and poor prognosis. Intriguingly, the signalling molecules perturbed by CCRK are divergent and cancer-specific, including the cell cycle regulators CDK2, cyclin D1, cyclin E and RB in glioblastoma, ovarian carcinoma and colorectal cancer, and KEAP1-NRF2 cytoprotective pathway in lung cancer. In hepatocellular carcinoma (HCC), CCRK mediates virus-host interaction to promote hepatitis B virus-associated tumorigenesis. Further mechanistic analyses reveal that CCRK orchestrates a self-reinforcing circuitry comprising of AR, GSK3β, β-catenin, AKT, EZH2, and NF-κB signalling for transcriptional and epigenetic regulation of oncogenes and tumor suppressor genes. Notably, EZH2 and NF-κB in this circuit have been recently shown to induce IL-6 production to facilitate tumor immune evasion. Concordantly, in a hepatoma preclinical model, ablation of Ccrk disrupts the immunosuppressive tumor microenvironment and enhances the therapeutic efficacy of immune checkpoint blockade via potentiation of anti-tumor T cell responses. In this review, we summarized the multifaceted tumor-intrinsic and -extrinsic functions of CCRK, which represents a novel signalling hub exploitable in cancer immunotherapy.
Collapse
Affiliation(s)
- Myth T Mok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jingying Zhou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenshu Tang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xuezhen Zeng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, Main Building, Cardiff, Wales, CF10 3AT, UK
| | - Alfred S Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
33
|
Yi P, Xie C, Ou G. The kinases male germ cell-associated kinase and cell cycle-related kinase regulate kinesin-2 motility inCaenorhabditis elegansneuronal cilia. Traffic 2018; 19:522-535. [DOI: 10.1111/tra.12572] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Peishan Yi
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
| | - Chao Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences and MOE Key Laboratory for Protein Science; Tsinghua University; Beijing China
| |
Collapse
|
34
|
Garcia G, Raleigh DR, Reiter JF. How the Ciliary Membrane Is Organized Inside-Out to Communicate Outside-In. Curr Biol 2018; 28:R421-R434. [PMID: 29689227 PMCID: PMC6434934 DOI: 10.1016/j.cub.2018.03.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cilia, organelles that move to execute functions like fertilization and signal to execute functions like photoreception and embryonic patterning, are composed of a core of nine-fold doublet microtubules overlain by a membrane. Distinct types of cilia display distinct membrane morphologies, ranging from simple domed cylinders to the highly ornate invaginations and membrane disks of photoreceptor outer segments. Critical for the ability of cilia to signal, both the protein and the lipid compositions of ciliary membranes are different from those of other cellular membranes. This specialization presents a unique challenge for the cell as, unlike membrane-bounded organelles, the ciliary membrane is contiguous with the surrounding plasma membrane. This distinct ciliary membrane is generated in concert with multiple membrane remodeling events that comprise the process of ciliogenesis. Once the cilium is formed, control of ciliary membrane composition relies on discrete molecular machines, including a barrier to membrane proteins entering the cilium at a specialized region of the base of the cilium called the transition zone and a trafficking adaptor that controls G protein-coupled receptor (GPCR) localization to the cilium called the BBSome. The ciliary membrane can be further remodeled by the removal of membrane proteins by the release of ciliary extracellular vesicles that may function in intercellular communication, removal of unneeded proteins or ciliary disassembly. Here, we review the structures and transport mechanisms that control ciliary membrane composition, and discuss how membrane specialization enables the cilium to function as the antenna of the cell.
Collapse
Affiliation(s)
- Galo Garcia
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - David R Raleigh
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Radiation Oncology, University of California, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
| |
Collapse
|
35
|
Wang C, Li J, Takemaru KI, Jiang X, Xu G, Wang B. Centrosomal protein Dzip1l binds Cby, promotes ciliary bud formation, and acts redundantly with Bromi to regulate ciliogenesis in the mouse. Development 2018; 145:dev.164236. [PMID: 29487109 DOI: 10.1242/dev.164236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/16/2018] [Indexed: 12/14/2022]
Abstract
The primary cilium is a microtubule-based organelle required for Hedgehog (Hh) signaling and consists of a basal body, a ciliary axoneme and a compartment between the first two structures, called the transition zone (TZ). The TZ serves as a gatekeeper to control protein composition in cilia, but less is known about its role in ciliary bud formation. Here, we show that centrosomal protein Dzip1l is required for Hh signaling between Smoothened and Sufu. Dzip1l colocalizes with basal body appendage proteins and Rpgrip1l, a TZ protein. Loss of Dzip1l results in reduced ciliogenesis and dysmorphic cilia in vivo Dzip1l interacts with, and acts upstream of, Cby, an appendage protein, in ciliogenesis. Dzip1l also has overlapping functions with Bromi (Tbc1d32) in ciliogenesis, cilia morphogenesis and neural tube patterning. Loss of Dzip1l arrests ciliogenesis at the stage of ciliary bud formation from the TZ. Consistent with this, Dzip1l mutant cells fail to remove the capping protein Cp110 (Ccp110) from the distal end of mother centrioles and to recruit Rpgrip1l to the TZ. Therefore, Dzip1l promotes ciliary bud formation and is required for the integrity of the TZ.
Collapse
Affiliation(s)
- Chengbing Wang
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA
| | - Jia Li
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA
| | - Ken-Ichi Takemaru
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Xiaogang Jiang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Baolin Wang
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA .,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA
| |
Collapse
|
36
|
Wiegering A, Rüther U, Gerhardt C. The Role of Hedgehog Signalling in the Formation of the Ventricular Septum. J Dev Biol 2017; 5:E17. [PMID: 29615572 PMCID: PMC5831794 DOI: 10.3390/jdb5040017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/08/2017] [Accepted: 12/09/2017] [Indexed: 12/11/2022] Open
Abstract
An incomplete septation of the ventricles in the vertebrate heart that disturbes the strict separation between the contents of the two ventricles is termed a ventricular septal defect (VSD). Together with bicuspid aortic valves, it is the most frequent congenital heart disease in humans. Until now, life-threatening VSDs are usually treated surgically. To avoid surgery and to develop an alternative therapy (e.g., a small molecule therapy), it is necessary to understand the molecular mechanisms underlying ventricular septum (VS) development. Consequently, various studies focus on the investigation of signalling pathways, which play essential roles in the formation of the VS. In the past decade, several reports found evidence for an involvement of Hedgehog (HH) signalling in VS development. In this review article, we will summarise the current knowledge about the association between HH signalling and VS formation and discuss the use of such knowledge to design treatment strategies against the development of VSDs.
Collapse
Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Ulrich Rüther
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
37
|
Lupu FI, Burnett JB, Eggenschwiler JT. Cell cycle-related kinase regulates mammalian eye development through positive and negative regulation of the Hedgehog pathway. Dev Biol 2017; 434:24-35. [PMID: 29166577 DOI: 10.1016/j.ydbio.2017.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/30/2017] [Accepted: 10/30/2017] [Indexed: 01/20/2023]
Abstract
Cell cycle-related kinase (CCRK) is a conserved regulator of ciliogenesis whose loss in mice leads to a wide range of developmental defects, including exencephaly, preaxial polydactyly, skeletal abnormalities, and microphthalmia. Here, we investigate the role of CCRK in mouse eye development. Ccrk mutants show dramatic patterning defects, with an expansion of the optic stalk domain into the optic cup, as well as an expansion of the retinal pigment epithelium (RPE) into neural retina (NR) territory. In addition, Ccrk mutants display a shortened optic stalk. These defects are associated with bimodal changes in Hedgehog (Hh) pathway activity within the eye, including the loss of proximal, high level responses but a gain in distal, low level responses. We simultaneously removed the Hh activator GLI2 in Ccrk mutants (Ccrk-/-;Gli2-/-), which resulted in rescue of optic cup patterning and exacerbation of optic stalk length defects. Next, we disrupted the Hh pathway antagonist GLI3 in mutants lacking CCRK (Ccrk-/-;Gli3-/-), which lead to even greater expansion of the RPE markers into the NR domain and a complete loss of NR specification within the optic cup. These results indicate that CCRK functions in eye development by both positively and negatively regulating the Hh pathway, and they reveal distinct requirements for Hh signaling in patterning and morphogenesis of the eyes.
Collapse
Affiliation(s)
- Floria I Lupu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Jacob B Burnett
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | |
Collapse
|
38
|
Hashimoto H, Jiang W, Yoshimura T, Moon KH, Bok J, Ikenaka K. Strong sonic hedgehog signaling in the mouse ventral spinal cord is not required for oligodendrocyte precursor cell (OPC) generation but is necessary for correct timing of its generation. Neurochem Int 2017; 119:178-183. [PMID: 29122585 DOI: 10.1016/j.neuint.2017.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 12/15/2022]
Abstract
In the mouse neural tube, sonic hedgehog (Shh) secreted from the floor plate (FP) and the notochord (NC) regulates ventral patterning of the neural tube, and later is essential for the generation of oligodendrocyte precursor cells (OPCs). During early development, the NC is adjacent to the neural tube and induces ventral domains in it, including the FP. In the later stage of development, during gliogenesis in the spinal cord, the pMN domain receives strong Shh signaling input. While this is considered to be essential for the generation of OPCs, the actual role of this strong input in OPC generation remains unclear. Here we studied OPC generation in bromi mutant mice which show abnormal ciliary structure. Shh signaling occurs within cilia and has been reported to be weak in bromi mutants. At E11.5, accumulation of Patched1 mRNA, a Shh signaling reporter, is observed in the pMN domain of wild type but not bromi mutants, whereas expression of Gli1 mRNA, another Shh reporter, disappeared. Thus, Shh signaling input to the pMN domain at E12.5 was reduced in bromi mutant mice. In these mutants, induction of the FP structure was delayed and its size was reduced compared to wild type mice. Furthermore, while the p3 and pMN domains were induced, the length of the Nkx2.2-positive region and the number of Olig2-positive cells decreased. The number of OPCs was also significantly decreased in the E12.5 and E14.5 bromi mutant spinal cord. In contrast, motor neuron (MN) production, detected by HB9 expression, significantly increased. It is likely that the transition from MN production to OPC generation in the pMN domain is impaired in bromi mutant mice. These results suggest that strong Shh input to the pMN domain is not required for OPC generation but is essential for producing a sufficient number of OPCs.
Collapse
Affiliation(s)
- Hirokazu Hashimoto
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Wen Jiang
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Takeshi Yoshimura
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Kyeong-Hye Moon
- Department of Anatomy, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea; BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea; Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea; BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Kazuhiro Ikenaka
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan.
| |
Collapse
|
39
|
Cell Cycle-Related Kinase (CCRK) regulates ciliogenesis and Hedgehog signaling in mice. PLoS Genet 2017; 13:e1006912. [PMID: 28817564 PMCID: PMC5574612 DOI: 10.1371/journal.pgen.1006912] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 08/29/2017] [Accepted: 07/06/2017] [Indexed: 01/04/2023] Open
Abstract
The Hedgehog (Hh) signaling pathway plays a key role in cell fate specification, proliferation, and survival during mammalian development. Cells require a small organelle, the primary cilium, to respond properly to Hh signals and the key regulators of Hh signal transduction exhibit dynamic localization to this organelle when the pathway is activated. Here, we investigate the role of Cell Cycle Related kinase (CCRK) in regulation of cilium-dependent Hh signaling in the mouse. Mice mutant for Ccrk exhibit a variety of developmental defects indicative of inappropriate regulation of this pathway. Cell biological, biochemical and genetic analyses indicate that CCRK is required to control the Hedgehog pathway at the level or downstream of Smoothened and upstream of the Gli transcription factors, Gli2 and Gli3. In vitro experiments indicate that Ccrk mutant cells show a greater deficit in response to signaling over long time periods than over short ones. Similar to Chlamydomonas mutants lacking the CCRK homolog, LF2, mouse Ccrk mutant cells show defective regulation of ciliary length and morphology. Ccrk mutant cells exhibit defects in intraflagellar transport (the transport mechanism used to assemble cilia), as well as slowed kinetics of ciliary enrichment of key Hh pathway regulators. Collectively, the data suggest that CCRK positively regulates the kinetics by which ciliary proteins such as Smoothened and Gli2 are imported into the cilium, and that the efficiency of ciliary recruitment allows for potent responses to Hedgehog signaling over long time periods. The importance of cilia in development and disease has become broadly appreciated in recent years due in part to their roles in signal transduction. Despite this attention, crucial aspects of ciliary assembly and function, such as the mechanisms controlling ciliary assembly and the signal transduction events occurring in cilia, remain unclear. Cilia play a central role in sensing and transducing Hedgehog signals in the context of mammalian embryogenesis and in a variety of cancers. Here, we investigate the functions of Cell Cycle Related Kinase (CCRK), which plays an evolutionarily conserved function in the assembly of cilia and flagella. We find that mouse CCRK positively and negatively regulates ciliary length. We show that CCRK controls multiple aspects of Hedgehog signaling in vivo and in vitro by regulating the processing and activities of the Gli transcription factors. Our data suggest that CCRK controls Hedgehog signaling by promoting the efficient ciliary import of core signaling components.
Collapse
|
40
|
Burnett JB, Lupu FI, Eggenschwiler JT. Proper ciliary assembly is critical for restricting Hedgehog signaling during early eye development in mice. Dev Biol 2017; 430:32-40. [PMID: 28778798 DOI: 10.1016/j.ydbio.2017.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 11/25/2022]
Abstract
Patterning of the vertebrate eye into optic stalk, retinal pigment epithelium (RPE) and neural retina (NR) territories relies on a number of signaling pathways, but how these signals are interpreted by optic progenitors is not well understood. The primary cilium is a microtubule-based organelle that is essential for Hedgehog (Hh) signaling, but it has also been implicated in the regulation of other signaling pathways. Here, we show that the optic primordium is ciliated during early eye development and that ciliogenesis is essential for proper patterning and morphogenesis of the mouse eye. Ift172 mutants fail to generate primary cilia and exhibit patterning defects that resemble those of Gli3 mutants, suggesting that cilia are required to restrict Hh activity during eye formation. Ift122 mutants, which produce cilia with abnormal morphology, generate optic vesicles that fail to invaginate to produce the optic cup. These mutants also lack formation of the lens, RPE and NR. Such phenotypic features are accompanied by strong, ectopic Hh pathway activity, evidenced by altered gene expression patterns. Removal of GLI2 from Ift122 mutants rescued several aspects of optic cup and lens morphogenesis as well as RPE and NR specification. Collectively, our data suggest that proper assembly of primary cilia is critical for restricting the Hedgehog pathway during eye formation in the mouse.
Collapse
Affiliation(s)
- Jacob B Burnett
- Department of Genetics, University of Georgia, Athens, GA 30602, United States
| | - Floria I Lupu
- Department of Genetics, University of Georgia, Athens, GA 30602, United States
| | | |
Collapse
|
41
|
Van De Weghe JC, Rusterholz TD, Latour B, Grout ME, Aldinger KA, Shaheen R, Dempsey JC, Maddirevula S, Cheng YHH, Phelps IG, Gesemann M, Goel H, Birk OS, Alanzi T, Rawashdeh R, Khan AO, Bamshad MJ, Nickerson DA, Neuhauss SC, Dobyns WB, Alkuraya FS, Roepman R, Bachmann-Gagescu R, Doherty D, Doherty D. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish. Am J Hum Genet 2017. [PMID: 28625504 DOI: 10.1016/j.ajhg.2017.05.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown. All of the gene products localize in and around the primary cilium, making JS a canonical ciliopathy. Ciliopathies are unified by their overlapping clinical features and underlying mechanisms involving ciliary dysfunction. In this work, we identify biallelic rare, predicted-deleterious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals with JS from 8 families, accounting for approximately 1% of the disorder. The associated phenotypes range from isolated neurological involvement to JS with retinal dystrophy, additional brain abnormalities (e.g., heterotopia, Dandy-Walker malformation), pituitary insufficiency, and/or synpolydactyly. We show that ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. Typical ciliopathy phenotypes (curved body shape, retinal dystrophy, coloboma, and decreased cilia) in a CRISPR/Cas9-engineered zebrafish mutant model provide additional support for ARMC9 as a ciliopathy-associated gene. Identifying ARMC9 mutations as a cause of JS takes us one step closer to a full genetic understanding of this important disorder and enables future functional work to define the central biological mechanisms underlying JS and other ciliopathies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
| |
Collapse
|
42
|
Lechtreck KF, Van De Weghe JC, Harris JA, Liu P. Protein transport in growing and steady-state cilia. Traffic 2017; 18:277-286. [PMID: 28248449 DOI: 10.1111/tra.12474] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 12/18/2022]
Abstract
Cilia and eukaryotic flagella are threadlike cell extensions with motile and sensory functions. Their assembly requires intraflagellar transport (IFT), a bidirectional motor-driven transport of protein carriers along the axonemal microtubules. IFT moves ample amounts of structural proteins including tubulin into growing cilia likely explaining its critical role for assembly. IFT continues in non-growing cilia contributing to a variety of processes ranging from axonemal maintenance and the export of non-ciliary proteins to cell locomotion and ciliary signaling. Here, we discuss recent data on cues regulating the type, amount and timing of cargo transported by IFT. A regulation of IFT-cargo interactions is critical to establish, maintain and adjust ciliary length, protein composition and function.
Collapse
Affiliation(s)
- Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia
| | | | | | - Peiwei Liu
- Department of Cellular Biology, University of Georgia, Athens, Georgia
| |
Collapse
|
43
|
Burnicka-Turek O, Steimle JD, Huang W, Felker L, Kamp A, Kweon J, Peterson M, Reeves RH, Maslen CL, Gruber PJ, Yang XH, Shendure J, Moskowitz IP. Cilia gene mutations cause atrioventricular septal defects by multiple mechanisms. Hum Mol Genet 2016; 25:3011-3028. [PMID: 27340223 DOI: 10.1093/hmg/ddw155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 01/13/2023] Open
Abstract
Atrioventricular septal defects (AVSDs) are a common severe form of congenital heart disease (CHD). In this study we identified deleterious non-synonymous mutations in two cilia genes, Dnah11 and Mks1, in independent N-ethyl-N-nitrosourea-induced mouse mutant lines with heritable recessive AVSDs by whole-exome sequencing. Cilia are required for left/right body axis determination and second heart field (SHF) Hedgehog (Hh) signaling, and we find that cilia mutations affect these requirements differentially. Dnah11avc4 did not disrupt SHF Hh signaling and caused AVSDs only concurrently with heterotaxy, a left/right axis abnormality. In contrast, Mks1avc6 disrupted SHF Hh signaling and caused AVSDs without heterotaxy. We performed unbiased whole-genome SHF transcriptional profiling and found that cilia motility genes were not expressed in the SHF whereas cilia structural and signaling genes were highly expressed. SHF cilia gene expression predicted the phenotypic concordance between AVSDs and heterotaxy in mice and humans with cilia gene mutations. A two-step model of cilia action accurately predicted the AVSD/heterotaxyu phenotypic expression pattern caused by cilia gene mutations. We speculate that cilia gene mutations contribute to both syndromic and non-syndromic AVSDs in humans and provide a model that predicts the phenotypic consequences of specific cilia gene mutations.
Collapse
Affiliation(s)
- Ozanna Burnicka-Turek
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA,
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Wenhui Huang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lindsay Felker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anna Kamp
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Junghun Kweon
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Michael Peterson
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Roger H Reeves
- Department of Physiology and Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cheryl L Maslen
- Knight Cardiovascular Institute and Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA and
| | - Peter J Gruber
- Department of Cardiothoracic Surgery, University of Iowa, Iowa City, IA 52245, USA
| | - Xinan H Yang
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA,
| |
Collapse
|
44
|
Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TMT, Texier Y, van Beersum SEC, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJC, Coene KLM, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJF, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJP, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, Roepman R. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nat Commun 2016; 7:11491. [PMID: 27173435 PMCID: PMC4869170 DOI: 10.1038/ncomms11491] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/01/2016] [Indexed: 01/12/2023] Open
Abstract
Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine. Mutations in proteins that localize to primary cilia cause devastating diseases, yet the primary cilium is a poorly understood organelle. Here the authors use interaction proteomics to identify a network of human ciliary proteins that provides new insights into several biological processes and diseases.
Collapse
Affiliation(s)
- Karsten Boldt
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Jeroen van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Qianhao Lu
- Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.,Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Konstantinos Koutroumpas
- Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Evry, 91030 Evry, France
| | - Thanh-Minh T Nguyen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Yves Texier
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.,Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science, 81377 Munich, Germany
| | - Sylvia E C van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Nicola Horn
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Dorus A Mans
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Gerard Dougherty
- Department of General Pediatrics, University Children's Hospital Muenster, 48149 Muenster, Germany
| | - Ideke J C Lamers
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Heleen H Arts
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Matthew J Betts
- Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.,Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Tina Beyer
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Emine Bolat
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholz Association, Otfried-Müller Strasse 23, 72076 Tuebingen, Germany
| | - Khatera Haidari
- Department of Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Lisette Hetterschijt
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Daniela Iaconis
- Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy
| | - Dagan Jenkins
- Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Franziska Klose
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Barbara Knapp
- Cell and Matrix Biology, Inst. of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany
| | - Brooke Latour
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Stef J F Letteboer
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Carlo L Marcelis
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Dragana Mitic
- Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy.,Department of Translational Medicine Federico II University, 80131 Naples, Italy
| | - Machteld M Oud
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Moniek Riemersma
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Susan Rix
- Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Grischa Toedt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Yasmin Wissinger
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Ka Man Wu
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Gordana Apic
- Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
| | - Philip L Beales
- Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Oliver E Blacque
- School of Biomolecular &Biomed Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Hannie Kremer
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Heymut Omran
- Department of General Pediatrics, University Children's Hospital Muenster, 48149 Muenster, Germany
| | - Erwin van Wijk
- Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Uwe Wolfrum
- Cell and Matrix Biology, Inst. of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany
| | - François Kepes
- Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Evry, 91030 Evry, France
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy.,Department of Translational Medicine Federico II University, 80131 Naples, Italy
| | - Rachel H Giles
- Department of Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Marius Ueffing
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany
| | - Robert B Russell
- Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.,Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | | |
Collapse
|
45
|
Franco B, Thauvin-Robinet C. Update on oral-facial-digital syndromes (OFDS). Cilia 2016; 5:12. [PMID: 27141300 PMCID: PMC4852435 DOI: 10.1186/s13630-016-0034-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
Oral-facial-digital syndromes (OFDS) represent a heterogeneous group of rare developmental disorders affecting the mouth, the face and the digits. Additional signs may involve brain, kidneys and other organs thus better defining the different clinical subtypes. With the exception of OFD types I and VIII, which are X-linked, the majority of OFDS is transmitted as an autosomal recessive syndrome. A number of genes have already found to be mutated in OFDS and most of the encoded proteins are predicted or proven to be involved in primary cilia/basal body function. Preliminary data indicate a physical interaction among some of those proteins and future studies will clarify whether all OFDS proteins are part of a network functionally connected to cilia. Mutations in some of the genes can also lead to other types of ciliopathies with partially overlapping phenotypes, such as Joubert syndrome (JS) and Meckel syndrome (MKS), supporting the concept that cilia-related diseases might be a continuous spectrum of the same phenotype with different degrees of severity. To date, seven of the described OFDS still await a molecular definition and two unclassified forms need further clinical and molecular validation. Next-generation sequencing (NGS) approaches are expected to shed light on how many OFDS geneticists should consider while evaluating oral-facial-digital cases. Functional studies will establish whether the non-ciliary functions of the transcripts mutated in OFDS might contribute to any of the phenotypic abnormalities observed in OFDS.
Collapse
Affiliation(s)
- Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, Pozzuoli, 80078 Naples, Italy ; Medical Genetics, Department of Medical Translational Sciences, University of Naples Federico II, Naples, Italy
| | - Christel Thauvin-Robinet
- EA GAD, IFR Santé-STIC, Université de Bourgogne, Dijon, France ; Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » de l'Est, Centre de Génétique et Pédiatrie 1, Hôpital d'Enfants, CHU Dijon, Dijon, France
| |
Collapse
|
46
|
Gibbs BC, Damerla RR, Vladar EK, Chatterjee B, Wan Y, Liu X, Cui C, Gabriel GC, Zahid M, Yagi H, Szabo-Rogers HL, Suyama KL, Axelrod JD, Lo CW. Prickle1 mutation causes planar cell polarity and directional cell migration defects associated with cardiac outflow tract anomalies and other structural birth defects. Biol Open 2016; 5:323-35. [PMID: 26883626 PMCID: PMC4810743 DOI: 10.1242/bio.015750] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Planar cell polarity (PCP) is controlled by a conserved pathway that regulates directional cell behavior. Here, we show that mutant mice harboring a newly described mutation termed Beetlejuice (Bj) in Prickle1 (Pk1), a PCP component, exhibit developmental phenotypes involving cell polarity defects, including skeletal, cochlear and congenital cardiac anomalies. Bj mutants die neonatally with cardiac outflow tract (OFT) malalignment. This is associated with OFT shortening due to loss of polarized cell orientation and failure of second heart field cell intercalation mediating OFT lengthening. OFT myocardialization was disrupted with cardiomyocytes failing to align with the direction of cell invasion into the outflow cushions. The expression of genes mediating Wnt signaling was altered. Also noted were shortened but widened bile ducts and disruption in canonical Wnt signaling. Using an in vitro wound closure assay, we showed Bj mutant fibroblasts cannot establish polarized cell morphology or engage in directional cell migration, and their actin cytoskeleton failed to align with the direction of wound closure. Unexpectedly, Pk1 mutants exhibited primary and motile cilia defects. Given Bj mutant phenotypes are reminiscent of ciliopathies, these findings suggest Pk1 may also regulate ciliogenesis. Together these findings show Pk1 plays an essential role in regulating cell polarity and directional cell migration during development. Summary: Outflow tract malalignment and multiple birth defects observed in the Prickle1 mutant may arise from cell polarity perturbation, which may involve disruptions in Wnt signaling and of cilia function.
Collapse
Affiliation(s)
- Brian C Gibbs
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Rama Rao Damerla
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Eszter K Vladar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bishwanath Chatterjee
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Yong Wan
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15261, USA
| | - Xiaoqin Liu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Cheng Cui
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Maliha Zahid
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Hisato Yagi
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| | - Heather L Szabo-Rogers
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15261, USA
| | - Kaye L Suyama
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey D Axelrod
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
| |
Collapse
|
47
|
Schock EN, Chang CF, Youngworth IA, Davey MG, Delany ME, Brugmann SA. Utilizing the chicken as an animal model for human craniofacial ciliopathies. Dev Biol 2015; 415:326-337. [PMID: 26597494 DOI: 10.1016/j.ydbio.2015.10.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/13/2015] [Accepted: 10/21/2015] [Indexed: 11/30/2022]
Abstract
The chicken has been a particularly useful model for the study of craniofacial development and disease for over a century due to their relatively large size, accessibility, and amenability for classical bead implantation and transplant experiments. Several naturally occurring mutant lines with craniofacial anomalies also exist and have been heavily utilized by developmental biologist for several decades. Two of the most well known lines, talpid(2) (ta(2)) and talpid(3) (ta(3)), represent the first spontaneous mutants to have the causative genes identified. Despite having distinct genetic causes, both mutants have recently been identified as ciliopathic. Excitingly, both of these mutants have been classified as models for human craniofacial ciliopathies: Oral-facial-digital syndrome (ta(2)) and Joubert syndrome (ta(3)). Herein, we review and compare these two models of craniofacial disease and highlight what they have revealed about the molecular and cellular etiology of ciliopathies. Furthermore, we outline how applying classical avian experiments and new technological advances (transgenics and genome editing) with naturally occurring avian mutants can add a tremendous amount to what we currently know about craniofacial ciliopathies.
Collapse
Affiliation(s)
- Elizabeth N Schock
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ching-Fang Chang
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ingrid A Youngworth
- College of Agricultural and Environmental Sciences, Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Megan G Davey
- Division of Developmental Biology, The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, UK
| | - Mary E Delany
- College of Agricultural and Environmental Sciences, Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Samantha A Brugmann
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| |
Collapse
|
48
|
Aleem E, Arceci RJ. Targeting cell cycle regulators in hematologic malignancies. Front Cell Dev Biol 2015; 3:16. [PMID: 25914884 PMCID: PMC4390903 DOI: 10.3389/fcell.2015.00016] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/25/2015] [Indexed: 12/20/2022] Open
Abstract
Hematologic malignancies represent the fourth most frequently diagnosed cancer in economically developed countries. In hematologic malignancies normal hematopoiesis is interrupted by uncontrolled growth of a genetically altered stem or progenitor cell (HSPC) that maintains its ability of self-renewal. Cyclin-dependent kinases (CDKs) not only regulate the mammalian cell cycle, but also influence other vital cellular processes, such as stem cell renewal, differentiation, transcription, epigenetic regulation, apoptosis, and DNA repair. Chromosomal translocations, amplification, overexpression and altered CDK activities have been described in different types of human cancer, which have made them attractive targets for pharmacological inhibition. Mouse models deficient for one or more CDKs have significantly contributed to our current understanding of the physiological functions of CDKs, as well as their roles in human cancer. The present review focuses on selected cell cycle kinases with recent emerging key functions in hematopoiesis and in hematopoietic malignancies, such as CDK6 and its role in MLL-rearranged leukemia and acute lymphocytic leukemia, CDK1 and its regulator WEE-1 in acute myeloid leukemia (AML), and cyclin C/CDK8/CDK19 complexes in T-cell acute lymphocytic leukemia. The knowledge gained from gene knockout experiments in mice of these kinases is also summarized. An overview of compounds targeting these kinases, which are currently in clinical development in various solid tumors and hematopoietic malignances, is presented. These include the CDK4/CDK6 inhibitors (palbociclib, LEE011, LY2835219), pan-CDK inhibitors that target CDK1 (dinaciclib, flavopiridol, AT7519, TG02, P276-00, terampeprocol and RGB 286638) as well as the WEE-1 kinase inhibitor, MK-1775. The advantage of combination therapy of cell cycle inhibitors with conventional chemotherapeutic agents used in the treatment of AML, such as cytarabine, is discussed.
Collapse
Affiliation(s)
- Eiman Aleem
- Department of Child Health, The Ronald A. Matricaria Institute of Molecular Medicine at Phoenix Children's Hospital, University of Arizona College of Medicine-Phoenix Phoenix, AZ, USA ; Department of Zoology, Faculty of Science, Alexandria University Alexandria, Egypt
| | - Robert J Arceci
- Department of Child Health, The Ronald A. Matricaria Institute of Molecular Medicine at Phoenix Children's Hospital, University of Arizona College of Medicine-Phoenix Phoenix, AZ, USA
| |
Collapse
|
49
|
Craft JM, Harris JA, Hyman S, Kner P, Lechtreck KF. Tubulin transport by IFT is upregulated during ciliary growth by a cilium-autonomous mechanism. ACTA ACUST UNITED AC 2015; 208:223-37. [PMID: 25583998 PMCID: PMC4298693 DOI: 10.1083/jcb.201409036] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In Chlamydomonas cilia, IFT concentrates soluble tubulin by regulating IFT train occupancy and thereby promotes elongation of axonemal microtubules. The assembly of the axoneme, the structural scaffold of cilia and flagella, requires translocation of a vast quantity of tubulin into the growing cilium, but the mechanisms that regulate the targeting, quantity, and timing of tubulin transport are largely unknown. In Chlamydomonas, GFP-tagged α-tubulin enters cilia as an intraflagellar transport (IFT) cargo and by diffusion. IFT-based transport of GFP-tubulin is elevated in growing cilia and IFT trains carry more tubulin. Cells possessing both nongrowing and growing cilia selectively target GFP-tubulin into the latter. The preferential delivery of tubulin boosts the concentration of soluble tubulin in the matrix of growing versus steady-state cilia. Cilia length mutants show abnormal kinetics of tubulin transport. We propose that cells regulate the extent of occupancy of IFT trains by tubulin cargoes. During ciliary growth, IFT concentrates soluble tubulin in cilia and thereby promotes elongation of the axonemal microtubules.
Collapse
Affiliation(s)
- Julie M Craft
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - J Aaron Harris
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Sebastian Hyman
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Peter Kner
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| | - Karl F Lechtreck
- Department of Cellular Biology and College of Engineering, University of Georgia, Athens, GA 30602
| |
Collapse
|
50
|
Intestinal cell kinase, a protein associated with endocrine-cerebro-osteodysplasia syndrome, is a key regulator of cilia length and Hedgehog signaling. Proc Natl Acad Sci U S A 2014; 111:8541-6. [PMID: 24853502 DOI: 10.1073/pnas.1323161111] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Endocrine-cerebro-osteodysplasia (ECO) syndrome is a recessive genetic disorder associated with multiple congenital defects in endocrine, cerebral, and skeletal systems that is caused by a missense mutation in the mitogen-activated protein kinase-like intestinal cell kinase (ICK) gene. In algae and invertebrates, ICK homologs are involved in flagellar formation and ciliogenesis, respectively. However, it is not clear whether this role of ICK is conserved in mammals and how a lack of functional ICK results in the characteristic phenotypes of human ECO syndrome. Here, we generated Ick knockout mice to elucidate the precise role of ICK in mammalian development and to examine the pathological mechanisms of ECO syndrome. Ick null mouse embryos displayed cleft palate, hydrocephalus, polydactyly, and delayed skeletal development, closely resembling ECO syndrome phenotypes. In cultured cells, down-regulation of Ick or overexpression of kinase-dead or ECO syndrome mutant ICK resulted in an elongation of primary cilia and abnormal Sonic hedgehog (Shh) signaling. Wild-type ICK proteins were generally localized in the proximal region of cilia near the basal bodies, whereas kinase-dead ICK mutant proteins accumulated in the distal part of bulged ciliary tips. Consistent with these observations in cultured cells, Ick knockout mouse embryos displayed elongated cilia and reduced Shh signaling during limb digit patterning. Taken together, these results indicate that ICK plays a crucial role in controlling ciliary length and that ciliary defects caused by a lack of functional ICK leads to abnormal Shh signaling, resulting in congenital disorders such as ECO syndrome.
Collapse
|