1
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Claus LR, Chen C, Stallworth J, Turner JL, Slaats GG, Hawks AL, Mabillard H, Senum SR, Srikanth S, Flanagan-Steet H, Louie RJ, Silver J, Lerner-Ellis J, Morel C, Mighton C, Sleutels F, van Slegtenhorst M, van Ham T, Brooks AS, Dorresteijn EM, Barakat TS, Dahan K, Demoulin N, Goffin EJ, Olinger E, Larsen M, Hertz JM, Lilien MR, Obeidová L, Seeman T, Stone HK, Kerecuk L, Gurgu M, Yousef Yengej FA, Ammerlaan CME, Rookmaaker MB, Hanna C, Rogers RC, Duran K, Peters E, Sayer JA, van Haaften G, Harris PC, Ling K, Mason JM, van Eerde AM, Steet R. Certain heterozygous variants in the kinase domain of the serine/threonine kinase NEK8 can cause an autosomal dominant form of polycystic kidney disease. Kidney Int 2023; 104:995-1007. [PMID: 37598857 PMCID: PMC10592035 DOI: 10.1016/j.kint.2023.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/22/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) resulting from pathogenic variants in PKD1 and PKD2 is the most common form of PKD, but other genetic causes tied to primary cilia function have been identified. Biallelic pathogenic variants in the serine/threonine kinase NEK8 cause a syndromic ciliopathy with extra-kidney manifestations. Here we identify NEK8 as a disease gene for ADPKD in 12 families. Clinical evaluation was combined with functional studies using fibroblasts and tubuloids from affected individuals. Nek8 knockout mouse kidney epithelial (IMCD3) cells transfected with wild type or variant NEK8 were further used to study ciliogenesis, ciliary trafficking, kinase function, and DNA damage responses. Twenty-one affected monoallelic individuals uniformly exhibited cystic kidney disease (mostly neonatal) without consistent extra-kidney manifestations. Recurrent de novo mutations of the NEK8 missense variant p.Arg45Trp, including mosaicism, were seen in ten families. Missense variants elsewhere within the kinase domain (p.Ile150Met and p.Lys157Gln) were also identified. Functional studies demonstrated normal localization of the NEK8 protein to the proximal cilium and no consistent cilia formation defects in patient-derived cells. NEK8-wild type protein and all variant forms of the protein expressed in Nek8 knockout IMCD3 cells were localized to cilia and supported ciliogenesis. However, Nek8 knockout IMCD3 cells expressing NEK8-p.Arg45Trp and NEK8-p.Lys157Gln showed significantly decreased polycystin-2 but normal ANKS6 localization in cilia. Moreover, p.Arg45Trp NEK8 exhibited reduced kinase activity in vitro. In patient derived tubuloids and IMCD3 cells expressing NEK8-p.Arg45Trp, DNA damage signaling was increased compared to healthy passage-matched controls. Thus, we propose a dominant-negative effect for specific heterozygous missense variants in the NEK8 kinase domain as a new cause of PKD.
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Affiliation(s)
- Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Joshua L Turner
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Gisela G Slaats
- Department of Nephrology and Hypertension, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandra L Hawks
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Holly Mabillard
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Sujata Srikanth
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Raymond J Louie
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Josh Silver
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Chantal Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Frank Sleutels
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tjakko van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eiske M Dorresteijn
- Department of Pediatric Nephrology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Karin Dahan
- Institute Pathology and Genetic, Center of Human Genetics, Charleroi, Belgium
| | - Nathalie Demoulin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Jean Goffin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Olinger
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Martin Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marc R Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Lena Obeidová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomas Seeman
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pediatrics, University Hospital Ostrava, Ostrava, Czech Republic; Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Hillarey K Stone
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Larissa Kerecuk
- Birmingham Women's and Children's National Health Services (NHS) Foundation Trust, National Institute for Health Care and Research (NIHR) Clinical Research Network (CRN) West Midlands, Birmingham, UK
| | - Mihai Gurgu
- Fundeni Clinical Institute, Bucharest, Romania
| | - Fjodor A Yousef Yengej
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Carola M E Ammerlaan
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Christian Hanna
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA; Division of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - R Curtis Rogers
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Karen Duran
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Edith Peters
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - John A Sayer
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK; National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Newcastle, UK
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
| | - Jennifer M Mason
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA.
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Richard Steet
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA.
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Chen Y, Zhang Y, Zhou X. Non-classical functions of nuclear pore proteins in ciliopathy. Front Mol Biosci 2023; 10:1278976. [PMID: 37908226 PMCID: PMC10614291 DOI: 10.3389/fmolb.2023.1278976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Nucleoporins (NUPs) constitute integral nuclear pore protein (NPC) elements. Although traditional NUP functions have been extensively researched, evidence of additional vital non-NPC roles, referred to herein as non-classical NUP functions, is also emerging. Several NUPs localise at the ciliary base. Indeed, Nup188, Nup93 or Nup205 knockdown results in cilia loss, impacting cardiac left-right patterning in models and cell lines. Genetic variants of Nup205 and Nup188 have been identified in patients with congenital heart disease and situs inversus totalis or heterotaxy, a prevalent human ciliopathy. These findings link non-classical NUP functions to human diseases. This mini-review summarises pivotal NUP interactions with NIMA-related kinases or nephronophthisis proteins that regulate ciliary function and explores other NUPs potentially implicated in cilia-related disorders. Overall, elucidating the non-classical roles of NUPs will enhance comprehension of ciliopathy aetiology.
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Affiliation(s)
- Yan Chen
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| | - Yuan Zhang
- Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiangyu Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
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Garaycoechea JI, Quinlan C, Luijsterburg MS. Pathological consequences of DNA damage in the kidney. Nat Rev Nephrol 2023; 19:229-243. [PMID: 36702905 DOI: 10.1038/s41581-022-00671-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 01/27/2023]
Abstract
DNA lesions that evade repair can lead to mutations that drive the development of cancer, and cellular responses to DNA damage can trigger senescence and cell death, which are associated with ageing. In the kidney, DNA damage has been implicated in both acute and chronic kidney injury, and in renal cell carcinoma. The susceptibility of the kidney to chemotherapeutic agents that damage DNA is well established, but an unexpected link between kidney ciliopathies and the DNA damage response has also been reported. In addition, human genetic deficiencies in DNA repair have highlighted DNA crosslinks, DNA breaks and transcription-blocking damage as lesions that are particularly toxic to the kidney. Genetic tools in mice, as well as advances in kidney organoid and single-cell RNA sequencing technologies, have provided important insights into how specific kidney cell types respond to DNA damage. The emerging view is that in the kidney, DNA damage affects the local microenvironment by triggering a damage response and cell proliferation to replenish injured cells, as well as inducing systemic responses aimed at reducing exposure to genotoxic stress. The pathological consequences of DNA damage are therefore key to the nephrotoxicity of DNA-damaging agents and the kidney phenotypes observed in human DNA repair-deficiency disorders.
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Affiliation(s)
- Juan I Garaycoechea
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Catherine Quinlan
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
- Department of Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Australia
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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4
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Nguyen K, Boehling J, Tran MN, Cheng T, Rivera A, Collins-Burow BM, Lee SB, Drewry DH, Burow ME. NEK Family Review and Correlations with Patient Survival Outcomes in Various Cancer Types. Cancers (Basel) 2023; 15:cancers15072067. [PMID: 37046733 PMCID: PMC10093199 DOI: 10.3390/cancers15072067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
The Never in Mitosis Gene A (NIMA)–related kinases (NEKs) are a group of serine/threonine kinases that are involved in a wide array of cellular processes including cell cycle regulation, DNA damage repair response (DDR), apoptosis, and microtubule organization. Recent studies have identified the involvement of NEK family members in various diseases such as autoimmune disorders, malignancies, and developmental defects. Despite the existing literature exemplifying the importance of the NEK family of kinases, this family of protein kinases remains understudied. This report seeks to provide a foundation for investigating the role of different NEKs in malignancies. We do this by evaluating the 11 NEK family kinase gene expression associations with patients’ overall survival (OS) from various cancers using the Kaplan–Meier Online Tool (KMPlotter) to correlate the relationship between mRNA expression of NEK1-11 in various cancers and patient survival. Furthermore, we use the Catalog of Somatic Mutations in Cancer (COSMIC) database to identify NEK family mutations in cancers of different tissues. Overall, the data suggest that the NEK family has varying associations with patient survival in different cancers with tumor-suppressive and tumor-promoting effects being tissue-dependent.
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5
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Yuan G, Yang ST, Yang S. Regulator of G protein signaling 12 drives inflammatory arthritis by activating synovial fibroblasts through MYCBP2/KIF2A signaling. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:197-210. [PMID: 36700049 PMCID: PMC9843488 DOI: 10.1016/j.omtn.2022.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Synovial fibroblasts are the active and aggressive drivers in the progression of arthritis, but the cellular and molecular mechanisms remain unknown. Here, our results showed that regulator of G protein signaling 12 (RGS12) maintained ciliogenesis in synovial fibroblasts, which is critical for the development of inflammatory arthritis. Deletion of RGS12 led to a significant decrease in ciliogenesis, adhesion, migration, and secretion of synovial fibroblasts. Mechanistically, RGS12 overexpression in synovial fibroblasts increased the length and number of cilia but decreased the protein level of kinesin family member 2A (KIF2A). The results of LC-MS analyses showed that RGS12 interacted with MYC binding protein 2 to enhance its ubiquitination activity, through which the KIF2A protein was degraded in synovial fibroblasts. Moreover, overexpression of KIF2A blocked the increases in cilia length and number. Mice with RGS12 deficiency or treatment of RGS12 shRNA nanoparticles significantly decreased the clinical score, paw swelling, synovitis, and cartilage destruction during inflammatory arthritis by inhibiting the activation of synovial fibroblasts. Therefore, this study provides evidence that RGS12 activates synovial fibroblasts' pathological function via promoting MCYBP2-mediated degradation of KIF2A and ciliogenesis. Our data suggest that RGS12 may be a potential drug target for the treatment of inflammatory arthritis.
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Affiliation(s)
- Gongsheng Yuan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shu-ting Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shuying Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Penn Center for Musculoskeletal Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Innovation & Precision Dentistry, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Wang J, Thomas HR, Thompson RG, Waldrep SC, Fogerty J, Song P, Li Z, Ma Y, Santra P, Hoover JD, Yeo NC, Drummond IA, Yoder BK, Amack JD, Perkins B, Parant JM. Variable phenotypes and penetrance between and within different zebrafish ciliary transition zone mutants. Dis Model Mech 2022; 15:dmm049568. [PMID: 36533556 PMCID: PMC9844136 DOI: 10.1242/dmm.049568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022] Open
Abstract
Meckel syndrome, nephronophthisis, Joubert syndrome and Bardet-Biedl syndrome are caused by mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest that these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes, suggesting that the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants, including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1 and nphp4, as well as mutants in ift88 and ift172. Our data indicate that variations in phenotypes exist between different TZ mutants, supporting different tissue-specific functions of these TZ genes. Further, we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants, the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We also demonstrated that multiple-guide-derived CRISPR/Cas9 F0 'crispant' embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12 and cfap52).
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Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Joseph Fogerty
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Zhang Li
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Yongjie Ma
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Peu Santra
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jonathan D. Hoover
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Iain A. Drummond
- Davis Center for Aging and Regeneration, Mount Desert Island Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA
| | - Bradley K. Yoder
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Jeffrey D. Amack
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Brian Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
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7
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Letavernier E, Flamant M, Marsault C, Haymann JP, Müller G, Villa L, Cloutier J, Traxer O, Daudon M. Lateralization of uric acid stones on the left side. CR CHIM 2022. [DOI: 10.5802/crchim.91] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Wells JR, Padua MB, Ware SM. The genetic landscape of cardiovascular left-right patterning defects. Curr Opin Genet Dev 2022; 75:101937. [PMID: 35777348 PMCID: PMC10698510 DOI: 10.1016/j.gde.2022.101937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/11/2022] [Accepted: 05/19/2022] [Indexed: 11/26/2022]
Abstract
Heterotaxy is a disorder with complex congenital heart defects and diverse left-right (LR) patterning defects in other organ systems. Despite evidence suggesting a strong genetic component in heterotaxy, the majority of molecular causes remain unknown. Established genes often involve a ciliated, embryonic structure known as the left-right organizer (LRO). Herein, we focus on genetic discoveries in heterotaxy in the past two years. These include complex genetic architecture, novel mechanisms regulating cilia formation, and evidence for conservation of LR patterning between distant species. We feature new insights regarding established LR signaling pathways, bring attention to heterotaxy candidate genes in novel pathways, and provide an extensive overview of genes previously associated with laterality phenotypes in humans.
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Affiliation(s)
- John R Wells
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Maria B Padua
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
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9
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Joseph BB, Edeen PT, Meadows S, Binti S, Fay DS. An unexpected role for the conserved ADAM-family metalloprotease ADM-2 in Caenorhabditis elegans molting. PLoS Genet 2022; 18:e1010249. [PMID: 35639786 PMCID: PMC9187072 DOI: 10.1371/journal.pgen.1010249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/10/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022] Open
Abstract
Molting is a widespread developmental process in which the external extracellular matrix (ECM), the cuticle, is remodeled to allow for organismal growth and environmental adaptation. Studies in the nematode Caenorhabditis elegans have identified a diverse set of molting-associated factors including signaling molecules, intracellular trafficking regulators, ECM components, and ECM-modifying enzymes such as matrix metalloproteases. C. elegans NEKL-2 and NEKL-3, two conserved members of the NEK family of protein kinases, are essential for molting and promote the endocytosis of environmental steroid-hormone precursors by the epidermis. Steroids in turn drive the cyclic induction of many genes required for molting. Here we report a role for the sole C. elegans ADAM–meltrin metalloprotease family member, ADM-2, as a mediator of molting. Loss of adm-2, including mutations that disrupt the metalloprotease domain, led to the strong suppression of molting defects in partial loss-of-function nekl mutants. ADM-2 is expressed in the epidermis, and its trafficking through the endo-lysosomal network was disrupted after NEKL depletion. We identified the epidermally expressed low-density lipoprotein receptor–related protein, LRP-1, as a candidate target of ADM-2 regulation. Whereas loss of ADM-2 activity led to the upregulation of apical epidermal LRP-1, ADM-2 overexpression caused a reduction in LRP-1 levels. Consistent with this, several mammalian ADAMs, including the meltrin ADAM12, have been shown to regulate mammalian LRP1 via proteolysis. In contrast to mammalian homologs, however, the regulation of LRP-1 by ADM-2 does not appear to involve the metalloprotease function of ADM-2, nor is proteolytic processing of LRP-1 strongly affected in adm-2 mutants. Our findings suggest a noncanonical role for an ADAM family member in the regulation of a lipoprotein-like receptor and lead us to propose that endocytic trafficking may be important for both the internalization of factors that promote molting as well as the removal of proteins that can inhibit the process. The molecular and cellular features of molting in nematodes share many similarities with cellular and developmental processes that occur in mammals. This includes the degradation and reorganization of extracellular matrix materials that surround cells, as well as the intracellular machineries that allow cells to sample and modify their environments. In the current study, we found an unexpected function for a conserved protein that cleaves other proteins on the external surface of cells. Rather than promoting molting through extracellular matrix reorganization, however, the ADM-2 protease appears to function as a negative regulator of molting. This observation can be explained in part by data showing that ADM-2 negatively regulates a cell surface receptor required for molting. Surprisingly, it appears to do so through a mechanism that does not involve proteolysis. Our data provide insights into the mechanisms controlling molting and link several conserved proteins to show how they function together during development.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Phillip T. Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sarina Meadows
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Shaonil Binti
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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10
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In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals. Int J Mol Sci 2022; 23:ijms23074041. [PMID: 35409400 PMCID: PMC8999480 DOI: 10.3390/ijms23074041] [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: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of this family was initially identified in Aspergillus and was found to play important roles in mitosis and cell division. The yeast family has one member each, Fin1p in fission yeast and Kin3p in budding yeast, also with functions in mitotic processes, but, overall, these are poorly studied kinases. The mammalian family, the main focus of this review, consists of 11 members named Nek1 to Nek11. With the exception of a few members, the functions of the mammalian Neks are poorly understood but appear to be quite diverse. Like the prototypical NIMA, many members appear to play important roles in mitosis and meiosis, but their functions in the cell go well beyond these well-established activities. In this review, we explore the roles of fungal and mammalian NIMA kinases and highlight the most recent findings in the field.
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11
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Whole-Exome Sequencing Identifies the VHL Mutation (c.262T > C, p.Try88Arg) in Non-Obstructive Azoospermia-Associated Cystic Renal Cell Carcinoma. Curr Oncol 2022; 29:2376-2384. [PMID: 35448166 PMCID: PMC9030033 DOI: 10.3390/curroncol29040192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 03/10/2022] [Indexed: 11/17/2022] Open
Abstract
Von Hippel-Lindau (VHL) genes are intimately involved in renal cell carcinoma (RCC), including clear cell RCC (ccRCC) pathogenesis. However, the contribution of pathogenic VHL mutations to ccRCC remains poorly understood. We report a xanthoderm with non-obstructive azoospermia (NOA)-associated cystic ccRCC, and the missense VHL mutation (c.262T > C, p.Try88Arg). In a 34-year-old patient, a urologic physical examination identified hard epididymis, and imaging tests revealed deferens-associated NOA, as well as multi-organ hydatid cysts, including bilateral epididymal cysts, bilateral testicular cysts, bilateral renal cysts, and pancreatic cysts. Five years later, ccRCC was developed based on clinical and radiologic evidence. Two different prediction models of protein structure and multiple sequence alignment across species were applied to assess the pathological effects of the VHL mutation. The reliability of the assessment in silico was determined by both the cellular location and protein levels of the mutant products, using IF and Western blot, respectively. Our study shows that the missense VHL mutation (c.262T > C, p.Try88Arg) plays a deleterious role in pVHL functions, as predicted by multiple sequence alignment across species. While a structural analysis identified no significant structural alterations in pVHL, the detrimental effects of this mutation were determined by exogenous expression, evidenced by a markedly different spatial distribution and reduced expression of mutant pVHL. This is the first report of the VHL gene mutation (c.475T > C, p.Try88Arg) in a xanthoderm.
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12
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Schwarz H, Popp B, Airik R, Torabi N, Knaup KX, Stoeckert J, Wiech T, Amann K, Reis A, Schiffer M, Wiesener MS, Schueler M. Biallelic ANKS6 mutations cause late onset ciliopathy with chronic kidney disease through YAP dysregulation. Hum Mol Genet 2021; 31:1357-1369. [PMID: 34740236 DOI: 10.1093/hmg/ddab322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Nephronophthisis-related ciliopathies (NPHP-RC) comprises a group of inherited kidney diseases, caused by mutations in genes encoding proteins localizing to primary cilia. NPHP-RC represent the one of the most frequent monogenic causes of renal failure within the first three decades of life, but its molecular disease mechanisms remains unclear. Here, we identified biallelic ANKS6 mutations in two affected siblings with late onset chronic kidney disease by whole exome sequencing. We employed patient derived fibroblasts generating an in vitro model to study the precise biological impact of distinct human ANKS6 mutations, completed by immunohistochemistry studies on renal biopsy samples. Functional studies using patient derived cells showed an impaired integrity of the ciliary Inversin compartment with reduced cilia length. Further analyses demonstrated that ANKS6 deficiency leads to a dysregulation of Hippo-signaling through nuclear YAP imbalance, and disrupted ciliary localization of YAP. Additionally an altered transcriptional activity of canonical Wnt target genes and altered expression of non-phosphorylated (active) β-catenin and phosphorylated GSK3β were observed. Upon ciliation ANKS6 deficiency revealed a deranged subcellular localization and expression of components of the endocytic recycling compartment. Our results demonstrate that ANKS6 plays a key role in regulating the Hippo pathway and ANKS6 deficiency is linked to dysregulation of signaling pathways. Our study provides molecular clues in understanding pathophysiological mechanisms of NPHP-RC and may offer new therapeutic targets.
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Affiliation(s)
- Hannah Schwarz
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Bernt Popp
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, 04103, Germany.,Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Rannar Airik
- Department of Pediatrics, Division of Nephrology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, 15224, USA
| | - Nasrin Torabi
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Karl X Knaup
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Johanna Stoeckert
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Thorsten Wiech
- Institute of Pathology, Nephropathology Section, University Hospital Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology, University of Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Michael S Wiesener
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Markus Schueler
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
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13
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Gupta S, Ozimek-Kulik JE, Phillips JK. Nephronophthisis-Pathobiology and Molecular Pathogenesis of a Rare Kidney Genetic Disease. Genes (Basel) 2021; 12:genes12111762. [PMID: 34828368 PMCID: PMC8623546 DOI: 10.3390/genes12111762] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The exponential rise in our understanding of the aetiology and pathophysiology of genetic cystic kidney diseases can be attributed to the identification of cystogenic genes over the last three decades. The foundation of this was laid by positional cloning strategies which gradually shifted towards next-generation sequencing (NGS) based screenings. This shift has enabled the discovery of novel cystogenic genes at an accelerated pace unlike ever before and, most notably, the past decade has seen the largest increase in identification of the genes which cause nephronophthisis (NPHP). NPHP is a monogenic autosomal recessive cystic kidney disease caused by mutations in a diverse clade of over 26 identified genes and is the most common genetic cause of renal failure in children. NPHP gene types present with some common pathophysiological features alongside a diverse range of extra-renal phenotypes associated with specific syndromic presentations. This review provides a timely update on our knowledge of this disease, including epidemiology, pathophysiology, anatomical and molecular features. We delve into the diversity of the NPHP causing genes and discuss known molecular mechanisms and biochemical pathways that may have possible points of intersection with polycystic kidney disease (the most studied renal cystic pathology). We delineate the pathologies arising from extra-renal complications and co-morbidities and their impact on quality of life. Finally, we discuss the current diagnostic and therapeutic modalities available for disease management, outlining possible avenues of research to improve the prognosis for NPHP patients.
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Affiliation(s)
- Shabarni Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- Correspondence:
| | - Justyna E. Ozimek-Kulik
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia
- Department of Paediatric Nephrology, Sydney Children’s Hospital Network, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Jacqueline Kathleen Phillips
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.E.O.-K.); (J.K.P.)
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14
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Stokman MF, Saunier S, Benmerah A. Renal Ciliopathies: Sorting Out Therapeutic Approaches for Nephronophthisis. Front Cell Dev Biol 2021; 9:653138. [PMID: 34055783 PMCID: PMC8155538 DOI: 10.3389/fcell.2021.653138] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in in vitro and/or in vivo models. Despite identification of numerous candidate drugs in rodent models, there has been a lack of clinical trials and there is currently no therapy that halts disease progression in NPH patients. This review covers the most important findings of therapeutic approaches in NPH model systems to date, including hypothesis-driven therapies and untargeted drug screens, approached from the pathophysiology of NPH. Importantly, most animal models used in these studies represent the cystic infantile form of NPH, which is less prevalent than the juvenile form. It appears therefore important to develop new models relevant for juvenile/adult NPH. Alternative non-orthologous animal models and developments in patient-based in vitro model systems are discussed, as well as future directions in personalized therapy for NPH.
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Affiliation(s)
- Marijn F Stokman
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Sophie Saunier
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Alexandre Benmerah
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
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15
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Zhang Y, Chen W, Zeng W, Lu Z, Zhou X. Biallelic loss of function NEK3 mutations deacetylate α-tubulin and downregulate NUP205 that predispose individuals to cilia-related abnormal cardiac left-right patterning. Cell Death Dis 2020; 11:1005. [PMID: 33230144 PMCID: PMC7684299 DOI: 10.1038/s41419-020-03214-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/05/2020] [Indexed: 12/18/2022]
Abstract
Defective left–right (LR) organization involving abnormalities in cilia ultrastructure causes laterality disorders including situs inversus (SI) and heterotaxy (Htx) with the prevalence approximately 1/10,000 births. In this study, we describe two unrelated family trios with abnormal cardiac LR patterning. Through whole-exome sequencing (WES), we identified compound heterozygous mutations (c.805-1G >C; p. Ile269GlnfsTer8/c.1117dupA; p.Thr373AsnfsTer19) (c.29T>C; p.Ile10Thr/c.356A>G; p.His119Arg) of NEK3, encoding a NIMA (never in mitosis A)-related kinase, in two affected individuals, respectively. Protein levels of NEK3 were abrogated in Patient-1 with biallelic loss-of function (LoF) NEK3 mutations that causes premature stop codon. Subsequence transcriptome analysis revealed that NNMT (nicotinamide N-methyltransferase) and SIRT2 (sirtuin2) was upregulated by NEK3 knockdown in human retinal pigment epithelial (RPE) cells in vitro, which associates α-tubulin deacetylation by western blot and immunofluorescence. Transmission electron microscopy (TEM) analysis further identified defective ciliary ultrastructure in Patient-1. Furthermore, inner ring components of nuclear pore complex (NPC) including nucleoporin (NUP)205, NUP188, and NUP155 were significantly downregulated in NEK3-silenced cells. In conclusion, we identified biallelic mutations of NEK3 predispose individual to abnormal cardiac left–right patterning via SIRT2-mediated α-tubulin deacetylation and downregulation of inner ring nucleoporins. Our study suggested that NEK3 could be a candidate gene for human ciliopathies.
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Affiliation(s)
- Yuan Zhang
- Department of Assisted Reproduction, and Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 201204, Shanghai, China
| | - Weicheng Chen
- Pediatric Cardiovascular Center, Children's Hospital of Fudan University, 201102, Shanghai, China
| | - Weijia Zeng
- School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Zhouping Lu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 201204, Shanghai, China
| | - Xiangyu Zhou
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 201204, Shanghai, China.
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16
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Chambers JM, Addiego A, Flores-Mireles AL, Wingert RA. Ppargc1a Controls Ciliated Cell Development by Regulating Prostaglandin Biosynthesis. Cell Rep 2020; 33:108370. [PMID: 33176142 PMCID: PMC7731726 DOI: 10.1016/j.celrep.2020.108370] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 07/23/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022] Open
Abstract
Cilia are microtubule-based organelles that function in a multitude of physiological contexts to perform chemosensing, mechanosensing, and fluid propulsion. The process of ciliogenesis is highly regulated, and disruptions result in disease states termed ciliopathies. Here, we report that peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (ppargc1a) is essential for ciliogenesis in nodal, mono-, and multiciliated cells (MCCs) and for discernment of renal tubule ciliated cell fate during embryogenesis. ppargc1a performs these functions by affecting prostaglandin signaling, whereby cilia formation and renal MCC fate are restored with prostaglandin E2 (PGE2) treatment in ppargc1a-deficient animals. Genetic disruption of ppargc1a specifically reduces expression of the prostanoid biosynthesis gene prostaglandin-endoperoxide synthase 1 (ptgs1), and suboptimal knockdown of both genes shows this synergistic effect. Furthermore, ptgs1 overexpression rescues ciliogenesis and renal MCCs in ppargc1a-deficient embryos. These findings position Ppargc1a as a key genetic regulator of prostaglandin signaling during ciliated cell ontogeny.
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Affiliation(s)
- Joseph M Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Amanda Addiego
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Ana L Flores-Mireles
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN 46556, USA.
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17
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Clinical and pathological features and varied mutational spectra of pathogenic genes in 55 Chinese patients with nephronophthisis. Clin Chim Acta 2020; 506:136-144. [PMID: 32173348 DOI: 10.1016/j.cca.2020.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Nephronophthisis (NPHP) is the most common genetic cause of end-stage renal disease (ESRD) in children. This study was performed to explore the pathogenic gene mutations and clinical and pathological features of Chinese patients with NPHP. METHODS Patients for whom causative mutations were not identified in our previous study, as well as those recruited later, were subjected to whole-exome next-generation sequencing (NGS) or the exome of 63 primary cilia disease genes. RESULTS We recruited 55 patients (27 boys and 28 girls) from 48 families, mainly from South China. We subjected 35 patients to NGS. Disease-causing mutations were revealed in seven more families (nine patients) by NGS. In total, disease-causing mutations were identified in 25 patients from 19 families, accounting for 39.6% (19/48) of all families, and novel mutation rate was 77.8% (35/45). NPHP1 and NPHP3 mutations were identified in 14.6% (7/48) and 12.5% (6/48) of all families, respectively. The patient with CEP83 mutations presented with prominent glomerular cysts and glomeruli dysplasia without extrarenal involvement. CONCLUSION A high novel mutation rate was identified, and disease-causing mutations of NPHP3 prevailed in this group of Chinese NPHP patients. This is the second report of a patient with CEP83 mutations.
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18
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Joseph BB, Wang Y, Edeen P, Lažetić V, Grant BD, Fay DS. Control of clathrin-mediated endocytosis by NIMA family kinases. PLoS Genet 2020; 16:e1008633. [PMID: 32069276 PMCID: PMC7048319 DOI: 10.1371/journal.pgen.1008633] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/28/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022] Open
Abstract
Endocytosis, the process by which cells internalize plasma membrane and associated cargo, is regulated extensively by posttranslational modifications. Previous studies suggested the potential involvement of scores of protein kinases in endocytic control, of which only a few have been validated in vivo. Here we show that the conserved NIMA-related kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (the NEKLs) control clathrin-mediated endocytosis in C. elegans. Loss of NEKL-2 or NEKL-3 activities leads to penetrant larval molting defects and to the abnormal localization of trafficking markers in arrested larvae. Using an auxin-based degron system, we also find that depletion of NEKLs in adult-stage C. elegans leads to gross clathrin mislocalization and to a dramatic reduction in clathrin mobility at the apical membrane. Using a non-biased genetic screen to identify suppressors of nekl molting defects, we identified several components and regulators of AP2, the major clathrin adapter complex acting at the plasma membrane. Strikingly, reduced AP2 activity rescues both nekl mutant molting defects as well as associated trafficking phenotypes, whereas increased levels of active AP2 exacerbate nekl defects. Moreover, in a unique example of mutual suppression, NEKL inhibition alleviates defects associated with reduced AP2 activity, attesting to the tight link between NEKL and AP2 functions. We also show that NEKLs are required for the clustering and internalization of membrane cargo required for molting. Notably, we find that human NEKs can rescue molting and trafficking defects in nekl mutant worms, suggesting that the control of intracellular trafficking is an evolutionarily conserved function of NEK family kinases. In order to function properly, cells must continually import materials from the outside. This process, termed endocytosis, is necessary for the uptake of nutrients and for interpreting signals coming from the external environment or from within the body. These signals are critical during animal development but also affect many types of cell behaviors throughout life. In our current work, we show that several highly conserved proteins in the nematode Caenorhabditis elegans, NEKL-2 and NEKL-3, regulate endocytosis. The human counterparts of NEKL-2 and NEKL-3 have been implicated in cardiovascular and renal diseases as well as many types of cancers. However, their specific functions within cells is incompletely understood and very little is known about their role in endocytosis or how this role might impact disease processes. Here we use several complementary approaches to characterize the specific functions of C. elegans NEKL-2 and NEKL-3 in endocytosis and show that their human counterparts likely have very similar functions. This work paves the way to a better understanding of fundamental biological processes and to determining the cellular functions of proteins connected to human diseases.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Yu Wang
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Phil Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Barth D. Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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19
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Bennett HW, Gustavsson AK, Bayas CA, Petrov PN, Mooney N, Moerner WE, Jackson PK. Novel fibrillar structure in the inversin compartment of primary cilia revealed by 3D single-molecule superresolution microscopy. Mol Biol Cell 2020; 31:619-639. [PMID: 31895004 PMCID: PMC7202064 DOI: 10.1091/mbc.e19-09-0499] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary cilia in many cell types contain a periaxonemal subcompartment called the inversin compartment. Four proteins have been found to assemble within the inversin compartment: INVS, ANKS6, NEK8, and NPHP3. The function of the inversin compartment is unknown, but it appears to be critical for normal development, including left–right asymmetry and renal tissue homeostasis. Here we combine superresolution imaging of human RPE1 cells, a classic model for studying primary cilia in vitro, with a genetic dissection of the protein–protein binding relationships that organize compartment assembly to develop a new structural model. We observe that INVS is the core structural determinant of a compartment composed of novel fibril-like substructures, which we identify here by three-dimensional single-molecule superresolution imaging. We find that NEK8 and ANKS6 depend on INVS for localization to these fibrillar assemblies and that ANKS6-NEK8 density within the compartment is regulated by NEK8. Together, NEK8 and ANKS6 are required downstream of INVS to localize and concentrate NPHP3 within the compartment. In the absence of these upstream components, NPHP3 is redistributed within cilia. These results provide a more detailed structure for the inversin compartment and introduce a new example of a membraneless compartment organized by protein–protein interactions.
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Affiliation(s)
- Henrietta W Bennett
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Anna-Karin Gustavsson
- Department of Chemistry, Stanford University, Stanford, CA 94305.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE 17177, Sweden
| | - Camille A Bayas
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nancie Mooney
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
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20
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Rothé B, Gagnieux C, Leal-Esteban LC, Constam DB. Role of the RNA-binding protein Bicaudal-C1 and interacting factors in cystic kidney diseases. Cell Signal 2019; 68:109499. [PMID: 31838063 DOI: 10.1016/j.cellsig.2019.109499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/03/2023]
Abstract
Polycystic kidneys frequently associate with mutations in individual components of cilia, basal bodies or centriolar satellites that perturb complex protein networks. In this review, we focus on the RNA-binding protein Bicaudal-C1 (BICC1) which was found mutated in renal cystic dysplasia, and on its interactions with the ankyrin repeat and sterile α motif (SAM)-containing proteins ANKS3 and ANKS6 and associated kinases and their partially overlapping ciliopathy phenotypes. After reviewing BICC1 homologs in model organisms and their functions in mRNA and cell metabolism during development and in renal tubules, we discuss recent insights from cell-based assays and from structure analysis of the SAM domains, and how SAM domain oligomerization might influence multivalent higher order complexes that are implicated in ciliary signal transduction.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Céline Gagnieux
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Lucia Carolina Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel B Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland.
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21
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Zhu C, Guo Z, Zhang Y, Liu M, Chen B, Cao K, Wu Y, Yang M, Yin W, Zhao H, Tai H, Ou Y, Yu X, Liu C, Li S, Su B, Feng Y, Huang S. Aplnra/b Sequentially Regulate Organ Left-Right Patterning via Distinct Mechanisms. Int J Biol Sci 2019; 15:1225-1239. [PMID: 31223282 PMCID: PMC6567806 DOI: 10.7150/ijbs.30100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/12/2019] [Indexed: 12/16/2022] Open
Abstract
The G protein-coupled receptor APJ/Aplnr has been widely reported to be involved in heart and vascular development and disease, but whether it contributes to organ left-right patterning is largely unknown. Here, we show that in zebrafish, aplnra/b coordinates organ LR patterning in an apela/apln ligand-dependent manner using distinct mechanisms at different stages. During gastrulation and early somitogenesis, aplnra/b loss of function results in heart and liver LR asymmetry defects, accompanied by disturbed KV/cilia morphogenesis and disrupted left-sided Nodal/spaw expression in the LPM. In this process, only aplnra loss of function results in KV/cilia morphogenesis defect. In addition, only apela works as the early endogenous ligand to regulate KV morphogenesis, which then contributes to left-sided Nodal/spaw expression and subsequent organ LR patterning. The aplnra-apela cascade regulates KV morphogenesis by enhancing the expression of foxj1a, but not fgf8 or dnh9, during KV development. At the late somite stage, both aplnra and aplnrb contribute to the expression of lft1 in the trunk midline but do not regulate KV formation, and this role is possibly mediated by both endogenous ligands, apela and apln. In conclusion, our study is the first to identify a role for aplnra/b and their endogenous ligands apela/apln in LR patterning, and it clarifies the distinct roles of aplnra-apela and aplnra/b-apela/apln in orchestrating organ LR patterning.
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Affiliation(s)
- Chengke Zhu
- College of Animal Science in Rongchang Campus, Southwest University, Key Laboratary of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 402460, China.,UoE Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Zhenghua Guo
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, 400014, Chongqing, China
| | - Yu Zhang
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Min Liu
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Bingyu Chen
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Kang Cao
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Yongmei Wu
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Min Yang
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Wenqing Yin
- Renal Division, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts. USA
| | - Haixia Zhao
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Haoran Tai
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Yu Ou
- School of Public Health, Chengdu Medical College , Chengdu 610500, China
| | - Xiaoping Yu
- School of Public Health, Chengdu Medical College , Chengdu 610500, China
| | - Chi Liu
- Department of Nephrology, Institute of Nephrology of Chongqing and Kidney Center of PLA, Xinqiao Hospital, Third Military Medical University, Chongqing, PR China
| | - Shurong Li
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Bingyin Su
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
| | - Yi Feng
- UoE Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Sizhou Huang
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu 610500, China
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Hoff S, Epting D, Falk N, Schroda S, Braun DA, Halbritter J, Hildebrandt F, Kramer-Zucker A, Bergmann C, Walz G, Lienkamp SS. The nucleoside-diphosphate kinase NME3 associates with nephronophthisis proteins and is required for ciliary function during renal development. J Biol Chem 2018; 293:15243-15255. [PMID: 30111592 PMCID: PMC6166740 DOI: 10.1074/jbc.ra117.000847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 08/07/2018] [Indexed: 01/12/2023] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive renal disease leading to kidney failure in children and young adults. The protein products of the corresponding genes (NPHPs) are localized in primary cilia or their appendages. Only about 70% of affected individuals have a mutation in one of 100 renal ciliopathy genes, and no unifying pathogenic mechanism has been identified. Recently, some NPHPs, including NIMA-related kinase 8 (NEK8) and centrosomal protein 164 (CEP164), have been found to act in the DNA-damage response pathway and to contribute to genome stability. Here, we show that NME/NM23 nucleoside-diphosphate kinase 3 (NME3) that has recently been found to facilitate DNA-repair mechanisms binds to several NPHPs, including NEK8, CEP164, and ankyrin repeat and sterile α motif domain-containing 6 (ANKS6). Depletion of nme3 in zebrafish and Xenopus resulted in typical ciliopathy-associated phenotypes, such as renal malformations and left-right asymmetry defects. We further found that endogenous NME3 localizes to the basal body and that it associates also with centrosomal proteins, such as NEK6, which regulates cell cycle arrest after DNA damage. The ciliopathy-typical manifestations of NME3 depletion in two vertebrate in vivo models, the biochemical association of NME3 with validated NPHPs, and its localization to the basal body reveal a role for NME3 in ciliary function. We conclude that mutations in the NME3 gene may aggravate the ciliopathy phenotypes observed in humans.
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Affiliation(s)
- Sylvia Hoff
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Daniel Epting
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Nathalie Falk
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sophie Schroda
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Jan Halbritter
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Albrecht Kramer-Zucker
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Carsten Bergmann
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany, and
| | - Gerd Walz
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signaling Studies (BIOSS), 79104 Freiburg, Germany
| | - Soeren S Lienkamp
- From the Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany,
- Center for Biological Signaling Studies (BIOSS), 79104 Freiburg, Germany
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23
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Ta-Shma A, Hjeij R, Perles Z, Dougherty GW, Abu Zahira I, Letteboer SJF, Antony D, Darwish A, Mans DA, Spittler S, Edelbusch C, Cindrić S, Nöthe-Menchen T, Olbrich H, Stuhlmann F, Aprea I, Pennekamp P, Loges NT, Breuer O, Shaag A, Rein AJJT, Gulec EY, Gezdirici A, Abitbul R, Elias N, Amirav I, Schmidts M, Roepman R, Elpeleg O, Omran H. Homozygous loss-of-function mutations in MNS1 cause laterality defects and likely male infertility. PLoS Genet 2018; 14:e1007602. [PMID: 30148830 PMCID: PMC6128653 DOI: 10.1371/journal.pgen.1007602] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/07/2018] [Accepted: 08/02/2018] [Indexed: 12/22/2022] Open
Abstract
The clinical spectrum of ciliopathies affecting motile cilia spans impaired mucociliary clearance in the respiratory system, laterality defects including heart malformations, infertility and hydrocephalus. Using linkage analysis and whole exome sequencing, we identified two recessive loss-of-function MNS1 mutations in five individuals from four consanguineous families: 1) a homozygous nonsense mutation p.Arg242* in four males with laterality defects and infertility and 2) a homozygous nonsense mutation p.Gln203* in one female with laterality defects and recurrent respiratory infections additionally carrying homozygous mutations in DNAH5. Consistent with the laterality defects observed in these individuals, we found Mns1 to be expressed in mouse embryonic ventral node. Immunofluorescence analysis further revealed that MNS1 localizes to the axonemes of respiratory cilia as well as sperm flagella in human. In-depth ultrastructural analyses confirmed a subtle outer dynein arm (ODA) defect in the axonemes of respiratory epithelial cells resembling findings reported in Mns1-deficient mice. Ultrastructural analyses in the female carrying combined mutations in MNS1 and DNAH5 indicated a role for MNS1 in the process of ODA docking (ODA-DC) in the distal respiratory axonemes. Furthermore, co-immunoprecipitation and yeast two hybrid analyses demonstrated that MNS1 dimerizes and interacts with the ODA docking complex component CCDC114. Overall, we demonstrate that MNS1 deficiency in humans causes laterality defects (situs inversus) and likely male infertility and that MNS1 plays a role in the ODA-DC assembly.
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Affiliation(s)
- Asaf Ta-Shma
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Rim Hjeij
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Zeev Perles
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Gerard W. Dougherty
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Ibrahim Abu Zahira
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Stef J. F. Letteboer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Dinu Antony
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Alaa Darwish
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Dorus A. Mans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Sabrina Spittler
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Christine Edelbusch
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Sandra Cindrić
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Tabea Nöthe-Menchen
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Heike Olbrich
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Friederike Stuhlmann
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Isabella Aprea
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Petra Pennekamp
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Niki T. Loges
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Oded Breuer
- Pediatric Pulmonology Unit, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avraham Shaag
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Azaria J. J. T. Rein
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Elif Yilmaz Gulec
- University of Health Sciences, Kanuni Sultan Suleyman, Training and Research Hospital, Department of Medical Genetics, Istanbul, Turkey
| | - Alper Gezdirici
- University of Health Sciences, Kanuni Sultan Suleyman, Training and Research Hospital, Department of Medical Genetics, Istanbul, Turkey
| | - Revital Abitbul
- Pediatric Department, Ziv Medical Center, Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Nael Elias
- Saint Vincent Hospital, Nazareth, Faculty of Medicine, Bar Ilan University, Israel
| | - Israel Amirav
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
- Pediatric Pulmonology Unit, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Miriam Schmidts
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
- * E-mail:
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Abstract
TGF-β family ligands function in inducing and patterning many tissues of the early vertebrate embryonic body plan. Nodal signaling is essential for the specification of mesendodermal tissues and the concurrent cellular movements of gastrulation. Bone morphogenetic protein (BMP) signaling patterns tissues along the dorsal-ventral axis and simultaneously directs the cell movements of convergence and extension. After gastrulation, a second wave of Nodal signaling breaks the symmetry between the left and right sides of the embryo. During these processes, elaborate regulatory feedback between TGF-β ligands and their antagonists direct the proper specification and patterning of embryonic tissues. In this review, we summarize the current knowledge of the function and regulation of TGF-β family signaling in these processes. Although we cover principles that are involved in the development of all vertebrate embryos, we focus specifically on three popular model organisms: the mouse Mus musculus, the African clawed frog of the genus Xenopus, and the zebrafish Danio rerio, highlighting the similarities and differences between these species.
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Affiliation(s)
- Joseph Zinski
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Benjamin Tajer
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Mary C Mullins
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
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25
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Nakajima Y, Kiyonari H, Mukumoto Y, Yokoyama T. The Inv compartment of renal cilia is an intraciliary signal-activating center to phosphorylate ANKS6. Kidney Int 2018; 93:1108-1117. [DOI: 10.1016/j.kint.2017.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 10/26/2017] [Accepted: 11/09/2017] [Indexed: 12/28/2022]
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26
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Lažetić V, Joseph BB, Bernazzani SM, Fay DS. Actin organization and endocytic trafficking are controlled by a network linking NIMA-related kinases to the CDC-42-SID-3/ACK1 pathway. PLoS Genet 2018; 14:e1007313. [PMID: 29608564 PMCID: PMC5897031 DOI: 10.1371/journal.pgen.1007313] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 04/12/2018] [Accepted: 03/19/2018] [Indexed: 01/07/2023] Open
Abstract
Molting is an essential process in the nematode Caenorhabditis elegans during which the epidermal apical extracellular matrix, termed the cuticle, is detached and replaced at each larval stage. The conserved NIMA-related kinases NEKL-2/NEK8/NEK9 and NEKL-3/NEK6/NEK7, together with their ankyrin repeat partners, MLT-2/ANKS6, MLT-3/ANKS3, and MLT-4/INVS, are essential for normal molting. In nekl and mlt mutants, the old larval cuticle fails to be completely shed, leading to entrapment and growth arrest. To better understand the molecular and cellular functions of NEKLs during molting, we isolated genetic suppressors of nekl molting-defective mutants. Using two independent approaches, we identified CDC-42, a conserved Rho-family GTPase, and its effector protein kinase, SID-3/ACK1. Notably, CDC42 and ACK1 regulate actin dynamics in mammals, and actin reorganization within the worm epidermis has been proposed to be important for the molting process. Inhibition of NEKL-MLT activities led to strong defects in the distribution of actin and failure to form molting-specific apical actin bundles. Importantly, this phenotype was reverted following cdc-42 or sid-3 inhibition. In addition, repression of CDC-42 or SID-3 also suppressed nekl-associated defects in trafficking, a process that requires actin assembly and disassembly. Expression analyses indicated that components of the NEKL-MLT network colocalize with both actin and CDC-42 in specific regions of the epidermis. Moreover, NEKL-MLT components were required for the normal subcellular localization of CDC-42 in the epidermis as well as wild-type levels of CDC-42 activation. Taken together, our findings indicate that the NEKL-MLT network regulates actin through CDC-42 and its effector SID-3. Interestingly, we also observed that downregulation of CDC-42 in a wild-type background leads to molting defects, suggesting that there is a fine balance between NEKL-MLT and CDC-42-SID-3 activities in the epidermis.
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Affiliation(s)
- Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY
| | - Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY
| | - Sarina M. Bernazzani
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY
- * E-mail:
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27
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Petersen MB, Gonçalves CA, Kim YH, Grapin-Botton A. Recapitulating and Deciphering Human Pancreas Development From Human Pluripotent Stem Cells in a Dish. Curr Top Dev Biol 2018; 129:143-190. [DOI: 10.1016/bs.ctdb.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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28
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Catana A, Apostu AP. The determination factors of left-right asymmetry disorders- a short review. ACTA ACUST UNITED AC 2017; 90:139-146. [PMID: 28559696 PMCID: PMC5433564 DOI: 10.15386/cjmed-701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/02/2016] [Accepted: 11/23/2016] [Indexed: 12/17/2022]
Abstract
Laterality defects in humans, situs inversus and heterotaxy, are rare disorders, with an incidence of 1:8000 to 1:10 000 in the general population, and a multifactorial etiology. It has been proved that 1.44/10 000 of all cardiac problems are associated with malformations of left-right asymmetry and heterotaxy accounts for 3% of all congenital heart defects. It is considered that defects of situs appear due to genetic and environmental factors. Also, there is evidence that the ciliopathies (defects of structure or function) are involved in development abnormalities. Over 100 genes have been reported to be involved in left-right patterning in model organisms, but only a few are likely to candidate for left-right asymmetry defects in humans. Left-right asymmetry disorders are genetically heterogeneous and have variable manifestations (from asymptomatic to serious clinical problems). The discovery of the right mechanism of left-right development will help explain the clinical complexity and may contribute to a therapy of these disorders.
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Affiliation(s)
- Andreea Catana
- Genetics Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adina Patricia Apostu
- Genetics Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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29
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Mizuno K, Sloboda RD. Protein arginine methyltransferases interact with intraflagellar transport particles and change location during flagellar growth and resorption. Mol Biol Cell 2017; 28:1208-1222. [PMID: 28298486 PMCID: PMC5415017 DOI: 10.1091/mbc.e16-11-0774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/03/2017] [Accepted: 03/08/2017] [Indexed: 01/09/2023] Open
Abstract
Protein arginine methyl transferases are located at specific sites in the flagellum. They change location during changes in flagellar dynamics (i.e., resorption and regeneration) via interaction with intraflagellar transport trains. Changes in protein by posttranslational modifications comprise an important mechanism for the control of many cellular processes. Several flagellar proteins are methylated on arginine residues during flagellar resorption; however, the function is not understood. To learn more about the role of protein methylation during flagellar dynamics, we focused on protein arginine methyltransferases (PRMTs) 1, 3, 5, and 10. These PRMTs localize to the tip of flagella and in a punctate pattern along the length, very similar, but not identical, to that of intraflagellar transport (IFT) components. In addition, we found that PRMT 1 and 3 are also highly enriched at the base of the flagella, and the basal localization of these PRMTs changes during flagellar regeneration and resorption. Proteins with methyl arginine residues are also enriched at the tip and base of flagella, and their localization also changes during flagellar assembly and disassembly. PRMTs are lost from the flagella of fla10-1 cells, which carry a temperature-sensitive mutation in the anterograde motor for IFT. The data define the distribution of specific PRMTs and their target proteins in flagella and demonstrate that PRMTs are cargo for translocation within flagella by the process of IFT.
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Affiliation(s)
- Katsutoshi Mizuno
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Roger D Sloboda
- Marine Biological Laboratory, Woods Hole, MA 02543 .,Marine Biological Laboratory, Woods Hole, MA 02543
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30
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Lažetić V, Fay DS. Conserved Ankyrin Repeat Proteins and Their NIMA Kinase Partners Regulate Extracellular Matrix Remodeling and Intracellular Trafficking in Caenorhabditis elegans. Genetics 2017; 205:273-293. [PMID: 27799278 PMCID: PMC5223508 DOI: 10.1534/genetics.116.194464] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/28/2016] [Indexed: 12/27/2022] Open
Abstract
Molting is an essential developmental process in nematodes during which the epidermal apical extracellular matrix, the cuticle, is remodeled to accommodate further growth. Using genetic approaches, we identified a requirement for three conserved ankyrin repeat-rich proteins, MLT-2/ANKS6, MLT-3/ANKS3, and MLT-4/INVS, in Caenorhabditis elegans molting. Loss of mlt function resulted in severe defects in the ability of larvae to shed old cuticle and led to developmental arrest. Genetic analyses demonstrated that MLT proteins functionally cooperate with the conserved NIMA kinase family members NEKL-2/NEK8 and NEKL-3/NEK6/NEK7 to promote cuticle shedding. MLT and NEKL proteins were specifically required within the hyp7 epidermal syncytium, and fluorescently tagged mlt and nekl alleles were expressed in puncta within this tissue. Expression studies further showed that NEKL-2-MLT-2-MLT-4 and NEKL-3-MLT-3 colocalize within largely distinct assemblies of apical foci. MLT-2 and MLT-4 were required for the normal accumulation of NEKL-2 at the hyp7-seam cell boundary, and loss of mlt-2 caused abnormal nuclear accumulation of NEKL-2 Correspondingly, MLT-3, which bound directly to NEKL-3, prevented NEKL-3 nuclear localization, supporting the model that MLT proteins may serve as molecular scaffolds for NEKL kinases. Our studies additionally showed that the NEKL-MLT network regulates early steps in clathrin-mediated endocytosis at the apical surface of hyp7, which may in part account for molting defects observed in nekl and mlt mutants. This study has thus identified a conserved NEKL-MLT protein network that regulates remodeling of the apical extracellular matrix and intracellular trafficking, functions that may be conserved across species.
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Affiliation(s)
- Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming 82071
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming 82071
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31
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Abstract
Primary cilia are small, antenna-like structures that detect mechanical and chemical cues and transduce extracellular signals. While mammalian primary cilia were first reported in the late 1800s, scientific interest in these sensory organelles has burgeoned since the beginning of the twenty-first century with recognition that primary cilia are essential to human health. Among the most common clinical manifestations of ciliary dysfunction are renal cysts. The molecular mechanisms underlying renal cystogenesis are complex, involving multiple aberrant cellular processes and signaling pathways, while initiating molecular events remain undefined. Autosomal Dominant Polycystic Kidney Disease is the most common renal cystic disease, caused by disruption of polycystin-1 and polycystin-2 transmembrane proteins, which evidence suggests must localize to primary cilia for proper function. To understand how the absence of these proteins in primary cilia may be remediated, we review intracellular trafficking of polycystins to the primary cilium. We also examine the controversial mechanisms by which primary cilia transduce flow-mediated mechanical stress into intracellular calcium. Further, to better understand ciliary function in the kidney, we highlight the LKB1/AMPK, Wnt, and Hedgehog developmental signaling pathways mediated by primary cilia and misregulated in renal cystic disease.
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32
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Abeyta A, Castella M, Jacquemont C, Taniguchi T. NEK8 regulates DNA damage-induced RAD51 foci formation and replication fork protection. Cell Cycle 2016; 16:335-347. [PMID: 27892797 PMCID: PMC5324754 DOI: 10.1080/15384101.2016.1259038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Proteins essential for homologous recombination play a pivotal role in the repair of DNA double strand breaks, DNA inter-strand crosslinks and replication fork stability. Defects in homologous recombination also play a critical role in the development of cancer and the sensitivity of these cancers to chemotherapy. RAD51, an essential factor for homologous recombination and replication fork protection, accumulates and forms immunocytochemically detectable nuclear foci at sites of DNA damage. To identify kinases that may regulate RAD51 localization to sites of DNA damage, we performed a human kinome siRNA library screen, using DNA damage-induced RAD51 foci formation as readout. We found that NEK8, a NIMA family kinase member, is required for efficient DNA damage-induced RAD51 foci formation. Interestingly, knockout of Nek8 in murine embryonic fibroblasts led to cellular sensitivity to the replication inhibitor, hydroxyurea, and inhibition of the ATR kinase. Furthermore, NEK8 was required for proper replication fork protection following replication stall with hydroxyurea. Loading of RAD51 to chromatin was decreased in NEK8-depleted cells and Nek8-knockout cells. Single-molecule DNA fiber analyses revealed that nascent DNA tracts were degraded in the absence of NEK8 following treatment with hydroxyurea. Consistent with this, Nek8-knockout cells showed increased chromosome breaks following treatment with hydroxyurea. Thus, NEK8 plays a critical role in replication fork stability through its regulation of the DNA repair and replication fork protection protein RAD51.
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Affiliation(s)
- Antonio Abeyta
- a Divisions of Human Biology and Public Health Sciences , Fred Hutchinson Cancer Research Center , Seattle , WA , USA.,b Molecular & Cellular Biology Graduate Program , University of Washington , Seattle , WA , USA
| | - Maria Castella
- a Divisions of Human Biology and Public Health Sciences , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Celine Jacquemont
- a Divisions of Human Biology and Public Health Sciences , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Toshiyasu Taniguchi
- a Divisions of Human Biology and Public Health Sciences , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
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Gallegos LL, Ng MR, Sowa ME, Selfors LM, White A, Zervantonakis IK, Singh P, Dhakal S, Harper JW, Brugge JS. A protein interaction map for cell-cell adhesion regulators identifies DUSP23 as a novel phosphatase for β-catenin. Sci Rep 2016; 6:27114. [PMID: 27255161 PMCID: PMC4891818 DOI: 10.1038/srep27114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 05/10/2016] [Indexed: 01/13/2023] Open
Abstract
Cell-cell adhesion is central to morphogenesis and maintenance of epithelial cell state. We previously identified 27 candidate cell-cell adhesion regulatory proteins (CCARPs) whose down-regulation disrupts epithelial cell-cell adhesion during collective migration. Using a protein interaction mapping strategy, we found that 18 CCARPs link to core components of adherens junctions or desmosomes. We further mapped linkages between the CCARPs and other known cell-cell adhesion proteins, including hits from recent screens uncovering novel components of E-cadherin adhesions. Mechanistic studies of one novel CCARP which links to multiple cell-cell adhesion proteins, the phosphatase DUSP23, revealed that it promotes dephosphorylation of β-catenin at Tyr 142 and enhances the interaction between α- and β-catenin. DUSP23 knockdown specifically diminished adhesion to E-cadherin without altering adhesion to fibronectin matrix proteins. Furthermore, DUSP23 knockdown produced “zipper-like” cell-cell adhesions, caused defects in transmission of polarization cues, and reduced coordination during collective migration. Thus, this study identifies multiple novel connections between proteins that regulate cell-cell interactions and provides evidence for a previously unrecognized role for DUSP23 in regulating E-cadherin adherens junctions through promoting the dephosphorylation of β-catenin.
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Affiliation(s)
| | - Mei Rosa Ng
- Cell Biology, Harvard Med School, Boston, MA, USA
| | | | | | - Anne White
- Cell Biology, Harvard Med School, Boston, MA, USA
| | | | - Pragya Singh
- Cell Biology, Harvard Med School, Boston, MA, USA
| | - Sabin Dhakal
- Cell Biology, Harvard Med School, Boston, MA, USA
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High-resolution genetic localization of a modifying locus affecting disease severity in the juvenile cystic kidneys (jck) mouse model of polycystic kidney disease. Mamm Genome 2016; 27:191-9. [PMID: 27114383 DOI: 10.1007/s00335-016-9633-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/07/2016] [Indexed: 12/31/2022]
Abstract
We have previously demonstrated that a locus on proximal Chr 4 modifies disease severity in the juvenile cystic kidney (jck) mouse, a model of polycystic kidney disease (PKD) that carries a mutation of the Nek8 serine-threonine kinase. In this study, we used QTL analysis of independently constructed B6.D2 congenic lines to confirm this and showed that this locus has a highly significant effect. We constructed sub-congenic lines to more specifically localize the modifier and have determined it resides in a 3.2 Mb interval containing 28 genes. These include Invs and Anks6, which are both excellent candidates for the modifier as mutations in these genes result in PKD and both genes are known to genetically and physically interact with Nek8. However, examination of strain-specific DNA sequence and kidney expression did not reveal clear differences that might implicate either gene as a modifier of PKD severity. The fact that our high-resolution analysis did not yield an unambiguous result highlights the challenge of establishing the causality of strain-specific variants as genetic modifiers, and suggests that alternative strategies be considered.
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Husson H, Moreno S, Smith LA, Smith MM, Russo RJ, Pitstick R, Sergeev M, Ledbetter SR, Bukanov NO, Lane M, Zhang K, Billot K, Carlson G, Shah J, Meijer L, Beier DR, Ibraghimov-Beskrovnaya O. Reduction of ciliary length through pharmacologic or genetic inhibition of CDK5 attenuates polycystic kidney disease in a model of nephronophthisis. Hum Mol Genet 2016; 25:2245-2255. [PMID: 27053712 PMCID: PMC5081056 DOI: 10.1093/hmg/ddw093] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/17/2016] [Indexed: 02/06/2023] Open
Abstract
Polycystic kidney diseases (PKDs) comprise a subgroup of ciliopathies characterized by the formation of fluid-filled kidney cysts and progression to end-stage renal disease. A mechanistic understanding of cystogenesis is crucial for the development of viable therapeutic options. Here, we identify CDK5, a kinase active in post mitotic cells, as a new and important mediator of PKD progression. We show that long-lasting attenuation of PKD in the juvenile cystic kidneys (jck) mouse model of nephronophthisis by pharmacological inhibition of CDK5 using either R-roscovitine or S-CR8 is accompanied by sustained shortening of cilia and a more normal epithelial phenotype, suggesting this treatment results in a reprogramming of cellular differentiation. Also, a knock down of Cdk5 in jck cells using small interfering RNA results in significant shortening of ciliary length, similar to what we observed with R-roscovitine. Finally, conditional inactivation of Cdk5 in the jck mice significantly attenuates cystic disease progression and is associated with shortening of ciliary length as well as restoration of cellular differentiation. Our results suggest that CDK5 may regulate ciliary length by affecting tubulin dynamics via its substrate collapsin response mediator protein 2. Taken together, our data support therapeutic approaches aimed at restoration of ciliogenesis and cellular differentiation as a promising strategy for the treatment of renal cystic diseases.
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Affiliation(s)
- Hervé Husson
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Sarah Moreno
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Laurie A Smith
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Mandy M Smith
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Ryan J Russo
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Rose Pitstick
- McLaughlin Research Institute, 1520 23rd Street South, Great Falls, Montana 59405, USA
| | - Mikhail Sergeev
- Harvard Institutes of Medicine, 4 Blackfan Circle HIM568, Boston, MA 02115, USA
| | - Steven R Ledbetter
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Nikolay O Bukanov
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Monica Lane
- Department of Biological Mass Spectrometry & Biomarker Research, Sanofi-Genzyme R&D Center, 1 Mountain Road, Framingham, MA 01701, USA
| | - Kate Zhang
- Department of Biological Mass Spectrometry & Biomarker Research, Sanofi-Genzyme R&D Center, 1 Mountain Road, Framingham, MA 01701, USA
| | - Katy Billot
- ManRos Therapeutics, Hotel de Recherche-Centre de Perharidy, 29680 Roscoff, France
| | - George Carlson
- McLaughlin Research Institute, 1520 23rd Street South, Great Falls, Montana 59405, USA
| | - Jagesh Shah
- Harvard Institutes of Medicine, 4 Blackfan Circle HIM568, Boston, MA 02115, USA
| | - Laurent Meijer
- ManRos Therapeutics, Hotel de Recherche-Centre de Perharidy, 29680 Roscoff, France
| | - David R Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA 98101, USA
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Grampa V, Delous M, Zaidan M, Odye G, Thomas S, Elkhartoufi N, Filhol E, Niel O, Silbermann F, Lebreton C, Collardeau-Frachon S, Rouvet I, Alessandri JL, Devisme L, Dieux-Coeslier A, Cordier MP, Capri Y, Khung-Savatovsky S, Sigaudy S, Salomon R, Antignac C, Gubler MC, Benmerah A, Terzi F, Attié-Bitach T, Jeanpierre C, Saunier S. Novel NEK8 Mutations Cause Severe Syndromic Renal Cystic Dysplasia through YAP Dysregulation. PLoS Genet 2016; 12:e1005894. [PMID: 26967905 PMCID: PMC4788435 DOI: 10.1371/journal.pgen.1005894] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/02/2016] [Indexed: 01/01/2023] Open
Abstract
Ciliopathies are a group of genetic multi-systemic disorders related to dysfunction of the primary cilium, a sensory organelle present at the cell surface that regulates key signaling pathways during development and tissue homeostasis. In order to identify novel genes whose mutations would cause severe developmental ciliopathies, >500 patients/fetuses were analyzed by a targeted high throughput sequencing approach allowing exome sequencing of >1200 ciliary genes. NEK8/NPHP9 mutations were identified in five cases with severe overlapping phenotypes including renal cystic dysplasia/hypodysplasia, situs inversus, cardiopathy with hypertrophic septum and bile duct paucity. These cases highlight a genotype-phenotype correlation, with missense and nonsense mutations associated with hypodysplasia and enlarged cystic organs, respectively. Functional analyses of NEK8 mutations in patient fibroblasts and mIMCD3 cells showed that these mutations differentially affect ciliogenesis, proliferation/apoptosis/DNA damage response, as well as epithelial morphogenesis. Notably, missense mutations exacerbated some of the defects due to NEK8 loss of function, highlighting their likely gain-of-function effect. We also showed that NEK8 missense and loss-of-function mutations differentially affect the regulation of the main Hippo signaling effector, YAP, as well as the expression of its target genes in patient fibroblasts and renal cells. YAP imbalance was also observed in enlarged spheroids of Nek8-invalidated renal epithelial cells grown in 3D culture, as well as in cystic kidneys of Jck mice. Moreover, co-injection of nek8 MO with WT or mutated NEK8-GFP RNA in zebrafish embryos led to shortened dorsally curved body axis, similar to embryos injected with human YAP RNA. Finally, treatment with Verteporfin, an inhibitor of YAP transcriptional activity, partially rescued the 3D spheroid defects of Nek8-invalidated cells and the abnormalities of NEK8-overexpressing zebrafish embryos. Altogether, our study demonstrates that NEK8 human mutations cause major organ developmental defects due to altered ciliogenesis and cell differentiation/proliferation through deregulation of the Hippo pathway. Genes mutated in ciliopathies encode proteins with various localizations and functions at the primary cilium. Here we report novel NEK8 mutations in patients with renal cystic hypodysplasia and associated ciliopathy defects. NEK8 belongs to a protein complex defining the Inversin compartment of the cilium. It is also a negative regulator of the Hippo signaling pathway that controls organ growth. We report genotype-phenotype correlation in the patients. We functionally demonstrate that the two types of mutations (missense versus nonsense) differentially affect ciliogenesis, cell apoptosis and epithelialisation. We also show that all the mutations lead to dysregulation of the Hippo pathway through nuclear YAP imbalance but that the nature of this imbalance is different according to the type of mutation. We confirm alteration of the Hippo pathway associated with Nek8 mutation in vivo in Jck mice. Remarkably, we show that morphogenesis defects observed in Nek8 knockdown epithelial cells or zebrafish embryos are rescued by Verteporfin, a specific inhibitor of YAP transcriptional activity, demonstrating the causative role of YAP dysregulation in the occurrence of these defects. Altogether, this study links NEK8 mutations to dysregulation of the Hippo pathway and provide molecular clues to understand the variability of the multiorgan defects in the patients.
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Affiliation(s)
- Valentina Grampa
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marion Delous
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Mohamad Zaidan
- INSERM U1151, CNRS UMR8253, Paris Descartes—Sorbonne Paris Cité University, Necker-Enfants Malades Institute, Mechanisms and Therapeutic Strategies of Chronic Kidney Diseases, Necker Hospital, Paris, France
| | - Gweltas Odye
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Sophie Thomas
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris, France
| | - Nadia Elkhartoufi
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris, France
- Department of Genetics, AP-HP, Necker Hospital, Paris, France
| | - Emilie Filhol
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Olivier Niel
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatric Nephrology, AP-HP, Robert Debré Hospital, Paris, France
| | - Flora Silbermann
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Corinne Lebreton
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Intestinal Immunity, Paris, France
| | | | - Isabelle Rouvet
- Cellular Biotechnology Department and Biobank, Hospices Civils de Lyon, CHU de Lyon, Lyon, France
| | | | - Louise Devisme
- Anatomopathological Department, CHRU Lille, University Hospital, Lille, France
| | | | - Marie-Pierre Cordier
- Department of Genetics, Femme Mère-Enfant Hospital, University of Lyon 1, Bron, France
| | - Yline Capri
- Department of Genetics, CHU Robert-Debré, Paris, France
| | | | - Sabine Sigaudy
- Multidisciplinary Department of Prenatal Diagnosis, La Timone Children’s Hospital, Marseille, France
| | - Rémi Salomon
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatric Nephrology, AP-HP, Necker Hospital, Paris, France
| | - Corinne Antignac
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Department of Genetics, AP-HP, Necker Hospital, Paris, France
| | - Marie-Claire Gubler
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Alexandre Benmerah
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Fabiola Terzi
- INSERM U1151, CNRS UMR8253, Paris Descartes—Sorbonne Paris Cité University, Necker-Enfants Malades Institute, Mechanisms and Therapeutic Strategies of Chronic Kidney Diseases, Necker Hospital, Paris, France
| | - Tania Attié-Bitach
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- INSERM UMR1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris, France
- Department of Histology-Embryology and Cytogenetics, AP-HP, Necker Hospital, Paris, France
| | - Cécile Jeanpierre
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Sophie Saunier
- INSERM UMR1163, Laboratory of Inherited Kidney Diseases, Necker-Enfants Malades Hospital, Paris, France
- Paris Descartes—Sorbonne Paris Cité University, Imagine Institute, Paris, France
- * E-mail:
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Meng D, Pan J. A NIMA-related kinase, CNK4, regulates ciliary stability and length. Mol Biol Cell 2016; 27:838-47. [PMID: 26764095 PMCID: PMC4803309 DOI: 10.1091/mbc.e15-10-0707] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/07/2015] [Accepted: 01/04/2016] [Indexed: 02/02/2023] Open
Abstract
NIMA-related kinases (Nrks or Neks) have emerged as key regulators of ciliogenesis. In human, mutations in Nek1 and Nek8 cause cilia-related disorders. The ciliary functions of Nrks are mostly revealed by genetic studies; however, the underlying mechanisms are not well understood. Here we show that a Chlamydomonas Nrk, CNK4, regulates ciliary stability and length. CNK4 is localized to the basal body region and the flagella. The cnk4-null mutant exhibited long flagella, with formation of flagellar bulges. The flagella gradually became curled at the bulge formation site, leading to flagellar loss. Electron microscopy shows that the curled flagella involved curling and degeneration of axonemal microtubules. cnk4 mutation resulted in flagellar increases of IFT trains, as well as its accumulation at the flagellar bulges. IFT speeds were not affected, however, IFT trains frequently stalled, leading to reduced IFT frequencies. These data are consistent with a model in which CNK4 regulates microtubule dynamics and IFT to control flagellar stability and length.
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Affiliation(s)
- Dan Meng
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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38
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Ciliary subcompartments and cysto-proteins. Anat Sci Int 2015; 92:207-214. [DOI: 10.1007/s12565-015-0302-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/14/2015] [Indexed: 11/26/2022]
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Worley KE, Shieh D, Wan LQ. Inhibition of cell–cell adhesion impairs directional epithelial migration on micropatterned surfaces. Integr Biol (Camb) 2015; 7:580-90. [DOI: 10.1039/c5ib00073d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Kathryn E. Worley
- Department of Biomedical Engineering, Laboratory for Tissue Engineering and Morphogenesis, 2147 Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA. Web: http://www.rpi.edu/∼wanq; Fax: +1-518-276-3035; Tel: +1-518-276-2505
| | - David Shieh
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Leo Q. Wan
- Department of Biomedical Engineering, Laboratory for Tissue Engineering and Morphogenesis, 2147 Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA. Web: http://www.rpi.edu/∼wanq; Fax: +1-518-276-3035; Tel: +1-518-276-2505
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
- Center for Modeling, Simulation and Imaging in Medicine, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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Abstract
Humans and other vertebrates exhibit left-right (LR) asymmetric arrangement of the internal organs, and failure to establish normal LR asymmetry leads to internal laterality disorders, including situs inversus and heterotaxy. Situs inversus is complete mirror-imaged arrangement of the internal organs along LR axis, whereas heterotaxy is abnormal arrangement of the internal thoraco-abdominal organs across LR axis of the body, most of which are associated with complex cardiovascular malformations. Both disorders are genetically heterogeneous with reduced penetrance, presumably because of monogenic, polygenic or multifactorial causes. Research in genetics of LR asymmetry disorders has been extremely prolific over the past 17 years, and a series of loci and disease genes involved in situs inversus and heterotaxy have been described. The review highlights the classification, chromosomal abnormalities, pathogenic genes and the possible mechanism of human LR asymmetry disorders.
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Czarnecki PG, Gabriel GC, Manning DK, Sergeev M, Lemke K, Klena NT, Liu X, Chen Y, Li Y, San Agustin JT, Garnaas MK, Francis RJ, Tobita K, Goessling W, Pazour GJ, Lo CW, Beier DR, Shah JV. ANKS6 is the critical activator of NEK8 kinase in embryonic situs determination and organ patterning. Nat Commun 2015; 6:6023. [PMID: 25599650 PMCID: PMC4361001 DOI: 10.1038/ncomms7023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
The ciliary kinase NEK8 plays a critical role in situs determination and cystic kidney disease, yet its exact function remains unknown. In this study, we identify ANKS6 as a target and activator of NEK8. ANKS6 requires NEK8 for localizing to the ciliary inversin compartment (IC) and activates NEK8 by binding to its kinase domain. Here we demonstrate the functional importance of this interaction through the analysis of two novel mouse mutations, Anks6(Streaker) and Nek8(Roc). Both display heterotaxy, cardiopulmonary malformations and cystic kidneys, a syndrome also characteristic of mutations in Invs and Nphp3, the other known components of the IC. The Anks6(Strkr) mutation decreases ANKS6 interaction with NEK8, precluding NEK8 activation. The Nek8(Roc) mutation inactivates NEK8 kinase function while preserving ANKS6 localization to the IC. Together, these data reveal the crucial role of NEK8 kinase activation within the IC, promoting proper left-right patterning, cardiopulmonary development and renal morphogenesis.
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Affiliation(s)
- Peter G Czarnecki
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA [3] Renal Division, Beth Israel Deaconess Medical Center, Boston, Massachussetts 02215, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Danielle K Manning
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Mikhail Sergeev
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Kristi Lemke
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Nikolai T Klena
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Xiaoqin Liu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Yu Chen
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - You Li
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Jovenal T San Agustin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachussetts 01655, USA
| | - Maija K Garnaas
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Richard J Francis
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Kimimasa Tobita
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Wolfram Goessling
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachussetts 01655, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - David R Beier
- 1] Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA [2] Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington 98101, USA
| | - Jagesh V Shah
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
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Ding XF, Zhou J, Hu QY, Liu SC, Chen G. The tumor suppressor pVHL down-regulates never-in-mitosis A-related kinase 8 via hypoxia-inducible factors to maintain cilia in human renal cancer cells. J Biol Chem 2014; 290:1389-94. [PMID: 25451921 DOI: 10.1074/jbc.m114.589226] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
NEK8 (never in mitosis gene A (NIMA)-related kinase 8) is involved in cytoskeleton, cilia, and DNA damage response/repair. Abnormal expression and/or dysfunction of NEK8 are related to cancer development and progression. However, the mechanisms that regulate NEK8 are not well declared. We demonstrated here that pVHL may be involved in regulating NEK8. We found that CAK-I cells with wild-type vhl expressed a lower level of NEK8 than the cells loss of vhl, such as 786-O, 769-P, and A-498 cells. Moreover, pVHL overexpression down-regulated the NEK8 protein in 786-O cells, whereas pVHL knockdown up-regulated NEK8 in CAK-I cells. In addition, we found that the positive hypoxia response elements (HREs) are located in the promoter of the nek8 sequence and hypoxia could induce nek8 expression in different cell types. Consistent with this, down-regulation of hypoxia-inducible factors α (HIF-1α or HIF-2α) by isoform-specific siRNA reduced the ability of hypoxia inducing nek8 expression. In vivo, NEK8 and HIF-1α expression were increased in kidneys of rats subjected to an experimental hypoxia model of ischemia and reperfusion. Furthermore, NEK8 siRNA transfection significantly blocked pVHL-knockdown-induced cilia disassembling, through impairing the pVHL-knockdown-up-regulated NEK8 expression. These results support that nek8 may be a novel hypoxia-inducible gene. In conclusion, our findings show that nek8 may be a new HIF target gene and pVHL can down-regulate NEK8 via HIFs to maintain the primary cilia structure in human renal cancer cells.
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Affiliation(s)
| | - Jun Zhou
- From the School of Medicine, the Institute of Tumor, and
| | | | - Shuang-Chun Liu
- the Taizhou Municipal Hospital, Taizhou, Zhejiang, 318000 China
| | - Guang Chen
- From the School of Medicine, the Institute of Tumor, and the School of Pharmaceutical and Chemical Engineering, Taizhou University, Taizhou, Zhejiang 318000 and
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Abstract
Cilia are force-generating and -sensing organelles that serve as mechanical interfaces between the cell and the extracellular environment. Cilia are present in tissues that adaptively respond to mechanical loading and fluid flow, and defects in ciliary function can lead to diseases affecting these tissues. As might be expected for a mechanical interface, the formation of cilia is, itself, regulated by mechanical forces, and these links between mechanics and ciliary formation are providing new entry points for dissecting the regulatory pathways of ciliogenesis.
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Affiliation(s)
- Hiroaki Ishikawa
- Hiroaki Ishikawa and Wallace F. Marshall are affiliated with the Department of Biochemistry and Biophysics at the University of California San Francisco
| | - Wallace F Marshall
- Hiroaki Ishikawa and Wallace F. Marshall are affiliated with the Department of Biochemistry and Biophysics at the University of California San Francisco
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45
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Madhivanan K, Aguilar RC. Ciliopathies: the trafficking connection. Traffic 2014; 15:1031-56. [PMID: 25040720 DOI: 10.1111/tra.12195] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/28/2014] [Accepted: 07/08/2014] [Indexed: 12/15/2022]
Abstract
The primary cilium (PC) is a very dynamic hair-like membrane structure that assembles/disassembles in a cell-cycle-dependent manner and is present in almost every cell type. Despite being continuous with the plasma membrane, a diffusion barrier located at the ciliary base confers the PC properties of a separate organelle with very specific characteristics and membrane composition. Therefore, vesicle trafficking is the major process by which components are acquired for cilium formation and maintenance. In fact, a system of specific sorting signals controls the right of cargo admission into the cilia. Disruption to the ciliary structure or its function leads to multiorgan diseases known as ciliopathies. These illnesses arise from a spectrum of mutations in any of the more than 50 loci linked to these conditions. Therefore, it is not surprising that symptom variability (specific manifestations and severity) among and within ciliopathies appears to be an emerging characteristic. Nevertheless, one can speculate that mutations occurring in genes whose products contribute to the overall vesicle trafficking to the PC (i.e. affecting cilia assembly) will lead to more severe symptoms, whereas those involved in the transport of specific cargoes will result in milder phenotypes. In this review, we summarize the trafficking mechanisms to the cilia and also provide a description of the trafficking defects observed in some ciliopathies which can be correlated to the severity of the pathology.
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Tran PV, Sharma M, Li X, Calvet JP. Developmental signaling: does it bridge the gap between cilia dysfunction and renal cystogenesis? ACTA ACUST UNITED AC 2014; 102:159-73. [PMID: 24861210 DOI: 10.1002/bdrc.21065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 04/14/2014] [Indexed: 01/05/2023]
Abstract
For more than a decade, evidence has accumulated linking dysfunction of primary cilia to renal cystogenesis, yet molecular mechanisms remain undefined. The pathogenesis of renal cysts is complex, involving multiple cellular aberrations and signaling pathways. Adding to this complexity, primary cilia exhibit multiple roles in a context-dependent manner. On renal epithelial cells, primary cilia act as mechanosensors and trigger extracellular Ca(2+) influx in response to laminar fluid flow. During mammalian development, primary cilia mediate the Hedgehog (Hh), Wnt, and Notch pathways, which control cell proliferation and differentiation, and tissue morphogenesis. Further, experimental evidence suggests the developmental state of the kidney strongly influences renal cystic disease. Thus, we review evidence for regulation of Ca(2+) and cAMP, key molecules in renal cystogenesis, at the primary cilium, the role of Hh, Wnt, and Notch signaling in renal cystic disease, and the interplay between these developmental pathways and Ca(2+) signaling. Indeed if these developmental pathways influence renal cystogenesis, these may represent novel therapeutic targets that can be integrated into a combination therapy for renal cystic disease.
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Affiliation(s)
- Pamela V Tran
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas; The Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas
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Taskiran EZ, Korkmaz E, Gucer S, Kosukcu C, Kaymaz F, Koyunlar C, Bryda EC, Chaki M, Lu D, Vadnagara K, Candan C, Topaloglu R, Schaefer F, Attanasio M, Bergmann C, Ozaltin F. Mutations in ANKS6 cause a nephronophthisis-like phenotype with ESRD. J Am Soc Nephrol 2014; 25:1653-61. [PMID: 24610927 DOI: 10.1681/asn.2013060646] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nephronophthisis (NPHP) is one of the most common genetic causes of CKD; however, the underlying genetic abnormalities have been established in <50% of patients. We performed genome-wide analysis followed by targeted resequencing in a Turkish consanguineous multiplex family and identified a canonic splice site mutation in ANKS6 associated with an NPHP-like phenotype. Furthermore, we identified four additional ANKS6 variants in a cohort of 56 unrelated patients diagnosed with CKD due to nephronophthisis, chronic GN, interstitial nephritis, or unknown etiology. Immunohistochemistry in human embryonic kidney tissue demonstrated that the expression patterns of ANKS6 change substantially during development. Furthermore, we detected increased levels of both total and active β-catenin in precystic tubuli in Han:SPRD Cy/+ rats. Overall, these data indicate the importance of ANKS6 in human kidney development and suggest a mechanism by which mutations in ANKS6 may contribute to an NPHP-like phenotype in humans.
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Affiliation(s)
- Ekim Z Taskiran
- Nephrogenetics Laboratory, andDepartments of Medical Genetics
| | | | | | | | | | | | - Elizabeth C Bryda
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri
| | | | | | | | - Cengiz Candan
- **Department of Pediatric Nephrology, Istanbul Medeniyet University, Istanbul, Turkey
| | - Rezan Topaloglu
- Pediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Franz Schaefer
- Pediatric Nephrology Division, Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany
| | - Massimo Attanasio
- Department of Internal Medicine, andEugene McDermott Center for Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carsten Bergmann
- Center for Human Genetics, Bioscientia, Ingelheim, Germany; Department of Nephrology and Center for Clinical Research, University Hospital, Freiburg, Germany; and
| | - Fatih Ozaltin
- Nephrogenetics Laboratory, andPediatric Nephrology, Hacettepe University Faculty of Medicine, Ankara, Turkey; Hacettepe University Center for Biobanking and Genomics, Ankara, Turkey
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48
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Huang S, Xu W, Su B, Luo L. Distinct mechanisms determine organ left-right asymmetry patterning in an uncoupled way. Bioessays 2014; 36:293-304. [PMID: 24464475 DOI: 10.1002/bies.201300128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Disruption of Nodal in the lateral plate mesoderm (LPM) usually leads to left-right (LR) patterning defects in multiple organs. However, whether the LR patterning of organs is always regulated in a coupled way has largely not yet been elucidated. In addition, whether other crucial regulators exist in the LPM that coordinate with Nodal in regulating organ LR patterning is also undetermined. In this paper, after briefly summarizing the common process of LR patterning, the most puzzling question regarding the initiation of asymmetry is considered and the divergent mechanisms underlying the uncoupled LR patterning in different organs are discussed. On the basis of cases in which different organ LR patterning is determined in an uncoupled way via an independent mechanism or at a different time, we propose that there are other critical factors in the LPM that coordinate with Nodal to regulate heart LR asymmetry patterning during early LR patterning.
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Affiliation(s)
- Sizhou Huang
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, Chengdu Medical College, Chengdu, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Beibei, Chongqing, China
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49
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Choi HJC, Lin JR, Vannier JB, Slaats GG, Kile AC, Paulsen RD, Manning DK, Beier DR, Giles RH, Boulton SJ, Cimprich KA. NEK8 links the ATR-regulated replication stress response and S phase CDK activity to renal ciliopathies. Mol Cell 2013; 51:423-39. [PMID: 23973373 PMCID: PMC3790667 DOI: 10.1016/j.molcel.2013.08.006] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/09/2013] [Accepted: 07/24/2013] [Indexed: 01/03/2023]
Abstract
Renal ciliopathies are a leading cause of kidney failure, but their exact etiology is poorly understood. NEK8/NPHP9 is a ciliary kinase associated with two renal ciliopathies in humans and mice, nephronophthisis (NPHP) and polycystic kidney disease. Here, we identify NEK8 as a key effector of the ATR-mediated replication stress response. Cells lacking NEK8 form spontaneous DNA double-strand breaks (DSBs) that further accumulate when replication forks stall, and they exhibit reduced fork rates, unscheduled origin firing, and increased replication fork collapse. NEK8 suppresses DSB formation by limiting cyclin A-associated CDK activity. Strikingly, a mutation in NEK8 that is associated with renal ciliopathies affects its genome maintenance functions. Moreover, kidneys of NEK8 mutant mice accumulate DNA damage, and loss of NEK8 or replication stress similarly disrupts renal cell architecture in a 3D-culture system. Thus, NEK8 is a critical component of the DNA damage response that links replication stress with cystic kidney disorders.
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Affiliation(s)
- Hyo Jei Claudia Choi
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Jia-Ren Lin
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Jean-Baptiste Vannier
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Gisela G. Slaats
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, the Netherlands
| | - Andrew C. Kile
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Renee D. Paulsen
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | | | - David R. Beier
- Brigham and Women's Hospital, Division of Genetics, Boston MA, 02115
| | - Rachel H. Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, the Netherlands
| | - Simon J. Boulton
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Karlene A. Cimprich
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
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50
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Yuan S, Zaidi S, Brueckner M. Congenital heart disease: emerging themes linking genetics and development. Curr Opin Genet Dev 2013; 23:352-9. [PMID: 23790954 PMCID: PMC4154700 DOI: 10.1016/j.gde.2013.05.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/13/2022]
Abstract
Although congenital heart disease (CHD) is the most common survivable birth defect, the etiology of most CHD remains unclear. Several lines of evidence from humans and vertebrate models have supported a genetic component for CHD, yet the extreme locus heterogeneity and lack of a distinct genotype-phenotype correlation have limited causative gene discovery. However, recent advances in genomic technologies are permitting detailed evaluation of the genetic abnormalities in large cohorts of CHD patients. This has led to the identification of copy-number variation and de novo mutations together accounting for up to 15% of CHD. Further, new strategies coupling human genetics with model organisms have provided mechanistic insights into the molecular and developmental pathways underlying CHD pathogenesis, notably chromatin remodeling and ciliary signaling.
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Affiliation(s)
- Shiaulou Yuan
- Department of Pediatrics, Yale University School of Medicine, 15 York St., New Haven, CT 06520
- Department of Genetics, Yale University School of Medicine, 15 York St., New Haven, CT 06520
| | - Samir Zaidi
- Department of Genetics, Yale University School of Medicine, 15 York St., New Haven, CT 06520
| | - Martina Brueckner
- Department of Pediatrics, Yale University School of Medicine, 15 York St., New Haven, CT 06520
- Department of Genetics, Yale University School of Medicine, 15 York St., New Haven, CT 06520
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