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Blue GM, Mekel M, Das D, Troup M, Rath E, Ip E, Gudkov M, Perumal G, Harvey RP, Sholler GF, Gecz J, Kirk EP, Liu J, Giannoulatou E, Hong H, Dunwoodie SL, Winlaw DS. Whole genome sequencing in transposition of the great arteries and associations with clinically relevant heart, brain and laterality genes. Am Heart J 2022; 244:1-13. [PMID: 34670123 DOI: 10.1016/j.ahj.2021.10.185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND The most common cyanotic congenital heart disease (CHD) requiring management as a neonate is transposition of great arteries (TGA). Clinically, up to 50% of TGA patients develop some form of neurodevelopmental disability (NDD), thought to have a significant genetic component. A "ciliopathy" and links with laterality disorders have been proposed. This first report of whole genome sequencing in TGA, sought to identify clinically relevant variants contributing to heart, brain and laterality defects. METHODS Initial whole genome sequencing analyses on 100 TGA patients focussed on established disease genes related to CHD (n = 107), NDD (n = 659) and heterotaxy (n = 74). Single variant as well as copy number variant analyses were conducted. Variant pathogenicity was assessed using the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. RESULTS Fifty-five putatively damaging variants were identified in established disease genes associated with CHD, NDD and heterotaxy; however, no clinically relevant variants could be attributed to disease. Notably, case-control analyses identified significantly more predicted-damaging, silent and total variants in TGA cases than healthy controls in established CHD genes (P < .001), NDD genes (P < .001) as well as across the three gene panels (P < .001). CONCLUSION We present compelling evidence that the majority of TGA is not caused by monogenic rare variants and is most likely oligogenic and/or polygenic in nature, highlighting the complex genetic architecture and multifactorial influences on this CHD sub-type and its long-term sequelae. Assessment of variant burden in key heart, brain and/or laterality genes may be required to unravel the genetic contributions to TGA and related disabilities.
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Garrity M, Kavus H, Rojas-Vasquez M, Valenzuela I, Larson A, Reed S, Bellus G, Mignot C, Munnich A, Isidor B, Chung WK. Neurodevelopmental phenotypes in individuals with pathogenic variants in CHAMP1. Cold Spring Harb Mol Case Stud 2021; 7:a006092. [PMID: 34021018 PMCID: PMC8327885 DOI: 10.1101/mcs.a006092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
De novo pathogenic variants in CHAMP1 (chromosome alignment maintaining phosphoprotein 1), which encodes kinetochore-microtubule associated protein on 13q34, cause a rare neurodevelopmental disorder. We enrolled 14 individuals with pathogenic variants in CHAMP1 that were documented by exome sequencing or gene panel sequencing. Medical history interviews, seizure surveys, Vineland Adapted Behavior Scales Second Edition, and other behavioral surveys were completed by primary caregivers of available participants in Simons Searchlight. Clinicians extracted clinical data from the medical record for two participants. We report on clinical features of 14 individuals (ages 2-26) with de novo predicted loss-of-function variants in CHAMP1 and compare them with previously reported cases (total n = 32). At least two individuals have the same de novo variant: p.(Ser181Cysfs*5), p.(Trp348*), p.(Arg398*), p.(Arg497*), or p.(Tyr709*). Common phenotypes include intellectual disability/developmental delay, language impairment, congenital and acquired microcephaly, behavioral problems including autism spectrum disorder, seizures, hypotonia, gastrointestinal issues of reflux and constipation, and ophthalmologic issues. Other rarely observed phenotypes include leukemia, failure to thrive, and high pain tolerance. Pathogenic variants in CHAMP1 are associated with a variable clinical phenotype of developmental delay/intellectual disability and seizures.
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Affiliation(s)
- Madison Garrity
- Columbia University School of Dental Medicine, New York, New York 10032, USA
| | - Haluk Kavus
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | - Marta Rojas-Vasquez
- Department of Pediatric Hematology-Oncology, Stollery Children's Hospital, Edmonton, Alberta T6G 2B7, Canada
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, 08035 Barcelona, Spain
| | - Austin Larson
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado 80045, USA
| | - Sara Reed
- Clinical Genetics and Genomic Medicine, Geisinger Health System, Danville, Pennsylvania 17821, USA
| | - Gary Bellus
- Clinical Genetics and Genomic Medicine, Geisinger Health System, Danville, Pennsylvania 17821, USA
| | - Cyril Mignot
- APHP-Sorbonne Université, Département de Génétique, Hôpital Trousseau et Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
| | - Arnold Munnich
- Imagine Institute, INSERM UMR 1163, Université de Paris; Fédération de Génétique Médicale, Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes Cedex 1, France
- L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
- Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
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3
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Abstract
Ciliopathies comprise a group of complex disorders, with involvement of the majority of organs and systems. In total, >180 causal genes have been identified and, in addition to Mendelian inheritance, oligogenicity, genetic modifications, epistatic interactions and retrotransposon insertions have all been described when defining the ciliopathic phenotype. It is remarkable how the structural and functional impairment of a single, minuscule organelle may lead to the pathogenesis of highly pleiotropic diseases. Thus, combined efforts have been made to identify the genetic substratum and to determine the pathophysiological mechanism underlying the clinical presentation, in order to diagnose and classify ciliopathies. Yet, predicting the phenotype, given the intricacy of the genetic cause and overlapping clinical characteristics, represents a major challenge. In the future, advances in proteomics, cell biology and model organisms may provide new insights that could remodel the field of ciliopathies.
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Affiliation(s)
- Ina Ofelia Focșa
- Department of Medical Genetics, University of Medicine and Pharmacy 'Carol Davila', 021901 Bucharest, Romania
| | - Magdalena Budișteanu
- Department of Pediatric Neurology, 'Prof. Dr. Alexandru Obregia' Clinical Hospital of Psychiatry, 041914 Bucharest, Romania
| | - Mihaela Bălgrădean
- Department of Pediatrics and Pediatric Nephrology, Emergency Clinical Hospital for Children 'Maria Skłodowska Curie', 077120 Bucharest, Romania
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4
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Drivas TG, Lucas A, Zhang X, Ritchie MD. Mendelian pathway analysis of laboratory traits reveals distinct roles for ciliary subcompartments in common disease pathogenesis. Am J Hum Genet 2021; 108:482-501. [PMID: 33636100 PMCID: PMC8008498 DOI: 10.1016/j.ajhg.2021.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/05/2021] [Indexed: 12/17/2022] Open
Abstract
Rare monogenic disorders of the primary cilium, termed ciliopathies, are characterized by extreme presentations of otherwise common diseases, such as diabetes, hepatic fibrosis, and kidney failure. However, despite a recent revolution in our understanding of the cilium's role in rare disease pathogenesis, the organelle's contribution to common disease remains largely unknown. Hypothesizing that common genetic variants within Mendelian ciliopathy genes might contribute to common complex diseases pathogenesis, we performed association studies of 16,874 common genetic variants across 122 ciliary genes with 12 quantitative laboratory traits characteristic of ciliopathy syndromes in 452,593 individuals in the UK Biobank. We incorporated tissue-specific gene expression analysis, expression quantitative trait loci, and Mendelian disease phenotype information into our analysis and replicated our findings in meta-analysis. 101 statistically significant associations were identified across 42 of the 122 examined ciliary genes (including eight novel replicating associations). These ciliary genes were widely expressed in tissues relevant to the phenotypes being studied, and eQTL analysis revealed strong evidence for correlation between ciliary gene expression levels and laboratory traits. Perhaps most interestingly, our analysis identified different ciliary subcompartments as being specifically associated with distinct sets of phenotypes. Taken together, our data demonstrate the utility of a Mendelian pathway-based approach to genomic association studies, challenge the widely held belief that the cilium is an organelle important mainly in development and in rare syndromic disease pathogenesis, and provide a framework for the continued integration of common and rare disease genetics to provide insight into the pathophysiology of human diseases of immense public health burden.
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Affiliation(s)
- Theodore George Drivas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA
| | - Xinyuan Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA
| | - Marylyn DeRiggi Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19194, USA.
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5
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Lebedev M, McEligot HA, Mutua VN, Walsh P, Carvallo Chaigneau FR, Gershwin LJ. Analysis of lung transcriptome in calves infected with Bovine Respiratory Syncytial Virus and treated with antiviral and/or cyclooxygenase inhibitor. PLoS One 2021; 16:e0246695. [PMID: 33600498 PMCID: PMC7891793 DOI: 10.1371/journal.pone.0246695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/22/2021] [Indexed: 12/15/2022] Open
Abstract
Bovine Respiratory Syncytial virus (BRSV) is one of the major infectious agents in the etiology of the bovine respiratory disease complex. BRSV causes a respiratory syndrome in calves, which is associated with severe bronchiolitis. In this study we describe the effect of treatment with antiviral fusion protein inhibitor (FPI) and ibuprofen, on gene expression in lung tissue of calves infected with BRSV. Calves infected with BRSV are an excellent model of human RSV in infants: we hypothesized that FPI in combination with ibuprofen would provide the best therapeutic intervention for both species. The following experimental treatment groups of BRSV infected calves were used: 1) ibuprofen day 3-10, 2) ibuprofen day 5-10, 3) placebo, 4) FPI day 5-10, 5) FPI and ibuprofen day 5-10, 6) FPI and ibuprofen day 3-10. All calves were infected with BRSV on day 0. Daily clinical evaluation with monitoring of virus shedding by qRT-PCR was conducted. On day10 lung tissue with lesions (LL) and non-lesional (LN) was collected at necropsy, total RNA extracted, and RNA sequencing performed. Differential gene expression analysis was conducted with Gene ontology (GO) and KEGG pathway enrichment analysis. The most significant differential gene expression in BRSV infected lung tissues was observed in the comparison of LL with LN; oxidative stress and cell damage was especially noticeable. Innate and adaptive immune functions were reduced in LL. As expected, combined treatment with FPI and Ibuprofen, when started early, made the most difference in gene expression patterns in comparison with placebo, especially in pathways related to the innate and adaptive immune response in both LL and LN. Ibuprofen, when used alone, negatively affected the antiviral response and caused higher virus loads as shown by increased viral shedding. In contrast, when used with FPI Ibuprofen enhanced the specific antiviral effect of FPI, due to its ability to reduce the damaging effect of prostanoids and oxidative stress.
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Affiliation(s)
- Maxim Lebedev
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Heather A. McEligot
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Victoria N. Mutua
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Paul Walsh
- Pediatric Emergency Medicine, Sutter Medical Center Sacramento, Sacramento, California, United States of America
| | - Francisco R. Carvallo Chaigneau
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech., Blacksburg, VA, United States of America
| | - Laurel J. Gershwin
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
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6
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Auckland P, Roscioli E, Coker HLE, McAinsh AD. CENP-F stabilizes kinetochore-microtubule attachments and limits dynein stripping of corona cargoes. J Cell Biol 2020; 219:e201905018. [PMID: 32207772 PMCID: PMC7199848 DOI: 10.1083/jcb.201905018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/04/2019] [Accepted: 02/19/2020] [Indexed: 01/14/2023] Open
Abstract
Accurate chromosome segregation demands efficient capture of microtubules by kinetochores and their conversion to stable bioriented attachments that can congress and then segregate chromosomes. An early event is the shedding of the outermost fibrous corona layer of the kinetochore following microtubule attachment. Centromere protein F (CENP-F) is part of the corona, contains two microtubule-binding domains, and physically associates with dynein motor regulators. Here, we have combined CRISPR gene editing and engineered separation-of-function mutants to define how CENP-F contributes to kinetochore function. We show that the two microtubule-binding domains make distinct contributions to attachment stability and force transduction but are dispensable for chromosome congression. We further identify a specialized domain that functions to limit the dynein-mediated stripping of corona cargoes through a direct interaction with Nde1. This antagonistic activity is crucial for maintaining the required corona composition and ensuring efficient kinetochore biorientation.
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Affiliation(s)
- Philip Auckland
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Emanuele Roscioli
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Helena Louise Elvidge Coker
- Computing and Advanced Microscopy Development Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Andrew D. McAinsh
- Centre for Mechanochemical Cell Biology & Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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7
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Haley CO, Waters AM, Bader DM. Malformations in the Murine Kidney Caused by Loss of CENP-F Function. Anat Rec (Hoboken) 2020; 302:163-170. [PMID: 30408335 DOI: 10.1002/ar.24018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/14/2018] [Accepted: 02/21/2018] [Indexed: 01/27/2023]
Abstract
Centromere-binding protein F (CENP-F) is a large and complex protein shown to play critical roles in mitosis and various other interphase functions. Previous studies have shown that the disruption of CENP-F function leads to detrimental effects on human development. Still, it is important to note the lack of studies focusing on the effects that the loss of this essential protein may have on specific adult organs. In the current study, we used a novel global knockout murine model to analyze the potential consequences deletion of CENP-F has on adult kidney structure and function. We discovered several structural abnormalities including loss of ciliary structure, tubule dilation, and disruption of the glomerulus. Along with these structural irregularities, renal dysfunction was also detected suggesting hydronephrosis and acute kidney injury in these knockout organs. Importantly, this is the first study linking CENP-F to kidney disease and hopefully these data will serve as a platform to further investigate the molecular mechanisms disrupted in the kidney by the loss of CENP-F. Anat Rec, 302:163-170, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Chanell O Haley
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Aoife M Waters
- Institute of Child Health, University College, London, UK.,Department of Nephrology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - D M Bader
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University, Nashville, Tennessee
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8
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Alghamdi M, Alkhamis WH, Bashiri FA, Jamjoom D, Al-Nafisah G, Tahir A, Abdouelhoda M. Expanding the phenotype and the genotype of Stromme syndrome: A novel variant of the CENPF gene and literature review. Eur J Med Genet 2020; 63:103844. [PMID: 31953238 DOI: 10.1016/j.ejmg.2020.103844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/25/2019] [Accepted: 01/11/2020] [Indexed: 01/08/2023]
Abstract
This report describes siblings with Stromme syndrome, a rare genetic condition that primarily presents with a triad of intestinal atresia, cranial and ocular malformations, and other organ systems could be involved. This clinical triad was initially named after the first person to describe it in 1993. Here, we report a family with two siblings who presented with unusual intestinal atresia and ocular and CNS abnormalities. The first patient is a 6-year-old-boy with apple peel duodeno-jejunal atresia, unilateral microphthalmia and microcephaly. The second patient, a younger brother, presented with intestinal atresia, corneal opacity and alobar holoprosencephaly and passed away at the age of 3 months. Exome sequencing showed a novel homozygous variant in the CENPF gene, NM_016343.3: c.1195-2 A > G that was detected in both of the affected siblings. This is a report and literature review of CENPF-related ciliopathy, which may result in Stromme syndrome. As this is the fourth report linking the CENPF gene variant with Stromme syndrome and first reported case presented with holoprosencephaly, it will expand the current knowledge on the genotype and the phenotype of Stromme syndrome.
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Affiliation(s)
- Malak Alghamdi
- Pediatric Genetics and Metabolic Disorders Division, Department of Pediatrics, College of Medicine, King Saud University, Saudi Arabia.
| | | | - Fahad A Bashiri
- Neurology Division, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Dima Jamjoom
- Department of Radiology, College of Medicine, Saudi Arabia
| | - Ghada Al-Nafisah
- Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Asma Tahir
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Saudi Arabia
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9
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Degrassi F, Damizia M, Lavia P. The Mitotic Apparatus and Kinetochores in Microcephaly and Neurodevelopmental Diseases. Cells 2019; 9:E49. [PMID: 31878213 DOI: 10.3390/cells9010049] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/18/2019] [Accepted: 12/21/2019] [Indexed: 12/15/2022] Open
Abstract
Regulators of mitotic division, when dysfunctional or expressed in a deregulated manner (over- or underexpressed) in somatic cells, cause chromosome instability, which is a predisposing condition to cancer that is associated with unrestricted proliferation. Genes encoding mitotic regulators are growingly implicated in neurodevelopmental diseases. Here, we briefly summarize existing knowledge on how microcephaly-related mitotic genes operate in the control of chromosome segregation during mitosis in somatic cells, with a special focus on the role of kinetochore factors. Then, we review evidence implicating mitotic apparatus- and kinetochore-resident factors in the origin of congenital microcephaly. We discuss data emerging from these works, which suggest a critical role of correct mitotic division in controlling neuronal cell proliferation and shaping the architecture of the central nervous system.
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10
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Filges I, Stromme P. CUGC for Stromme syndrome and CENPF-related disorders. Eur J Hum Genet 2020; 28:132-6. [PMID: 31488893 DOI: 10.1038/s41431-019-0498-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/16/2019] [Accepted: 08/02/2019] [Indexed: 11/09/2022] Open
Abstract
NAME OF THE DISEASE (SYNONYMS) Stromme syndrome.Jejunal atresia with microcephaly and ocular anomalies.Apple peel syndrome with microcephaly and ocular anomalies.Ciliopathy phenotype.Primary microcephaly and intellectual disability.OMIM# of the disease 243605.Name of the analysed genes or DNA/chromosome segments CENPF.OMIM# of the gene(s) 600236.Review of the analytical and clinical validity as well as of the clinical utility of DNA-based testing for mutations in CENPF genes in diagnostic, prenatal settings, and for risk assessment in relatives.
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11
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Peterka M, Kornmann B. Miro-dependent mitochondrial pool of CENP-F and its farnesylated C-terminal domain are dispensable for normal development in mice. PLoS Genet 2019; 15:e1008050. [PMID: 30856164 PMCID: PMC6428352 DOI: 10.1371/journal.pgen.1008050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/21/2019] [Accepted: 02/27/2019] [Indexed: 11/19/2022] Open
Abstract
CENP-F is a large, microtubule-binding protein that regulates multiple cellular processes including chromosome segregation and mitochondrial trafficking at cytokinesis. This multiplicity of functions is mediated through the binding of various partners, like Bub1 at the kinetochore and Miro at mitochondria. Due to the multifunctionality of CENP-F, the cellular phenotypes observed upon its depletion are difficult to interpret and there is a need to genetically separate its different functions by preventing binding to selected partners. Here we engineer a CENP-F point-mutant that is deficient in Miro binding and thus is unable to localize to mitochondria, but retains other localizations. We introduce this mutation in cultured human cells using CRISPR/Cas9 system and show it causes a defect in mitochondrial spreading similar to that observed upon Miro depletion. We further create a mouse model carrying this CENP-F variant, as well as truncated CENP-F mutants lacking the farnesylated C-terminus of the protein. Importantly, one of these truncations leads to ~80% downregulation of CENP-F expression. We observe that, despite the phenotypes apparent in cultured cells, mutant mice develop normally. Taken together, these mice will serve as important models to study CENP-F biology at organismal level. In addition, because truncations of CENP-F in humans cause a lethal disease termed Strømme syndrome, they might also be relevant disease models. CENP-F is a poorly characterized multifunctional regulator of metazoan cell division involved in chromosome segregation and mitochondrial dynamics. The physiological importance of CENP-F in both of these processes is not firmly established and numerous conflicting reports exist regarding its function in mitosis. Here we set out to investigate the function of CENP-F in vivo by CRISPR-mediated mutagenesis in mice where we specifically disrupt different domains of CENP-F important for mitosis and mitochondrial regulation. Surprisingly, contrasting to reported phenotypes in cultured cells, mutant animals display no obvious phenotypes. This argues against CENP-F being a major player in mammalian cell division and suggest context-specific roles of this protein. Importantly, in humans, truncations of CENP-F as small as 20 amino acids have recently emerged as a cause of human disease termed Strømme syndrome. Truncations in these mice might yield information relevant to the understanding of this disease and biology of CENP-F.
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Affiliation(s)
- Martin Peterka
- Institute of Biochemistry, ETH Zurich, Zürich, Switzerland
- Molecular Life Science Program, Zurich Life-Science Graduate School, Zürich, Switzerland
| | - Benoît Kornmann
- Institute of Biochemistry, ETH Zurich, Zürich, Switzerland
- * E-mail:
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12
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Meier N, Bruder E, Lapaire O, Hoesli I, Kang A, Hench J, Hoeller S, De Geyter J, Miny P, Heinimann K, Chaoui R, Tercanli S, Filges I. Exome sequencing of fetal anomaly syndromes: novel phenotype-genotype discoveries. Eur J Hum Genet 2019; 27:730-737. [PMID: 30679815 PMCID: PMC6461982 DOI: 10.1038/s41431-018-0324-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/02/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
The monogenic etiology of most severe fetal anomaly syndromes is poorly understood. Our objective was to use exome sequencing (ES) to increase our knowledge on causal variants and novel candidate genes associated with specific fetal phenotypes. We employed ES in a cohort of 19 families with one or more fetuses presenting with a distinctive anomaly pattern and/or phenotype recurrence at increased risk for lethal outcomes. Candidate variants were identified in 12 families (63%); in 6 of them a definite diagnosis was achieved including known or novel variants in recognized disease genes (MKS1, OTX2, FGFR2, and RYR1) and variants in novel disease genes describing new fetal phenotypes (CENPF, KIF14). We identified variants likely causal after clinical and functional review (SMAD3, KIF4A, and PIGW) and propose novel candidate genes (PTK7, DNHD1, and TTC28) for early human developmental disease supported by functional and cross-species phenotyping evidence. We describe rare and novel fetal anomaly syndromes and highlight the diagnostic utility of ES, but also its contribution to discovery. The diagnostic yield of the future application of prenatal ES will depend on our ability to increase our knowledge on the specific phenotype–genotype correlations during fetal development.
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Affiliation(s)
- Nicole Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Elisabeth Bruder
- University of Basel, Basel, Switzerland.,Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Olav Lapaire
- Department of Obstetrics and Gynecology, University Hospital Basel, Basel, Switzerland
| | - Irene Hoesli
- Department of Obstetrics and Gynecology, University Hospital Basel, Basel, Switzerland
| | - Anjeung Kang
- Centre for Prenatal Ultrasound, Freie Strasse, Basel, Switzerland
| | - Jürgen Hench
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Sylvia Hoeller
- University of Basel, Basel, Switzerland.,Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Julie De Geyter
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Peter Miny
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Karl Heinimann
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Rabih Chaoui
- Centre for Prenatal Diagnosis, Friedrichstrasse, Berlin, Germany
| | - Sevgi Tercanli
- University of Basel, Basel, Switzerland.,Centre for Prenatal Ultrasound, Freie Strasse, Basel, Switzerland
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland. .,Department of Clinical Research, University Hospital Basel, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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13
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Abstract
In metazoans, the assembly of kinetochores on centrometric chromatin and the dismantling of nuclear pore complexes are processes that have to be tightly coordinated to ensure the proper assembly of the mitotic spindle and a successful mitosis. It is therefore noteworthy that these two macromolecular assemblies share a subset of constituents. One of these multifaceted components is Cenp-F, a protein implicated in cancer and developmental pathologies. During the cell cycle, Cenp-F localizes in multiple cellular structures including the nuclear envelope in late G2/early prophase and kinetochores throughout mitosis. We recently characterized the molecular determinants of Cenp-F interaction with Nup133, a structural nuclear pore constituent. In parallel with two other independent studies, we further elucidated the mechanisms governing Cenp-F kinetochore recruitment that mainly relies on its interaction with Bub1, with redundant contribution of Cenp-E upon acute microtubule depolymerisation. Here we synthesize the current literature regarding the dual location of Cenp-F at nuclear pores and kinetochores and extend our discussion to the regulation of these NPC and kinetochore localizations by mitotic kinase and spindle microtubules.
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Affiliation(s)
- Alessandro Berto
- a Institut Jacques Monod , UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité , Paris , France.,b Ecole Doctorale Structure et Dynamique des Systèmes Vivants (#577) , Univ Paris Sud, Université Paris-Saclay , Orsay , France
| | - Valérie Doye
- a Institut Jacques Monod , UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité , Paris , France
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Paul AM, Acharya D, Neupane B, Thompson EA, Gonzalez-Fernandez G, Copeland KM, Garrett M, Liu H, Lopez ME, de Cruz M, Flynt A, Liao J, Guo YL, Gonzalez-Fernandez F, Vig PJS, Bai F. Congenital Zika Virus Infection in Immunocompetent Mice Causes Postnatal Growth Impediment and Neurobehavioral Deficits. Front Microbiol 2018; 9:2028. [PMID: 30210488 PMCID: PMC6124374 DOI: 10.3389/fmicb.2018.02028] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/10/2018] [Indexed: 02/04/2023] Open
Abstract
A small percentage of babies born to Zika virus (ZIKV)-infected mothers manifest severe defects at birth, including microcephaly. Among those who appeared healthy at birth, there are increasing reports of postnatal growth or developmental defects. However, the impact of congenital ZIKV infection in postnatal development is poorly understood. Here, we report that a mild congenital ZIKV-infection in pups born to immunocompetent pregnant mice did not display apparent defects at birth, but manifested postnatal growth impediments and neurobehavioral deficits, which include reduced locomotor and cognitive deficits that persisted into adulthood. We found that the brains of these pups were smaller, had a thinner cortical layer 1, displayed increased astrogliosis, decreased expression of microcephaly- and neuron development- related genes, and increased pathology as compared to mock-infected controls. In summary, our results showed that even a mild congenital ZIKV infection in immunocompetent mice could lead to postnatal deficits, providing definitive experimental evidence for a necessity to closely monitor postnatal growth and development of presumably healthy human infants, whose mothers were exposed to ZIKV infection during pregnancy.
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Affiliation(s)
- Amber M. Paul
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Dhiraj Acharya
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Biswas Neupane
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - E. Ashely Thompson
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | | | | | - Me’Lanae Garrett
- Department of Bioengineering, University of Texas, Arlington, TX, United States
| | - Haibei Liu
- Hattiesburg Clinic, Hattiesburg, MS, United States
| | - Mariper E. Lopez
- Department of Neurology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Matthew de Cruz
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Alex Flynt
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Jun Liao
- Department of Bioengineering, University of Texas, Arlington, TX, United States
| | - Yan-Lin Guo
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Federico Gonzalez-Fernandez
- Medical Research Service, G.V. (Sonny) Montgomery Veterans Affairs Medical Center, Jackson, MS, United States
- Department of Ophthalmology and Pathology, University of Mississippi Medical Center, Jackson, MS, United States
- Pathrd, Inc.,Jackson, MS, United States
| | - Parminder J. S. Vig
- Department of Neurology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Fengwei Bai
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
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15
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Bubien V, Bonnet F, Dupiot-Chiron J, Barouk-Simonet E, Jones N, de Reynies A, MacGrogan G, Sevenet N, Letouzé E, Longy M. Combined tumor genomic profiling and exome sequencing in a breast cancer family implicates ATM in tumorigenesis: A proof of principle study. Genes Chromosomes Cancer 2017; 56:788-799. [PMID: 28691344 DOI: 10.1002/gcc.22482] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 05/11/2017] [Accepted: 07/06/2017] [Indexed: 11/08/2022] Open
Abstract
Familial breast cancers (BCs) account for 10%-20% of all diagnosed BCs, yet only 20% of such tumors arise in the context of a germline mutation in known tumor suppressor genes such as BRCA1 or BRCA2. The vast genetic heterogeneity which characterizes non BRCA1 and non BRCA2 (or BRCAx) families makes grouped studies impossible to perform. Next generation sequencing techniques, however, allow individual families to be studied to identify rare and or private mutations but the high number of genetic variants identified need to be sorted using pathogenicity or recurrence criteria. An additional sorting criterion may be represented by the identification of candidate regions defined by tumor genomic rearrangements. Indeed, comparative genomic hybridization (CGH) using single nucleotide polymorphism (SNP) arrays allows the detection of conserved ancestral haplotypes within recurrent regions of loss of heterozygosity, common to several familial tumors, which can highlight genomic loci harboring a germline mutation in cancer predisposition genes. The combination of both exome sequencing and SNP array-CGH for a series of familial BC revealed a germline ATM mutation associated with a loss of the wild-type allele in two BC from a BRCAx family. The analysis of additional breast tumors from ten BC families in which a germline ATM mutation had been identified revealed a high frequency of wild-type allele loss. This result argues strongly in favor of the involvement of ATM in these tumors as a tumor suppressor gene and confirms that germline ATM mutations are involved in a subset of familial BC.
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Affiliation(s)
- Virginie Bubien
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | - Françoise Bonnet
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | | | | | - Natalie Jones
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | - Aurélien de Reynies
- Programme CIT, Bioinformatics Department, Ligue Nationale contre le Cancer (Cartes d'Identité des Tumeurs), Paris, France
| | - Gaëtan MacGrogan
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,BioPathology Department, Institut Bergonié, Bordeaux, France
| | - Nicolas Sevenet
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | - Eric Letouzé
- Programme CIT, Bioinformatics Department, Ligue Nationale contre le Cancer (Cartes d'Identité des Tumeurs), Paris, France
| | - Michel Longy
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
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16
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17
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Ozkinay F, Atik T, Isik E, Gormez Z, Sagiroglu M, Sahin OA, Corduk N, Onay H. A further family of Stromme syndrome carrying CENPF
mutation. Am J Med Genet A 2017; 173:1668-1672. [DOI: 10.1002/ajmg.a.38173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Ferda Ozkinay
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine; Ege University; Izmir Turkey
| | - Tahir Atik
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine; Ege University; Izmir Turkey
| | - Esra Isik
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine; Ege University; Izmir Turkey
| | - Zeliha Gormez
- Advanced Genomics and Bioinformatics Research Center; TUBITAK-BILGEM; Kocaeli Turkey
| | - Mahmut Sagiroglu
- Advanced Genomics and Bioinformatics Research Center; TUBITAK-BILGEM; Kocaeli Turkey
| | - Ozlem Atan Sahin
- Biochemistry and Molecular Biology, Institude of Health Sciences; Acibadem University; Istanbul Turkey
| | - Nergul Corduk
- Department of Pediatric Surgery, Faculty of Medicine; Pamukkale University; Denizli Turkey
| | - Huseyin Onay
- Department of Medical Genetics, Faculty of Medicine; Ege University; Izmir Turkey
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18
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Greer YE, Gao B, Yang Y, Nussenzweig A, Rubin JS. Lack of Casein Kinase 1 Delta Promotes Genomic Instability - The Accumulation of DNA Damage and Down-Regulation of Checkpoint Kinase 1. PLoS One 2017; 12:e0170903. [PMID: 28125685 PMCID: PMC5268481 DOI: 10.1371/journal.pone.0170903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/12/2017] [Indexed: 12/18/2022] Open
Abstract
Casein kinase 1 delta (CK1δ) is a conserved serine/threonine protein kinase that regulates diverse cellular processes. Mice lacking CK1δ have a perinatal lethal phenotype and typically weigh 30% less than their wild type littermates. However, the causes of death and small size are unknown. We observed cells with abnormally large nuclei in tissue from Csnk1d null embryos, and multiple centrosomes in mouse embryo fibroblasts (MEFs) deficient in CK1δ (MEFCsnk1d null). Results from γ-H2AX staining and the comet assay demonstrated significant DNA damage in MEFCsnk1d null cells. These cells often contain micronuclei, an indicator of genomic instability. Similarly, abrogation of CK1δ expression in control MEFs stimulated micronuclei formation after doxorubicin treatment, suggesting that CK1δ loss increases vulnerability to genotoxic stress. Cellular levels of total and activated checkpoint kinase 1 (Chk1), which functions in the DNA damage response and mitotic checkpoints, and its downstream effector, Cdc2/CDK1 kinase, were often decreased in MEFCsnk1d null cells as well as in control MEFs transfected with CK1δ siRNA. Hydroxyurea-induced Chk1 activation, as measured by Ser345 phosphorylation, and nuclear localization also were impaired in MEF cells following siRNA knockdown of CK1δ. Similar results were observed in the MCF7 human breast cancer cell line. The decreases in phosphorylated Chk1 were rescued by concomitant expression of siRNA-resistant CK1δ. Experiments with cycloheximide demonstrated that the stability of Chk1 protein was diminished in cells subjected to CK1δ knockdown. Together, these findings suggest that CK1δ contributes to the efficient repair of DNA damage and the proper functioning of mitotic checkpoints by maintaining appropriate levels of Chk1.
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Affiliation(s)
- Yoshimi Endo Greer
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bethesda, Maryland, United States of America
- Women’s Malignancies Branch, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail: (YEG); (JSR)
| | - Bo Gao
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Yingzi Yang
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jeffrey S. Rubin
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail: (YEG); (JSR)
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20
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Pfaltzgraff ER, Roth GM, Miller PM, Gintzig AG, Ohi R, Bader DM. Loss of CENP-F results in distinct microtubule-related defects without chromosomal abnormalities. Mol Biol Cell 2016; 27:1990-9. [PMID: 27146114 PMCID: PMC4927273 DOI: 10.1091/mbc.e15-12-0848] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/27/2016] [Indexed: 01/09/2023] Open
Abstract
Microtubule (MT)-binding centromere protein F (CENP-F) was previously shown to play a role exclusively in chromosome segregation during cellular division. Many cell models of CENP-F depletion show a lag in the cell cycle and aneuploidy. Here, using our novel genetic deletion model, we show that CENP-F also regulates a broader range of cellular functions outside of cell division. We characterized CENP-F(+/+) and CENP-F(-/-) mouse embryonic fibroblasts (MEFs) and found drastic differences in multiple cellular functions during interphase, including cell migration, focal adhesion dynamics, and primary cilia formation. We discovered that CENP-F(-/-) MEFs have severely diminished MT dynamics, which underlies the phenotypes we describe. These data, combined with recent biochemical research demonstrating the strong binding of CENP-F to the MT network, support the conclusion that CENP-F is a powerful regulator of MT dynamics during interphase and affects heterogeneous cell functions.
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Affiliation(s)
- Elise R Pfaltzgraff
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Gretchen M Roth
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Paul M Miller
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Anneelizabeth G Gintzig
- Division of Hematology-Oncology, Department of Pediatrics, Vanderbilt University, Nashville, TN 37232
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232
| | - David M Bader
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232
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