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D’Gama PP, Jeong I, Nygård AM, Trinh AT, Yaksi E, Jurisch-Yaksi N. Ciliogenesis defects after neurulation impact brain development and neuronal activity in larval zebrafish. iScience 2024; 27:110078. [PMID: 38868197 PMCID: PMC11167523 DOI: 10.1016/j.isci.2024.110078] [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: 09/25/2023] [Revised: 03/06/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024] Open
Abstract
Cilia are slender, hair-like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system, primary cilia contribute to signaling and sensory perception, while motile cilia facilitate cerebrospinal fluid flow. Here, we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects after neurulation affect neurogenesis and brain morphology, especially in the cerebellum, and lead to altered gene expression profiles. Using whole brain calcium imaging, we measured reduced light-evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish, our work highlights their evolutionary conserved role in the brain and sets the stage for future analysis of ciliopathy models.
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Affiliation(s)
- Percival P. D’Gama
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skalgssons gate 1, 7030 Trondheim, Norway
| | - Inyoung Jeong
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skalgssons gate 1, 7030 Trondheim, Norway
| | - Andreas Moe Nygård
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skalgssons gate 1, 7030 Trondheim, Norway
| | - Anh-Tuan Trinh
- Kavli Institute for Systems Neuroscience and Centre for Algorithms in the Cortex, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Emre Yaksi
- Kavli Institute for Systems Neuroscience and Centre for Algorithms in the Cortex, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
- Koç University Research Center for Translational Medicine, Koç University School of Medicine, Davutpaşa Caddesi, No:4, Topkapı 34010, Istanbul, Turkey
| | - Nathalie Jurisch-Yaksi
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skalgssons gate 1, 7030 Trondheim, Norway
- Kavli Institute for Systems Neuroscience and Centre for Algorithms in the Cortex, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
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2
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Lesnyak O, Marini F, Sokolnikova P, Sorokina M, Sukhareva K, Artamonova I, Kenis V, Tkach O, Kostareva A, Brandi ML. Skeletal abnormalities, pediatric-onset severe osteoporosis, and multiple fragility fractures in a patient with a novel CTNNB1 de novo variant. Bone Rep 2024; 21:101777. [PMID: 38952406 PMCID: PMC11215946 DOI: 10.1016/j.bonr.2024.101777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/28/2024] [Accepted: 06/01/2024] [Indexed: 07/03/2024] Open
Abstract
We report a case of a patient with a de novo germline heterozygous truncating variant of CTNNB1 gene (c.2172del, p.Tyr724Ter) causing neurodevelopmental disorder with spastic diplegia and visual defects syndrome (NEDSDV) associated with a new clinical feature - severe pediatric-onset osteoporosis and multiple fractures. A functional effect of the identified variant was demonstrated using adipose-tissue derived primary mesenchymal stem cells, where we detected the alteration of CTNNB1mRNA and β-catenin protein levels using real-time PCR and Western blot analysis.
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Affiliation(s)
- Olga Lesnyak
- North Western State Medical University named after I.I. Mechnikov, 41, Kirochnaya Street, St. Petersburg 191015, Russian Federation
- Clinical Rheumatological Hospital, # 25, 30, B.Pod'yacheskaya Street, St. Petersburg 190068, Russian Federation
| | - Francesca Marini
- Fondazione FIRMO Onlus, Fondazione Italiana per la Ricerca sulle Malattie dell'Osso, Via San Gallo 123, Florence 50129, Italy
| | - Polina Sokolnikova
- Almazov National Medical Research Centre, 2, Akkuratova Street, St. Petersburg 197341, Russian Federation
| | - Margarita Sorokina
- Almazov National Medical Research Centre, 2, Akkuratova Street, St. Petersburg 197341, Russian Federation
| | - Kseniya Sukhareva
- Almazov National Medical Research Centre, 2, Akkuratova Street, St. Petersburg 197341, Russian Federation
| | - Irina Artamonova
- Almazov National Medical Research Centre, 2, Akkuratova Street, St. Petersburg 197341, Russian Federation
| | - Vladimir Kenis
- North Western State Medical University named after I.I. Mechnikov, 41, Kirochnaya Street, St. Petersburg 191015, Russian Federation
- H.Turner National Medical Research Center for Children's Orthopedics and Trauma Surgery, 12, lit. a, Lakhtinskaya Street, St. Petersburg 197136, Russian Federation
| | - Olga Tkach
- Clinical Rheumatological Hospital, # 25, 30, B.Pod'yacheskaya Street, St. Petersburg 190068, Russian Federation
| | - Anna Kostareva
- Almazov National Medical Research Centre, 2, Akkuratova Street, St. Petersburg 197341, Russian Federation
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet (KI), Solna, 17176 Stockholm, Sweden
| | - Maria Luisa Brandi
- Fondazione FIRMO Onlus, Fondazione Italiana per la Ricerca sulle Malattie dell'Osso, Via San Gallo 123, Florence 50129, Italy
- Donatello Bone Clinic, Villa Donatello Hospital, Via Attilio Ragionieri 101, 50019, Sesto Fiorentino, Florence, Italy
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3
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Lai B, Jiang H, Gao Y, Zhou X. Skeletal ciliopathy: pathogenesis and related signaling pathways. Mol Cell Biochem 2024; 479:811-823. [PMID: 37188988 DOI: 10.1007/s11010-023-04765-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Cilia are tiny organelles with conserved structures and components in eukaryotic cells. Ciliopathy is a set of diseases resulting from cilium dysfunction classified into first-order and second-order ciliopathy. With the advancement of clinical diagnosis and radiography, numerous skeletal phenotypes, including polydactyly, short limbs, short ribs, scoliosis, a narrow thorax, and numerous anomalies in bone and cartilage, have been discovered in ciliopathies. Mutation in genes encoding cilia core components or other cilia-related molecules have been found in skeletal ciliopathies. Meanwhile, various signaling pathways associated with cilia and skeleton development have been deemed to be significant for the occurrence and progression of diseases. Herein, we review the structure and key components of the cilium and summarize several skeletal ciliopathies with their presumable pathology. We also emphasize the signaling pathways involved in skeletal ciliopathies, which may assist in developing potential therapies for these diseases.
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Affiliation(s)
- Bowen Lai
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Fengyang Road 415, Shanghai, 200003, China
| | - Heng Jiang
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Fengyang Road 415, Shanghai, 200003, China
| | - Yuan Gao
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Fengyang Road 415, Shanghai, 200003, China
| | - Xuhui Zhou
- Department of Orthopedics, Changzheng Hospital, Second Military Medical University, Fengyang Road 415, Shanghai, 200003, China.
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Kebschull JM, Casoni F, Consalez GG, Goldowitz D, Hawkes R, Ruigrok TJH, Schilling K, Wingate R, Wu J, Yeung J, Uusisaari MY. Cerebellum Lecture: the Cerebellar Nuclei-Core of the Cerebellum. CEREBELLUM (LONDON, ENGLAND) 2024; 23:620-677. [PMID: 36781689 PMCID: PMC10951048 DOI: 10.1007/s12311-022-01506-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/10/2022] [Indexed: 02/15/2023]
Abstract
The cerebellum is a key player in many brain functions and a major topic of neuroscience research. However, the cerebellar nuclei (CN), the main output structures of the cerebellum, are often overlooked. This neglect is because research on the cerebellum typically focuses on the cortex and tends to treat the CN as relatively simple output nuclei conveying an inverted signal from the cerebellar cortex to the rest of the brain. In this review, by adopting a nucleocentric perspective we aim to rectify this impression. First, we describe CN anatomy and modularity and comprehensively integrate CN architecture with its highly organized but complex afferent and efferent connectivity. This is followed by a novel classification of the specific neuronal classes the CN comprise and speculate on the implications of CN structure and physiology for our understanding of adult cerebellar function. Based on this thorough review of the adult literature we provide a comprehensive overview of CN embryonic development and, by comparing cerebellar structures in various chordate clades, propose an interpretation of CN evolution. Despite their critical importance in cerebellar function, from a clinical perspective intriguingly few, if any, neurological disorders appear to primarily affect the CN. To highlight this curious anomaly, and encourage future nucleocentric interpretations, we build on our review to provide a brief overview of the various syndromes in which the CN are currently implicated. Finally, we summarize the specific perspectives that a nucleocentric view of the cerebellum brings, move major outstanding issues in CN biology to the limelight, and provide a roadmap to the key questions that need to be answered in order to create a comprehensive integrated model of CN structure, function, development, and evolution.
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Affiliation(s)
- Justus M Kebschull
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Filippo Casoni
- Division of Neuroscience, San Raffaele Scientific Institute, and San Raffaele University, Milan, Italy
| | - G Giacomo Consalez
- Division of Neuroscience, San Raffaele Scientific Institute, and San Raffaele University, Milan, Italy
| | - Daniel Goldowitz
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Richard Hawkes
- Department of Cell Biology & Anatomy and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Tom J H Ruigrok
- Department of Neuroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Karl Schilling
- Department of Anatomy, Anatomy & Cell Biology, Rheinische Friedrich-Wilhelms-Universität, 53115, Bonn, Federal Republic of Germany
| | - Richard Wingate
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Joshua Wu
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Joanna Yeung
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Marylka Yoe Uusisaari
- Neuronal Rhythms in Movement Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-Son, Kunigami-Gun, Okinawa, 904-0495, Japan.
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5
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Bear RM, Caspary T. Uncovering cilia function in glial development. Ann Hum Genet 2024; 88:27-44. [PMID: 37427745 PMCID: PMC10776815 DOI: 10.1111/ahg.12519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
Primary cilia play critical roles in regulating signaling pathways that underlie several developmental processes. In the nervous system, cilia are known to regulate signals that guide neuron development. Cilia dysregulation is implicated in neurological diseases, and the underlying mechanisms remain poorly understood. Cilia research has predominantly focused on neurons and has overlooked the diverse population of glial cells in the brain. Glial cells play essential roles during neurodevelopment, and their dysfunction contributes to neurological disease; however, the relationship between cilia function and glial development is understudied. Here we review the state of the field and highlight the glial cell types where cilia are found and the ciliary functions that are linked to glial development. This work uncovers the importance of cilia in glial development and raises outstanding questions for the field. We are poised to make progress in understanding the function of glial cilia in human development and their contribution to neurological diseases.
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Affiliation(s)
- Rachel M. Bear
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta GA 30322
- Graduate Program in Neuroscience
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta GA 30322
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Peng C, Wu DD, Ren JL, Peng ZL, Ma Z, Wu W, Lv Y, Wang Z, Deng C, Jiang K, Parkinson CL, Qi Y, Zhang ZY, Li JT. Large-scale snake genome analyses provide insights into vertebrate development. Cell 2023; 186:2959-2976.e22. [PMID: 37339633 DOI: 10.1016/j.cell.2023.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 04/06/2023] [Accepted: 05/19/2023] [Indexed: 06/22/2023]
Abstract
Snakes are a remarkable squamate lineage with unique morphological adaptations, especially those related to the evolution of vertebrate skeletons, organs, and sensory systems. To clarify the genetic underpinnings of snake phenotypes, we assembled and analyzed 14 de novo genomes from 12 snake families. We also investigated the genetic basis of the morphological characteristics of snakes using functional experiments. We identified genes, regulatory elements, and structural variations that have potentially contributed to the evolution of limb loss, an elongated body plan, asymmetrical lungs, sensory systems, and digestive adaptations in snakes. We identified some of the genes and regulatory elements that might have shaped the evolution of vision, the skeletal system and diet in blind snakes, and thermoreception in infrared-sensitive snakes. Our study provides insights into the evolution and development of snakes and vertebrates.
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Affiliation(s)
- Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jin-Long Ren
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Zhong-Liang Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhifei Ma
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; College of Life Science, Neijiang Normal University, Neijiang, Sichuan 641100, China
| | - Zeng Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cao Deng
- Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 610000, China
| | - Ke Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | | | - Yin Qi
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Zhi-Yi Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar.
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7
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Holroyd NA, Walsh C, Gourmet L, Walker-Samuel S. Quantitative Image Processing for Three-Dimensional Episcopic Images of Biological Structures: Current State and Future Directions. Biomedicines 2023; 11:909. [PMID: 36979887 PMCID: PMC10045950 DOI: 10.3390/biomedicines11030909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Episcopic imaging using techniques such as High Resolution Episcopic Microscopy (HREM) and its variants, allows biological samples to be visualized in three dimensions over a large field of view. Quantitative analysis of episcopic image data is undertaken using a range of methods. In this systematic review, we look at trends in quantitative analysis of episcopic images and discuss avenues for further research. Papers published between 2011 and 2022 were analyzed for details about quantitative analysis approaches, methods of image annotation and choice of image processing software. It is shown that quantitative processing is becoming more common in episcopic microscopy and that manual annotation is the predominant method of image analysis. Our meta-analysis highlights where tools and methods require further development in this field, and we discuss what this means for the future of quantitative episcopic imaging, as well as how annotation and quantification may be automated and standardized across the field.
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Affiliation(s)
| | - Claire Walsh
- Centre for Computational Medicine, University College London, London WC1E 6DD, UK
- Department of Mechanical Engineering, University College London, London WC1E 7JE, UK
| | - Lucie Gourmet
- Centre for Computational Medicine, University College London, London WC1E 6DD, UK
| | - Simon Walker-Samuel
- Centre for Computational Medicine, University College London, London WC1E 6DD, UK
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Wang H, Nie W, Wang C, Wang Z, Zheng Y. Novel CPLANE1 c.8948dupT (p.P2984Tfs*7) variant in a child patient with Joubert syndrome. Open Life Sci 2023; 18:20220542. [PMID: 36789003 PMCID: PMC9896164 DOI: 10.1515/biol-2022-0542] [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: 07/28/2022] [Revised: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 02/04/2023] Open
Abstract
Joubert syndrome (JBTS) is a class of heterogeneous ciliopathy genetically associated with CPLANE1 mutations. The characteristics of clinical phenotypes and CPLANE1 variants were analyzed in a 2-month-old patient. A 2-month-old patient with JBTS was diagnosed after clinical evaluation including family history, physical examination, cerebral MRI, ultrasonography imaging, VEGG, ocular fundus examination, and comprehensive blood and urine testing. Whole exome sequencing (WES) was performed to detect CPLANE1 variants, and Sanger sequencing was used to confirm the variants. This JBTS patient presented with oculomotor apraxia, dysregulation of breathing pattern, and ataxia. MRI revealed poor continuity of cerebelli, batwing appearance, and molar tooth sign. This patient was noted with abnormal hematology, dysregulation of hepatic function, thyroid function, immunity, and renal function, and encephalopathy. CPLANE1 (c.8948dupT (p.P2984Tfs*7) and c.247G > T (p.G83X)) variants were noticed in the patient as a pathogenic variant and caused autosomal recessive inheritance. The JBTS patient with mutations in CPLANE1 (c.8948dupT (p.P2984Tfs*7) and c.247G > T (p.G83X)) developed JBTS phenotypes. The novel CPLANE1 c.8948dupT (p.P2984Tfs*7) variant will assist clinicians and geneticists in reaching a precise diagnosis for JBTS.
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Affiliation(s)
- Huiping Wang
- Department of Neurology, Kunming Children’s Hospital, Kunming Children’s Hospital Affiliated with Kunming Medical University, No. 288, Qianxing Road, Xishan District, Kunming 650228, China
| | - Wensha Nie
- Department of Neurology, Kunming Children’s Hospital, Kunming Children’s Hospital Affiliated with Kunming Medical University, No. 288, Qianxing Road, Xishan District, Kunming 650228, China
| | - Chunxia Wang
- Department of Neurology, Kunming Children’s Hospital, Kunming Children’s Hospital Affiliated with Kunming Medical University, No. 288, Qianxing Road, Xishan District, Kunming 650228, China
| | - Zuohua Wang
- Department of Neurology, Kunming Children’s Hospital, Kunming Children’s Hospital Affiliated with Kunming Medical University, No. 288, Qianxing Road, Xishan District, Kunming 650228, China
| | - Yuxia Zheng
- Department of Neurology, Kunming Children’s Hospital, Kunming Children’s Hospital Affiliated with Kunming Medical University, No. 288, Qianxing Road, Xishan District, Kunming 650228, China
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9
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Zhang J, Wang L, Chen W, Duan J, Meng Y, Yang H, Guo Q. Whole exome sequencing facilitated the diagnosis in four Chinese pediatric cases of Joubert syndrome related disorders. Am J Transl Res 2022; 14:5088-5097. [PMID: 35958498 PMCID: PMC9360900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES Joubert syndrome is a spectrum of rare genetic disorders, mainly characterized by a distinctive cerebellar and brain stem malformation called the "molar tooth sign" (MTS), hypotonia, and intellectual disability/developmental delay. METHODS In this study, 4 pediatric cases with developmental delay and oculomotor abnormities were recruited, and submitted to a clinical evaluation and magnetic resonance imaging (MRI) examination. Afterwards, genetic detection with whole exome sequencing (WES) was conducted on the 4 patients. RESULTS Imaging results demonstrated cerebellar dysplasia in all probands, yet the MTS findings varied in severity. WES detected diagnostic variations in all four probands, which were distributed in four genes, namely CC2D2A, NPHP1, AHI1, and C5orf42. Two variants were novelly identified, which were the CC2D2A: c.2444delC (p.P815fs*2) and the AIH1: exon (15-17) del. In silico analysis supported the pathogenicity of the variations in this study. CONCLUSIONS Our findings expanded the mutation spectrum of Joubert syndrome related disorders, and provided solid evidence to the affected families for further genetic counseling and pregnancy guidance.
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Affiliation(s)
- Jing Zhang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Medical University (Key Laboratory of Maternal and Fetal Medicine of Hebei Province)Shijiazhuang, Hebei, China
| | - Lihui Wang
- Neurology Department, Children’s Hospital of Hebei Province, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Wenqi Chen
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Medical University (Key Laboratory of Maternal and Fetal Medicine of Hebei Province)Shijiazhuang, Hebei, China
| | - Jun Duan
- Radiology Department, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Yanxin Meng
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Medical University (Key Laboratory of Maternal and Fetal Medicine of Hebei Province)Shijiazhuang, Hebei, China
| | - Huafang Yang
- Neurology Department, Children’s Hospital of Hebei Province, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Qing Guo
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Hebei Medical University (Key Laboratory of Maternal and Fetal Medicine of Hebei Province)Shijiazhuang, Hebei, China
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10
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Qian W, Liu X, Wang Z, Xu Y, Zhang J, Li H, Zhong Q, Li C, Zhu L, Zhou Z, Pan W. Whole-exome sequencing identified novel variants in CPLANE1 that causes oral-facial-digital syndrome Ⅵ by inducing primary cilia abnormality. J Cell Mol Med 2022; 26:3213-3222. [PMID: 35582950 PMCID: PMC9170817 DOI: 10.1111/jcmm.17326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/25/2022] [Accepted: 03/26/2022] [Indexed: 11/29/2022] Open
Abstract
Oral‐facial‐digital syndrome (OFDS) is a multisystemic ciliopathic disorder with an autosomal recessive mode of inheritance. OFDS usually manifests with typical craniofacial anomalies and variable occurrence of polydactyly. Germline variants in CPLANE1 cause OFDS VI. In this study, we investigated a 26‐year‐old Chinese female patient who was 23+1 weeks pregnant. She had a history of adverse pregnancy outcomes with multiple foetal malformations. We performed ultrasonography and identified the foetus as having a posterior fossa Blake cyst and postaxial polydactyly. The patient decided to terminate her pregnancy, and further genetic molecular analysis was performed. We identified the aborted foetus as having postaxial polydactyly. Whole‐exome sequencing identified a missense variant (c.3599C>T, p.A1200V) in exon 20 and a c.834+1G>T variant in exon 7 of CPLANE1 (NM_023073.3) in the foetus. Sanger sequencing confirmed that these variants came from the parents of the foetus. In this study, we investigated a family with OFDS VI through genetic testing and bioinformatics analysis, which provided powerful help for prenatal diagnosis. Then, we demonstrated that the cell migration rate and the number of cilia were decreased after interference with CPLANE1 expression in NIH/3T3 cells. After CPLANE1 knockdown, the Hh signalling pathway was inhibited, and the Hh pathway activator SAG reversed the inhibitory effect. This is the first report of a family with OFDS VI in the Chinese population.
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Affiliation(s)
- Wen Qian
- Prenatal Diagnosis Center in Guizhou Province, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xinlei Liu
- Prenatal Diagnosis Center in Guizhou Province, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhengrong Wang
- Prenatal Diagnosis Center in Guizhou Province, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.,School of Medical Laboratory, Guizhou Medical University, Guiyang, China
| | - Yongjie Xu
- School of Public Health, Key Laboratory of Environmental Pollution Monitoring and Disease Control, Guizhou Medical University, Guiyang, China
| | - Jingzhi Zhang
- School of Public Health, Key Laboratory of Environmental Pollution Monitoring and Disease Control, Guizhou Medical University, Guiyang, China
| | - Haizhi Li
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Qiang Zhong
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Chengcheng Li
- Prenatal Diagnosis Center in Guizhou Province, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Liying Zhu
- School of Medical Laboratory, Guizhou Medical University, Guiyang, China
| | - Zunlun Zhou
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Wei Pan
- Prenatal Diagnosis Center in Guizhou Province, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.,School of Medical Laboratory, Guizhou Medical University, Guiyang, China.,School of Public Health, Key Laboratory of Environmental Pollution Monitoring and Disease Control, Guizhou Medical University, Guiyang, China
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11
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Djenoune L, Berg K, Brueckner M, Yuan S. A change of heart: new roles for cilia in cardiac development and disease. Nat Rev Cardiol 2022; 19:211-227. [PMID: 34862511 PMCID: PMC10161238 DOI: 10.1038/s41569-021-00635-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/27/2022]
Abstract
Although cardiac abnormalities have been observed in a growing class of human disorders caused by defective primary cilia, the function of cilia in the heart remains an underexplored area. The primary function of cilia in the heart was long thought to be restricted to left-right axis patterning during embryogenesis. However, new findings have revealed broad roles for cilia in congenital heart disease, valvulogenesis, myocardial fibrosis and regeneration, and mechanosensation. In this Review, we describe advances in our understanding of the mechanisms by which cilia function contributes to cardiac left-right axis development and discuss the latest findings that highlight a broader role for cilia in cardiac development. Specifically, we examine the growing line of evidence connecting cilia function to the pathogenesis of congenital heart disease. Furthermore, we also highlight research from the past 10 years demonstrating the role of cilia function in common cardiac valve disorders, including mitral valve prolapse and aortic valve disease, and describe findings that implicate cardiac cilia in mechanosensation potentially linking haemodynamic and contractile forces with genetic regulation of cardiac development and function. Finally, given the presence of cilia on cardiac fibroblasts, we also explore the potential role of cilia in fibrotic growth and summarize the evidence implicating cardiac cilia in heart regeneration.
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Affiliation(s)
- Lydia Djenoune
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kathryn Berg
- Department of Paediatrics, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Martina Brueckner
- Department of Paediatrics, Yale University School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Shiaulou Yuan
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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12
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Chang CH, Chen TY, Tang TK. Using in vivo cerebellar electroporation to study neuronal cell proliferation and differentiation in a Joubert syndrome mouse model. Methods Cell Biol 2022; 175:235-249. [PMID: 36967143 DOI: 10.1016/bs.mcb.2022.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Joubert syndrome (JS) is an autosomal recessive ciliopathy that mainly affects the morphogenesis of the cerebellum and brain stem. To date, mutations in at least 39 genes have been identified in JS; all these gene-encoding proteins are involved in the biogenesis of the primary cilium and centrioles. Recent studies using the mouse model carrying deleted or mutated JS-related genes exhibited cerebellar hypoplasia with a reduction in neurogenesis; however, investigating specific neuronal behaviors during their development in vivo remains challenging. Here, we describe an in vivo cerebellar electroporation technique that can be used to deliver plasmids carrying GFP and/or shRNAs into the major cerebellar cell type, granule neurons, from their progenitor state to their maturation in a spatiotemporal-specific manner. By combining this method with cerebellar immunostaining and EdU incorporation, these approaches enable the investigation of the cell-autonomous effect of JS-related genes in granule neuron progenitors, including the pathogenesis of ectopic neurons and the defects in neuronal differentiation. This approach provides information toward understanding the multifaceted roles of JS-related genes during cerebellar development in vivo.
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Affiliation(s)
| | - Ting-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tang K Tang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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13
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Patel TN, Dhanyamraju PK. Role of aberrant Sonic hedgehog signaling pathway in cancers and developmental anomalies. J Biomed Res 2021; 36:1-9. [PMID: 34963676 PMCID: PMC8894283 DOI: 10.7555/jbr.35.20210139] [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] [Indexed: 12/02/2022] Open
Abstract
Development is a sophisticated process maintained by various signal transduction pathways, including the Hedgehog (Hh) pathway. Several important functions are executed by the Hh signaling cascade such as organogenesis, tissue regeneration, and tissue homeostasis, among various others. Considering the multiple functions carried out by this pathway, any mutation causing aberrant Hh signaling may lead to myriad developmental abnormalities besides cancers. In the present review article, we explored a wide range of diseases caused by aberrant Hh signaling, including developmental defects and cancers. Finally, we concluded this mini-review with various treatment strategies for Hh-induced diseases.
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Affiliation(s)
- Trupti N Patel
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Pavan Kumar Dhanyamraju
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA.,Penn State Cancer Institute, Hershey, PA 17033, USA
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14
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Rasheed M, Khan V, Harripaul R, Siddiqui M, Malik MA, Ullah Z, Zahid M, Vincent JB, Ansar M. Exome sequencing identifies novel and known mutations in families with intellectual disability. BMC Med Genomics 2021; 14:211. [PMID: 34452636 PMCID: PMC8399827 DOI: 10.1186/s12920-021-01066-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/25/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) is a phenotypically and genetically heterogeneous disorder. METHODS In this study, genome wide SNP microarray and whole exome sequencing are used for the variant identification in eight Pakistani families with ID. Beside ID, most of the affected individuals had speech delay, facial dysmorphism and impaired cognitive abilities. Repetitive behavior was observed in MRID143, while seizures were reported in affected individuals belonging to MRID137 and MRID175. RESULTS In two families (MRID137b and MRID175), we identified variants in the genes CCS and ELFN1, which have not previously been reported to cause ID. In four families, variants were identified in ARX, C5orf42, GNE and METTL4. A copy number variation (CNV) was identified in IL1RAPL1 gene in MRID165. CONCLUSION These findings expand the existing knowledge of variants and genes implicated in autosomal recessive and X linked ID.
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Affiliation(s)
- Memoona Rasheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Valeed Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Maimoona Siddiqui
- Division of Neurology, Shifa College of Medicine, H-8/1, Islamabad, Pakistan
| | - Madiha Amin Malik
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Zahid Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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15
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Conduit SE, Davies EM, Fulcher AJ, Oorschot V, Mitchell CA. Superresolution Microscopy Reveals Distinct Phosphoinositide Subdomains Within the Cilia Transition Zone. Front Cell Dev Biol 2021; 9:634649. [PMID: 33996795 PMCID: PMC8120242 DOI: 10.3389/fcell.2021.634649] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 04/06/2021] [Indexed: 11/30/2022] Open
Abstract
Primary cilia are evolutionary conserved microtubule-based organelles that protrude from the surface of most mammalian cells. Phosphoinositides (PI) are membrane-associated signaling lipids that regulate numerous cellular events via the recruitment of lipid-binding effectors. The temporal and spatial membrane distribution of phosphoinositides is regulated by phosphoinositide kinases and phosphatases. Recently phosphoinositide signaling and turnover has been observed at primary cilia. However, the precise localization of the phosphoinositides to specific ciliary subdomains remains undefined. Here we use superresolution microscopy (2D stimulated emission depletion microscopy) to map phosphoinositide distribution at the cilia transition zone. PI(3,4,5)P3 and PI(4,5)P2 localized to distinct subregions of the transition zone in a ring-shape at the inner transition zone membrane. Interestingly, the PI(3,4,5)P3 subdomain was more distal within the transition zone relative to PtdIns(4,5)P2. The phosphoinositide effector kinase pAKT(S473) localized in close proximity to these phosphoinositides. The inositol polyphosphate 5-phosphatase, INPP5E, degrades transition zone phosphoinositides, however, studies of fixed cells have reported recombinant INPP5E localizes to the ciliary axoneme, distant from its substrates. Notably, here using live cell imaging and optimized fixation/permeabilization protocols INPP5E was found concentrated at the cilia base, in a distribution characteristic of the transition zone in a ring-shaped domain of similar dimensions to the phosphoinositides. Collectively, this superresolution map places the phosphoinositides in situ with the transition zone proteins and reveals that INPP5E also likely localizes to a subdomain of the transition zone membrane, where it is optimally situated to control local phosphoinositide metabolism.
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Affiliation(s)
- Sarah E Conduit
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Elizabeth M Davies
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, VIC, Australia
| | - Viola Oorschot
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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16
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Wiegering A, Dildrop R, Vesque C, Khanna H, Schneider-Maunoury S, Gerhardt C. Rpgrip1l controls ciliary gating by ensuring the proper amount of Cep290 at the vertebrate transition zone. Mol Biol Cell 2021; 32:675-689. [PMID: 33625872 PMCID: PMC8108517 DOI: 10.1091/mbc.e20-03-0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A range of severe human diseases called ciliopathies is caused by the dysfunction of primary cilia. Primary cilia are cytoplasmic protrusions consisting of the basal body (BB), the axoneme, and the transition zone (TZ). The BB is a modified mother centriole from which the axoneme, the microtubule-based ciliary scaffold, is formed. At the proximal end of the axoneme, the TZ functions as the ciliary gate governing ciliary protein entry and exit. Since ciliopathies often develop due to mutations in genes encoding proteins that localize to the TZ, the understanding of the mechanisms underlying TZ function is of eminent importance. Here, we show that the ciliopathy protein Rpgrip1l governs ciliary gating by ensuring the proper amount of Cep290 at the vertebrate TZ. Further, we identified the flavonoid eupatilin as a potential agent to tackle ciliopathies caused by mutations in RPGRIP1L as it rescues ciliary gating in the absence of Rpgrip1l.
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Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.,Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Renate Dildrop
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Christine Vesque
- Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Hemant Khanna
- Department of Ophthalmology and Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sylvie Schneider-Maunoury
- Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
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17
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Liu Q, Wang H, Zhao J, Liu Z, Sun D, Yuan A, Luo G, Wei W, Hou M. Four novel compound heterozygous mutations in C5orf42 gene in patients with pure and mild Joubert syndrome. Int J Dev Neurosci 2020; 80:455-463. [PMID: 32233090 DOI: 10.1002/jdn.10029] [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: 02/03/2020] [Revised: 03/09/2020] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
Joubert syndrome (JS) is a rare clinically and genetically heterogeneous disease. Using whole or targeted exome sequencing, we identified four novel compound heterozygous mutations in chromosome 5 open reading frame 42 gene (C5orf42), including c.2876C>T (missense mutation) and c.3921+1G>A (splicing mutation), c.2292 -2delA (splicing mutation) and c.4067C>T (missense mutation), c.6997_6998insT (frameshift mutation) and c.8710C>T (nonsense mutation), c.3981G>C (nonsense mutation) and c.230 _233del (frameshift mutation), in four Chinese JS families. They were all inherited from their heterozygosis parents in the autosomal recessive inheritance mode. Pure JS clinical manifestations and mild neuroimaging findings were found in these patients. These verified the previous findings that C5orf42 mutations generally resulted in a purely neurological Joubert phenotype, and neuroimaging findings were mild in JS with C5orf42 mutations. Our report analyzed these C5orf42 mutations-associated phenotypes and neuroimaging findings in JS and updated the genetic variation spectrum of JS caused by C5orf42.These will help clinicians and geneticists reach a more accurate diagnosis for JS.
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Affiliation(s)
- Qiuyan Liu
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, P.R. China
| | - Haiqiao Wang
- Department of Traditional Chinese Medicine, School of Medicine, Ren Ji Hospital, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Jianhui Zhao
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, P.R. China
| | - Zhicui Liu
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, P.R. China
| | - Dianrong Sun
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, P.R. China
| | - Aiyun Yuan
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, P.R. China
| | - Guangjin Luo
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, P.R. China
| | - Wei Wei
- Kangso Medical Inspection Co., Ltd, Beijing, P.R. China
| | - Mei Hou
- Department of Neurology and Rehabilitation, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, P.R. China
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18
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Abstract
Our current understanding of genetic disease is often inadequate, largely due to genetic background effects that modify disease presentation. This is particularly challenging for rare diseases that lack sufficient numbers of patients for genome-wide association studies. We show in a series of experiments using a murine model of Joubert syndrome, a multisystem ciliopathy, that a single locus is a modifier of cystic kidney disease. We go on to show that the human homolog plays a similar role in disease using a cohort of patients. These findings make a significant contribution to the underplayed (and often ignored) role of genetic background in murine models and how this can be exploited to understand further rare inherited disease. Genetic and phenotypic heterogeneity and the lack of sufficiently large patient cohorts pose a significant challenge to understanding genetic associations in rare disease. Here we identify Bsnd (alias Barttin) as a genetic modifier of cystic kidney disease in Joubert syndrome, using a Cep290-deficient mouse model to recapitulate the phenotypic variability observed in patients by mixing genetic backgrounds in a controlled manner and performing genome-wide analysis of these mice. Experimental down-regulation of Bsnd in the parental mouse strain phenocopied the severe cystic kidney phenotype. A common polymorphism within human BSND significantly associates with kidney disease severity in a patient cohort with CEP290 mutations. The striking phenotypic modifications we describe are a timely reminder of the value of mouse models and highlight the significant contribution of genetic background. Furthermore, if appropriately managed, this can be exploited as a powerful tool to elucidate mechanisms underlying human disease heterogeneity.
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19
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Suzuki A, Yoshioka H, Summakia D, Desai NG, Jun G, Jia P, Loose DS, Ogata K, Gajera MV, Zhao Z, Iwata J. MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse. BMC Genomics 2019; 20:852. [PMID: 31727022 PMCID: PMC6854646 DOI: 10.1186/s12864-019-6238-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Background Cleft lip (CL), one of the most common congenital birth defects, shows considerable geographic and ethnic variation, with contribution of both genetic and environmental factors. Mouse genetic studies have identified several CL-associated genes. However, it remains elusive how these CL-associated genes are regulated and involved in CL. Environmental factors may regulate these genes at the post-transcriptional level through the regulation of non-coding microRNAs (miRNAs). In this study, we sought to identify miRNAs associated with CL in mice. Results Through a systematic literature review and a Mouse Genome Informatics (MGI) database search, we identified 55 genes that were associated with CL in mice. Subsequent bioinformatic analysis of these genes predicted that a total of 33 miRNAs target multiple CL-associated genes, with 20 CL-associated genes being potentially regulated by multiple miRNAs. To experimentally validate miRNA function in cell proliferation, we conducted cell proliferation/viability assays for the selected five candidate miRNAs (miR-124-3p, let-7a-5p, let-7b-5p, let-7c-5p, and let-7d-5p). Overexpression of miR-124-3p, but not of the others, inhibited cell proliferation through suppression of CL-associated genes in cultured mouse embryonic lip mesenchymal cells (MELM cells) isolated from the developing mouse lip region. By contrast, miR-124-3p knockdown had no effect on MELM cell proliferation. This miRNA-gene regulatory mechanism was mostly conserved in O9–1 cells, an established cranial neural crest cell line. Expression of miR-124-3p was low in the maxillary processes at E10.5, when lip mesenchymal cells proliferate, whereas it was greatly increased at later developmental stages, suggesting that miR-124-3p expression is suppressed during the proliferation phase in normal palate development. Conclusions Our findings indicate that upregulated miR-124-3p inhibits cell proliferation in cultured lip cells through suppression of CL-associated genes. These results will have a significant impact, not only on our knowledge about lip morphogenesis, but also on the development of clinical approaches for the diagnosis and prevention of CL.
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Affiliation(s)
- Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dima Summakia
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA
| | - Neha G Desai
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA.,Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Goo Jun
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David S Loose
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.,Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kenichi Ogata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mona V Gajera
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA.,Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhongming Zhao
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA. .,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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20
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Sasai N, Toriyama M, Kondo T. Hedgehog Signal and Genetic Disorders. Front Genet 2019; 10:1103. [PMID: 31781166 PMCID: PMC6856222 DOI: 10.3389/fgene.2019.01103] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
The hedgehog (Hh) family comprises sonic hedgehog (Shh), Indian hedgehog (Ihh), and desert hedgehog (Dhh), which are versatile signaling molecules involved in a wide spectrum of biological events including cell differentiation, proliferation, and survival; establishment of the vertebrate body plan; and aging. These molecules play critical roles from embryogenesis to adult stages; therefore, alterations such as abnormal expression or mutations of the genes involved and their downstream factors cause a variety of genetic disorders at different stages. The Hh family involves many signaling mediators and functions through complex mechanisms, and achieving a comprehensive understanding of the entire signaling system is challenging. This review discusses the signaling mediators of the Hh pathway and their functions at the cellular and organismal levels. We first focus on the roles of Hh signaling mediators in signal transduction at the cellular level and the networks formed by these factors. Then, we analyze the spatiotemporal pattern of expression of Hh pathway molecules in tissues and organs, and describe the phenotypes of mutant mice. Finally, we discuss the genetic disorders caused by malfunction of Hh signaling-related molecules in humans.
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Affiliation(s)
- Noriaki Sasai
- Developmental Biomedical Science, Division of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Michinori Toriyama
- Systems Neurobiology and Medicine, Division of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Toru Kondo
- Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
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21
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Gabriel GC, Lo CW. Novel insights into the genetic landscape of congenital heart disease with systems genetics. PROGRESS IN PEDIATRIC CARDIOLOGY 2019; 54. [PMID: 34404969 DOI: 10.1016/j.ppedcard.2019.101128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We recently conducted a large-scale mouse mutagenesis screen and uncovered a central role for cilia in the pathogenesis of congenital heart disease (CHD). Though our screen was phenotype based, most of the genes recovered were cilia-related, including genes encoding proteins important for ciliogenesis, cilia-transduced cell signaling, and vesicular trafficking. Also unexpected, many of the cilia related genes recovered are known direct protein-protein interactors, even though each gene was recovered independently in unrelated mouse lines. These findings suggest a cilia-based protein-protein interactome network may provide the context for congenital heart disease pathogenesis. This could explain the incomplete penetrance and variable expressivity of human CHD, and account for its complex non-Mendelian etiology. Supporting these findings in mice, a preponderance of cilia and cilia related cell signaling genes were observed among de novo pathogenic variants identified in a CHD patient cohort. Further clinical relevance unfolded with the observation of a high prevalence of respiratory cilia dysfunction in CHD patients. This was associated with increased postsurgical respiratory complications. Together these findings highlight the importance of cilia in CHD pathogenesis and suggest possible clinical translation with instituting pulmonary therapy to improve outcome for CHD patients undergoing congenital cardiac surgeries.
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Affiliation(s)
- George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States of America
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States of America
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22
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Hong H, Joo K, Park SM, Seo J, Kim MH, Shin E, Cheong HI, Lee JH, Kim J. Extraciliary roles of the ciliopathy protein JBTS17 in mitosis and neurogenesis. Ann Neurol 2019; 86:99-115. [PMID: 31004438 DOI: 10.1002/ana.25491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE JBTS17 is a major gene mutated in ciliopathies such as Joubert syndrome and oral-facial-digital syndrome type VI. Most patients with loss of function mutations in JBTS17 exhibit cerebellar vermis hypoplasia and brainstem malformation. However, some patients with JBTS17 mutations show microcephaly and abnormal gyration. We examined potential roles of JBTS17 in neurogenesis to understand the pathological mechanism of JBTS17-related cortical abnormalities. METHODS We examined subcellular localization and cell-cycle-dependent expression of JBTS17 proteins using anti-JBTS17 antibodies and JBTS17 expression vectors. We also performed knockdown experiments to determined roles of JBTS17 in human cells, and demonstrated mitotic functions of JBTS17 using immunostaining and live imaging. We examined the involvement of JBTS17 in cortical neurogenesis using a mouse in utero electroporation technique. RESULTS We found that JBTS17 localizes to the kinetochore and the level of JBTS17 is regulated by cell-cycle-dependent proteolysis. Depletion of JBTS17 disrupts chromosome alignment and spindle pole orientation, resulting in mitotic delay. JBTS17 interacts with LIS1 and influences LIS1 localization. Depletion of Jbts17 in the developing mouse cortex interferes with the mitotic progression of neural progenitors and the migration of postmitotic neurons. INTERPRETATION LIS1 is implicated in lissencephaly, but altered dosage of LIS1 has been also associated with microcephaly syndromes. Our results suggest that JBTS17 contributes to mitotic progression by interacting with LIS1, and abnormal mitosis is an underlying mechanism of the microcephaly phenotype in JBTS17-related ciliopathies. We propose that understanding extraciliary roles of ciliopathy proteins is important to elucidate pathological mechanisms underlying diverse ciliopathy phenotypes. ANN NEUROL 2019.
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Affiliation(s)
- Hyowon Hong
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam
| | - Sang Min Park
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon
| | - Jimyung Seo
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon
| | - Min Hwan Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon
| | - EunBie Shin
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon
| | - Hae Il Cheong
- Department Pediatrics, Seoul National University Children's Hospital, Seoul; and 5Research Coordination Center for Rare Disease, Seoul National University Hospital, Seoul, Korea
| | - Jeong Ho Lee
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon
| | - Joon Kim
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon
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23
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Buneeva O, Kopylov A, Kapitsa I, Ivanova E, Zgoda V, Medvedev A. The Effect of Neurotoxin MPTP and Neuroprotector Isatin on the Profile of Ubiquitinated Brain Mitochondrial Proteins. Cells 2018; 7:E91. [PMID: 30065189 PMCID: PMC6115780 DOI: 10.3390/cells7080091] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/30/2022] Open
Abstract
Mitochondria are a crucial target for the actions of neurotoxins, causing symptoms of Parkinson's disease in various experimental animal models, and also neuroprotectors. There is evidence that mitochondrial dysfunction induced by the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) influences functioning of the ubiquitin-proteasomal system (UPS) responsible for selective proteolytic degradation of proteins from various intracellular compartments (including mitochondria) and neuroprotective effects of certain anti-Parkisonian agents (monoamine oxidase inhibitors) may be associated with their effects on the UPS. In this study, we have investigated the effect of the neurotoxin MPTP and neuroprotector isatin, and their combination on the profile of ubiquitinated brain mitochondrial proteins. The development of movement disorders induced by MPTP administration caused dramatic changes in the profile of ubiquitinated proteins associated with mitochondria. Pretreatment with the neuroprotector isatin decreased manifestations of MPTP-induced Parkinsonism, and had a significant impact on the profile of ubiquitinated mitochondrial proteins (including oxidative modified proteins). Administration of isatin alone to intact mice also influenced the profile of ubiquitinated mitochondrial proteins, and increased the proportion of oxidized proteins carrying the ubiquitination signature. These alterations in the ubiquitination of mitochondrial proteins observed within 2 h after administration of MPTP and isatin obviously reflect immediate short-term biological responses to these treatments.
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Affiliation(s)
- Olga Buneeva
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
| | - Arthur Kopylov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
| | - Inga Kapitsa
- Zakusov Institute of Pharmacology, 8 Baltiskaya Street, Moscow 124315, Russia.
| | - Elena Ivanova
- Zakusov Institute of Pharmacology, 8 Baltiskaya Street, Moscow 124315, Russia.
| | - Victor Zgoda
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
| | - Alexei Medvedev
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
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24
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Song P, Perkins BD. Developmental expression of the zebrafish Arf-like small GTPase paralogs arl13a and arl13b. Gene Expr Patterns 2018; 29:82-87. [PMID: 30009987 DOI: 10.1016/j.gep.2018.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
Abstract
Members of the Arf-like (Arl) family of small GTP-binding proteins regulate a number of cellular functions and play important roles in cilia structure and signaling. The small GTPase Arl13a is a close paralog to Arl13b, a small GTPase required for normal cilia formation that causes Joubert Syndrome when mutated. As mutation of arl13b causes a slow retinal degeneration in zebrafish (Song et al., 2016), we hypothesized that expression of arl13a may provide functional redundancy. We determined the expression domains of arl13a and arl13b during zebrafish development and examined subcellular localization by expression of fluorescence fusion proteins. Both genes are widely expressed during early cell division and gastrulation and Arl13a and Arl13b both localize to microtubules in ciliated and dividing cells of the early zebrafish embryo. Between 2 and 5 days post fertilization (dpf), arl13b is expressed in neural tissues while expression of arl13a is downregulated by 2 dpf and restricted to craniofacial structures. These results indicate that arl13a and arl13b have evolved different roles and that arl13a does not function in the zebrafish retina.
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Affiliation(s)
- Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Brian D Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
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25
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Xu J, Wu Q, Wang L, Han J, Pei Y, Zhi W, Liu Y, Yin C, Jiang Y. Next-generation sequencing identified genetic variations in families with fetal non-syndromic atrioventricular septal defects. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3732-3743. [PMID: 31949757 PMCID: PMC6962893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/09/2018] [Indexed: 06/10/2023]
Abstract
Atrioventricular septal defects (AVSDs) account for approximately 5% of all congenital heart disease (CHD). About half of AVSDs are diagnosed in cases with trisomy 21 (Down's syndrome, DS). However, many AVSDs occur sporadically and manifest as non-syndromic. The pathogenesis is complex and has not yet been fully elucidated. In the present study, we applied two advanced applications of next-generation sequencing (NGS) to explore the genetic variations in families with fetal non-syndromic AVSDs. Our study was mainly divided into two steps: (1) low-pass whole-genome sequencing (WGS) was used to detect the genome-wide copy number variations (CNVs) for included subjects; (2) whole-exome sequencing (WES) was used to detect the gene mutations for the subjects without AVSD-associated CNVs. A total of 17 heterozygous de novo CNVs and 19 heterozygous de novo gene mutations were selected, and 15 candidate genes were involved in these variations. Among these heterozygous de novo variations, most have potential pathogenicity for AVSDs, but the others require further investigation to confirm their pathogenicity. Our study not only shows the genetic diversity and the etiological complexity of AVSDs but also shows the rationality and practicability of this sequential genetic detection and analysis strategy.
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Affiliation(s)
- Jinyu Xu
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Qingqing Wu
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Li Wang
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Jijing Han
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Yan Pei
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Wenxue Zhi
- Department of Pathology, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Yan Liu
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Chenghong Yin
- Department of Internal Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijing, China
| | - Yuxin Jiang
- Department of Ultrasound, Peking Union Medical College HospitalBeijing, China
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Christie KR, Blake JA. Sensing the cilium, digital capture of ciliary data for comparative genomics investigations. Cilia 2018; 7:3. [PMID: 29713460 PMCID: PMC5907423 DOI: 10.1186/s13630-018-0057-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 04/03/2018] [Indexed: 01/03/2023] Open
Abstract
Background Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work. Methods We focused on the capture of information about cilia as studied in the laboratory mouse, a primary model of human biology. The workflow developed establishes a standard for capture of comparative functional data relevant to human biology. We established the 310 closest mouse orthologs of the 302 human genes defined in the SYSCILIA Gold Standard set of ciliary genes. For the mouse genes, we identified biomedical literature for curation and used Gene Ontology (GO) curation paradigms to provide functional annotations from these publications. Results Employing a methodology for comprehensive capture of experimental data about cilia genes in structured, digital form, we established a workflow for curation of experimental literature detailing molecular function and roles of cilia proteins starting with the mouse orthologs of the human SYSCILIA gene set. We worked closely with the GO Consortium ontology development editors and the SYSCILIA Consortium to improve the representation of ciliary biology within the GO. During the time frame of the ontology improvement project, we have fully curated 134 of these 310 mouse genes, resulting in an increase in the number of ciliary and other experimental annotations. Conclusions We have improved the GO annotations available for mouse genes orthologous to the human genes in the SYSCILIA Consortium’s Gold Standard set. In addition, ciliary terminology in the GO itself was improved in collaboration with GO ontology developers and the SYSCILIA Consortium. These improvements to the GO terms for the functions and roles of ciliary proteins, along with the increase in annotations of the corresponding genes, enhance the representation of ciliary processes and localizations and improve access to these data during large-scale bioinformatic analyses. Electronic supplementary material The online version of this article (10.1186/s13630-018-0057-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karen R Christie
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Judith A Blake
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
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Clinical and experimental evidence suggest a link between KIF7 and C5orf42-related ciliopathies through Sonic Hedgehog signaling. Eur J Hum Genet 2018; 26:197-209. [PMID: 29321670 PMCID: PMC5839020 DOI: 10.1038/s41431-017-0019-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 09/11/2017] [Accepted: 09/19/2017] [Indexed: 01/03/2023] Open
Abstract
Acrocallosal syndrome (ACLS) is an autosomal recessive neurodevelopmental disorder caused by KIF7 defects and belongs to the heterogeneous group of ciliopathies related to Joubert syndrome (JBTS). While ACLS is characterized by macrocephaly, prominent forehead, depressed nasal bridge, and hypertelorism, facial dysmorphism has not been emphasized in JBTS cohorts with molecular diagnosis. To evaluate the specificity and etiology of ACLS craniofacial features, we performed whole exome or targeted Sanger sequencing in patients with the aforementioned overlapping craniofacial appearance but variable additional ciliopathy features followed by functional studies. We found (likely) pathogenic variants of KIF7 in 5 out of 9 families, including the original ACLS patients, and delineated 1000 to 4000-year-old Swiss founder alleles. Three of the remaining families had (likely) pathogenic variants in the JBTS gene C5orf42, and one patient had a novel de novo frameshift variant in SHH known to cause autosomal dominant holoprosencephaly. In accordance with the patients' craniofacial anomalies, we showed facial midline widening after silencing of C5orf42 in chicken embryos. We further supported the link between KIF7, SHH, and C5orf42 by demonstrating abnormal primary cilia and diminished response to a SHH agonist in fibroblasts of C5orf42-mutated patients, as well as axonal pathfinding errors in C5orf42-silenced chicken embryos similar to those observed after perturbation of Shh signaling. Our findings, therefore, suggest that beside the neurodevelopmental features, macrocephaly and facial widening are likely more general signs of disturbed SHH signaling. Nevertheless, long-term follow-up revealed that C5orf42-mutated patients showed catch-up development and fainting of facial features contrary to KIF7-mutated patients.
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28
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Klena NT, Gibbs BC, Lo CW. Cilia and Ciliopathies in Congenital Heart Disease. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028266. [PMID: 28159874 DOI: 10.1101/cshperspect.a028266] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A central role for cilia in congenital heart disease (CHD) was recently identified in a large-scale mouse mutagenesis screen. Although the screen was phenotype-driven, the majority of genes recovered were cilia-related, suggesting that cilia play a central role in CHD pathogenesis. This partly reflects the role of cilia as a hub for cell signaling pathways regulating cardiovascular development. Consistent with this, many cilia-transduced cell signaling genes were also recovered, and genes regulating vesicular trafficking, a pathway essential for ciliogenesis and cell signaling. Interestingly, among CHD-cilia genes recovered, some regulate left-right patterning, indicating cardiac left-right asymmetry disturbance may play significant roles in CHD pathogenesis. Clinically, CHD patients show a high prevalence of ciliary dysfunction and show enrichment for de novo mutations in cilia-related pathways. Combined with the mouse findings, this would suggest CHD may be a new class of ciliopathy.
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Affiliation(s)
- Nikolai T Klena
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201
| | - Brian C Gibbs
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201
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29
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Abstract
Motile and non-motile (primary) cilia are nearly ubiquitous cellular organelles. The dysfunction of cilia causes diseases known as ciliopathies. The number of reported ciliopathies (currently 35) is increasing, as is the number of established (187) and candidate (241) ciliopathy-associated genes. The characterization of ciliopathy-associated proteins and phenotypes has improved our knowledge of ciliary functions. In particular, investigating ciliopathies has helped us to understand the molecular mechanisms by which the cilium-associated basal body functions in early ciliogenesis, as well as how the transition zone functions in ciliary gating, and how intraflagellar transport enables cargo trafficking and signalling. Both basic biological and clinical studies are uncovering novel ciliopathies and the ciliary proteins involved. The assignment of these proteins to different ciliary structures, processes and ciliopathy subclasses (first order and second order) provides insights into how this versatile organelle is built, compartmentalized and functions in diverse ways that are essential for human health.
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30
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Bangs F, Anderson KV. Primary Cilia and Mammalian Hedgehog Signaling. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028175. [PMID: 27881449 DOI: 10.1101/cshperspect.a028175] [Citation(s) in RCA: 400] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
It has been a decade since it was discovered that primary cilia have an essential role in Hedgehog (Hh) signaling in mammals. This discovery came from screens in the mouse that identified a set of genes that are required for both normal Hh signaling and for the formation of primary cilia. Since then, dozens of mouse mutations have been identified that disrupt cilia in a variety of ways and have complex effects on Hedgehog signaling. Here, we summarize the genetic and developmental studies used to deduce how Hedgehog signal transduction is linked to cilia and the complex effects that perturbation of cilia structure can have on Hh signaling. We conclude by describing the current status of our understanding of the cell-type-specific regulation of ciliogenesis and how that determines the ability of cells to respond to Hedgehog ligands.
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Affiliation(s)
- Fiona Bangs
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Kathryn V Anderson
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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31
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Gonçalves J, Pelletier L. The Ciliary Transition Zone: Finding the Pieces and Assembling the Gate. Mol Cells 2017; 40:243-253. [PMID: 28401750 PMCID: PMC5424270 DOI: 10.14348/molcells.2017.0054] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cilia are organelles that project from the surface of cells to fulfill motility and sensory functions. In vertebrates, the functions of both motile and immotile cilia are critical for embryonic development and adult tissue homeostasis. Importantly, a multitude of human diseases is caused by abnormal cilia biogenesis and functions which rely on the compartmentalization of the cilium and the maintenance of its protein composition. The transition zone (TZ) is a specialized ciliary domain present at the base of the cilium and is part of a gate that controls protein entry and exit from this organelle. The relevance of the TZ is highlighted by the fact that several of its components are coded by ciliopathy genes. Here we review recent developments in the study of TZ proteomes, the mapping of individual components to the TZ structure and the establishment of the TZ as a lipid gate.
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Affiliation(s)
- João Gonçalves
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5,
Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8,
Canada
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32
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Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelley MR, Kim S, Park TJ, Braun D, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-lami HA, Yeung Y, Choi YJ, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB. The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Nat Genet 2016; 48:648-56. [PMID: 27158779 PMCID: PMC4978421 DOI: 10.1038/ng.3558] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/01/2016] [Indexed: 12/21/2022]
Abstract
Cilia use microtubule-based intraflagellar transport (IFT) to organize intercellular signaling. Ciliopathies are a spectrum of human diseases resulting from defects in cilia structure or function. The mechanisms regulating the assembly of ciliary multiprotein complexes and the transport of these complexes to the base of cilia remain largely unknown. Combining proteomics, in vivo imaging and genetic analysis of proteins linked to planar cell polarity (Inturned, Fuzzy and Wdpcp), we identified and characterized a new genetic module, which we term CPLANE (ciliogenesis and planar polarity effector), and an extensive associated protein network. CPLANE proteins physically and functionally interact with the poorly understood ciliopathy-associated protein Jbts17 at basal bodies, where they act to recruit a specific subset of IFT-A proteins. In the absence of CPLANE, defective IFT-A particles enter the axoneme and IFT-B trafficking is severely perturbed. Accordingly, mutation of CPLANE genes elicits specific ciliopathy phenotypes in mouse models and is associated with ciliopathies in human patients.
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Affiliation(s)
| | - Chanjae Lee
- Dept. of Molecular Biosciences, University of Texas at Austin
| | - S. Paige Taylor
- Departments of Orthopaedic Surgery, Human Genetics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Ivan Duran
- Departments of Orthopaedic Surgery, Human Genetics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Daniel H. Cohn
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, California, USA, 90095
| | - Ange-Line Bruel
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, F-21079 Dijon, France
| | | | - Kevin Drew
- Dept. of Molecular Biosciences, University of Texas at Austin
| | - Marcus R. Kelley
- Stanford University School of Medicine, Baxter Laboratory, Department of Microbiology & Immunology, Stanford, California 94305
| | - Sukyoung Kim
- Dept. of Molecular Biosciences, University of Texas at Austin
| | - Tae Joo Park
- Dept. of Molecular Biosciences, University of Texas at Austin
| | - Daniella Braun
- HHMI and Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Kerstin Wagner
- Cardiological Pediatric unit, Hospital Center, Luxemburg
| | - Anne Malfroot
- Clinic of Pediatric Respiratory Diseases, Infectious Diseases, Travel Clinic and Cystic Fibrosis Clinic at the Universitair Ziekenhuis UZ Brussel, Belgium
| | - Inusha Panigrahi
- Department of Pediatrics Advanced, Pediatric Centre Pigmer, Chandigarh, India
| | - Brunella Franco
- Department of Medical Translational Sciences, Division of Pediatrics, Federico II University of Naples, Italy
- Telethon Institute of Genetics and Medicine-TIGEM , Naples Italy
| | - Hadeel Adel Al-lami
- Dept. of Craniofacial and Stem Cell Biology, Dental Institute, King's College London
| | - Yvonne Yeung
- Dept. of Craniofacial and Stem Cell Biology, Dental Institute, King's College London
| | - Yeon Ja Choi
- Departments of Pathology and Dermatology, Stony Brook University, Stony Brook, NY 11794
| | | | - Yannis Duffourd
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, F-21079 Dijon, France
| | - Laurence Faivre
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, F-21079 Dijon, France
- Clinical genetics centre and Eastern referral centre for developmental anomalies and malformative syndromes, FHU-TRANSLAD, Children Hospital, CHU Dijon, F-21079 Dijon, France
| | - Jean-Baptiste Rivière
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, F-21079 Dijon, France
- Laboratory of Molecular Genetics, FHU-TRANSLAD, PTB, CHU Dijon, F-21079 Dijon, France
| | - Jiang Chen
- Departments of Pathology and Dermatology, Stony Brook University, Stony Brook, NY 11794
| | - Karen J. Liu
- Dept. of Craniofacial and Stem Cell Biology, Dental Institute, King's College London
| | | | - Friedhelm Hildebrandt
- HHMI and Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christel Thauvin-Robinet
- EA4271GAD Genetics of Developmental Anomalies, FHU-TRANSLAD, Medecine Faculty, Burgundy University, F-21079 Dijon, France
- Laboratory of Molecular Genetics, FHU-TRANSLAD, PTB, CHU Dijon, F-21079 Dijon, France
| | - Deborah Krakow
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, California, USA, 90095
| | - Peter K. Jackson
- Stanford University School of Medicine, Baxter Laboratory, Department of Microbiology & Immunology, Stanford, California 94305
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Abstract
The basal body is a highly organized structure essential for the formation of cilia. Basal bodies dock to a cellular membrane through their distal appendages (also known as transition fibers) and provide the foundation on which the microtubules of the ciliary axoneme are built. Consequently, basal body position and orientation dictates the position and orientation of its cilium. The heart of the basal body is the mother centriole, the older of the two centrioles inherited during mitosis and which is comprised of nine triplet microtubules arranged in a cylinder. Like all ciliated organisms, mice possess basal bodies, and studies of mouse basal body structure have made diverse important contributions to the understanding of how basal body structure impacts the function of cilia. The appendages and associated structures of mouse basal bodies can differ in their architecture from those of other organisms, and even between murine cell types. For example, basal bodies of immotile primary cilia are connected to daughter centrioles, whereas those of motile multiciliated cells are not. The last few years have seen the identification of many components of the basal body, and the mouse will continue to be an extremely valuable system for genetically defining their functions.
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Affiliation(s)
- Galo Garcia
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158 USA
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34
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Schock EN, Chang CF, Youngworth IA, Davey MG, Delany ME, Brugmann SA. Utilizing the chicken as an animal model for human craniofacial ciliopathies. Dev Biol 2015; 415:326-337. [PMID: 26597494 DOI: 10.1016/j.ydbio.2015.10.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/13/2015] [Accepted: 10/21/2015] [Indexed: 11/30/2022]
Abstract
The chicken has been a particularly useful model for the study of craniofacial development and disease for over a century due to their relatively large size, accessibility, and amenability for classical bead implantation and transplant experiments. Several naturally occurring mutant lines with craniofacial anomalies also exist and have been heavily utilized by developmental biologist for several decades. Two of the most well known lines, talpid(2) (ta(2)) and talpid(3) (ta(3)), represent the first spontaneous mutants to have the causative genes identified. Despite having distinct genetic causes, both mutants have recently been identified as ciliopathic. Excitingly, both of these mutants have been classified as models for human craniofacial ciliopathies: Oral-facial-digital syndrome (ta(2)) and Joubert syndrome (ta(3)). Herein, we review and compare these two models of craniofacial disease and highlight what they have revealed about the molecular and cellular etiology of ciliopathies. Furthermore, we outline how applying classical avian experiments and new technological advances (transgenics and genome editing) with naturally occurring avian mutants can add a tremendous amount to what we currently know about craniofacial ciliopathies.
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Affiliation(s)
- Elizabeth N Schock
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ching-Fang Chang
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ingrid A Youngworth
- College of Agricultural and Environmental Sciences, Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Megan G Davey
- Division of Developmental Biology, The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, UK
| | - Mary E Delany
- College of Agricultural and Environmental Sciences, Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Samantha A Brugmann
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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