1
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Arslanhan MD, Cengiz-Emek S, Odabasi E, Steib E, Hamel V, Guichard P, Firat-Karalar EN. CCDC15 localizes to the centriole inner scaffold and controls centriole length and integrity. J Cell Biol 2023; 222:e202305009. [PMID: 37934472 PMCID: PMC10630097 DOI: 10.1083/jcb.202305009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/23/2023] [Accepted: 09/23/2023] [Indexed: 11/08/2023] Open
Abstract
Centrioles are microtubule-based organelles responsible for forming centrosomes and cilia, which serve as microtubule-organizing, signaling, and motility centers. Biogenesis and maintenance of centrioles with proper number, size, and architecture are vital for their functions during development and physiology. While centriole number control has been well-studied, less is understood about their maintenance as stable structures with conserved size and architecture during cell division and ciliary motility. Here, we identified CCDC15 as a centriole protein that colocalizes with and interacts with the inner scaffold, a crucial centriolar subcompartment for centriole size control and integrity. Using ultrastructure expansion microscopy, we found that CCDC15 depletion affects centriole length and integrity, leading to defective cilium formation, maintenance, and response to Hedgehog signaling. Moreover, loss-of-function experiments showed CCDC15's role in recruiting both the inner scaffold protein POC1B and the distal SFI1/Centrin-2 complex to centrioles. Our findings reveal players and mechanisms of centriole architectural integrity and insights into diseases linked to centriolar defects.
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Affiliation(s)
- Melis D. Arslanhan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Seyma Cengiz-Emek
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Ezgi Odabasi
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Emmanuelle Steib
- Department of Bioengineering, Imperial College London, London, UK
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Paul Guichard
- Department of Molecular and Cellular Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
- Koç University School of Medicine, Istanbul, Turkey
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2
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Masek M, Bachmann-Gagescu R. Control of protein and lipid composition of photoreceptor outer segments-Implications for retinal disease. Curr Top Dev Biol 2023; 155:165-225. [PMID: 38043951 DOI: 10.1016/bs.ctdb.2023.09.001] [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] [Indexed: 12/05/2023]
Abstract
Vision is arguably our most important sense, and its loss brings substantial limitations to daily life for affected individuals. Light is perceived in retinal photoreceptors (PRs), which are highly specialized neurons subdivided into several compartments with distinct functions. The outer segments (OSs) of photoreceptors represent highly specialized primary ciliary compartments hosting the phototransduction cascade, which transforms incoming light into a neuronal signal. Retinal disease can result from various pathomechanisms originating in distinct subcompartments of the PR cell, or in the retinal pigment epithelium which supports the PRs. Dysfunction of primary cilia causes human disorders known as "ciliopathies", in which retinal disease is a common feature. This chapter focuses on PR OSs, discussing the mechanisms controlling their complex structure and composition. A sequence of tightly regulated sorting and trafficking events, both upstream of and within this ciliary compartment, ensures the establishment and maintenance of the adequate proteome and lipidome required for signaling in response to light. We discuss in particular our current understanding of the role of ciliopathy proteins involved in multi-protein complexes at the ciliary transition zone (CC2D2A) or BBSome (BBS1) and how their dysfunction causes retinal disease. While the loss of CC2D2A prevents the fusion of vesicles and delivery of the photopigment rhodopsin to the ciliary base, leading to early OS ultrastructural defects, BBS1 deficiency results in precocious accumulation of cholesterol in mutant OSs and decreased visual function preceding morphological changes. These distinct pathomechanisms underscore the central role of ciliary proteins involved in multiple processes controlling OS protein and lipid composition.
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Affiliation(s)
- Markus Masek
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; University Research Priority Program AdaBD, University of Zurich, Zurich, Switzerland.
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3
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Nudelman K, Nho K, Zhang M, McDonald BC, Zhai W, Small BJ, Wegel CE, Jacobsen PB, Jim HSL, Patel SK, Graham DMA, Ahles TA, Root JC, Foroud T, Breen EC, Carroll JE, Mandelblatt JS, Saykin AJ. Genetic Variants Associated with Longitudinal Cognitive Performance in Older Breast Cancer Patients and Controls. Cancers (Basel) 2023; 15:2877. [PMID: 37296840 PMCID: PMC10252108 DOI: 10.3390/cancers15112877] [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: 03/12/2023] [Revised: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 06/12/2023] Open
Abstract
Background: There have been no published genome-wide studies of the genetics of cancer- and treatment-related cognitive decline (CRCD); the purpose of this study is to identify genetic variants associated with CRCD in older female breast cancer survivors. Methods: Analyses included white non-Hispanic women with non-metastatic breast cancer aged 60+ (N = 325) and age-, racial/ethnic group-, and education-matched controls (N = 340) with pre-systemic treatment and one-year follow-up cognitive assessment. CRCD was evaluated using longitudinal domain scores on cognitive tests of attention, processing speed, and executive function (APE), and learning and memory (LM). Linear regression models of one-year cognition included an interaction term for SNP or gene SNP enrichment*cancer case/control status, controlling for demographic variables and baseline cognition. Results: Cancer patients carrying minor alleles for two SNPs, rs76859653 (chromosome 1) in the hemicentin 1 (HMCN1) gene (p = 1.624 × 10-8), and rs78786199 (chromosome 2, p = 1.925 × 10-8) in an intergenic region had lower one-year APE scores than non-carriers and controls. Gene-level analyses showed the POC5 centriolar protein gene was enriched for SNPs associated with differences in longitudinal LM performance between patients and controls. Conclusions: The SNPs associated with cognition in survivors, but not controls, were members of the cyclic nucleotide phosphodiesterase family, that play important roles in cell signaling, cancer risk, and neurodegeneration. These findings provide preliminary evidence that novel genetic loci may contribute to susceptibility to CRCD.
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Affiliation(s)
- Kelly Nudelman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kwangsik Nho
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brenna C. McDonald
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wanting Zhai
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Brent J. Small
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- School of Aging Studies, University of South Florida, Tampa, FL 33620, USA
| | - Claire E. Wegel
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Paul B. Jacobsen
- Division of Cancer Control and Population Studies, National Cancer Institute, Bethesda, MD 20892, USA
| | - Heather S. L. Jim
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Sunita K. Patel
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Deena M. A. Graham
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Tim A. Ahles
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James C. Root
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Genetics Biobank, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elizabeth C. Breen
- Cousins Center for Psychoneuroimmunology, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry & Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Judith E. Carroll
- Cousins Center for Psychoneuroimmunology, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry & Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA
| | - Jeanne S. Mandelblatt
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Andrew J. Saykin
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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4
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Tsekitsidou E, Wong CJ, Ulengin-Talkish I, Barth AIM, Stearns T, Gingras AC, Wang JT, Cyert MS. Calcineurin associates with centrosomes and regulates cilia length maintenance. J Cell Sci 2023; 136:jcs260353. [PMID: 37013443 PMCID: PMC10163345 DOI: 10.1242/jcs.260353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Calcineurin, or protein phosphatase 2B (PP2B), the Ca2+ and calmodulin-activated phosphatase and target of immunosuppressants, has many substrates and functions that remain uncharacterized. By combining rapid proximity-dependent labeling with cell cycle synchronization, we mapped the spatial distribution of calcineurin in different cell cycle stages. While calcineurin-proximal proteins did not vary significantly between interphase and mitosis, calcineurin consistently associated with multiple centrosomal and/or ciliary proteins. These include POC5, which binds centrins in a Ca2+-dependent manner and is a component of the luminal scaffold that stabilizes centrioles. We show that POC5 contains a calcineurin substrate motif (PxIxIT type) that mediates calcineurin binding in vivo and in vitro. Using indirect immunofluorescence and ultrastructure expansion microscopy, we demonstrate that calcineurin colocalizes with POC5 at the centriole, and further show that calcineurin inhibitors alter POC5 distribution within the centriole lumen. Our discovery that calcineurin directly associates with centriolar proteins highlights a role for Ca2+ and calcineurin signaling at these organelles. Calcineurin inhibition promotes elongation of primary cilia without affecting ciliogenesis. Thus, Ca2+ signaling within cilia includes previously unknown functions for calcineurin in maintenance of cilia length, a process that is frequently disrupted in ciliopathies.
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Affiliation(s)
| | - Cassandra J. Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | | | | | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jennifer T. Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Martha S. Cyert
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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5
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Wawrocka A, Socha M, Walczak-Sztulpa J, Koczyk G, Skorczyk-Werner A, Krawczyński MR. Molecular Re-Diagnosis with Whole-Exome Sequencing Increases the Diagnostic Yield in Patients with Non-Syndromic Retinitis Pigmentosa. Diagnostics (Basel) 2023; 13:diagnostics13040730. [PMID: 36832217 PMCID: PMC9954991 DOI: 10.3390/diagnostics13040730] [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: 01/16/2023] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of disorders with progressive loss of photoreceptor and pigment epithelial function. Nineteen unrelated Polish probands clinically diagnosed with nonsyndromic RP were recruited to this study. We used whole-exome sequencing (WES) to identify potential pathogenic gene variants in molecularly undiagnosed RP patients, as a molecular re-diagnosis after having performed targeted NGS in the past. Targeted NGS allowed for identification of the molecular background in only 5 out of 19 patients. Fourteen patients who remained unsolved despite the targeted NGS were subjected to WES. WES revealed potentially causative variants in RP-related genes in another 12 patients. Together, NGS methods revealed the coexistence of causal variants affecting distinct RP genes in 17 out of 19 RP families, with a very high efficiency of 89%. With the improvement of NGS methods, including higher sequencing depth, broader target enrichment, and better bioinformatic analysis capabilities, the ratio of identified causal gene variants has significantly increased. Therefore, it is important to consider repeating high-throughput sequencing analysis in those patients in whom the previously performed NGS did not reveal any pathogenic variants. The study confirmed the efficiency and clinical utility of re-diagnosis with WES in molecularly undiagnosed RP patients.
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Affiliation(s)
- Anna Wawrocka
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Correspondence:
| | - Magdalena Socha
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Joanna Walczak-Sztulpa
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Grzegorz Koczyk
- Biometry and Bioinformatics Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Anna Skorczyk-Werner
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Maciej R. Krawczyński
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Centers for Medical Genetics GENESIS, 60-529 Poznan, Poland
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6
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Mercey O, Kostic C, Bertiaux E, Giroud A, Sadian Y, Gaboriau DCA, Morrison CG, Chang N, Arsenijevic Y, Guichard P, Hamel V. The connecting cilium inner scaffold provides a structural foundation that protects against retinal degeneration. PLoS Biol 2022; 20:e3001649. [PMID: 35709082 PMCID: PMC9202906 DOI: 10.1371/journal.pbio.3001649] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/27/2022] [Indexed: 12/17/2022] Open
Abstract
Inherited retinal degeneration due to loss of photoreceptor cells is a leading cause of human blindness. These cells possess a photosensitive outer segment linked to the cell body through the connecting cilium (CC). While structural defects of the CC have been associated with retinal degeneration, its nanoscale molecular composition, assembly, and function are barely known. Here, using expansion microscopy and electron microscopy, we reveal the molecular architecture of the CC and demonstrate that microtubules are linked together by a CC inner scaffold containing POC5, CENTRIN, and FAM161A. Dissecting CC inner scaffold assembly during photoreceptor development in mouse revealed that it acts as a structural zipper, progressively bridging microtubule doublets and straightening the CC. Furthermore, we show that Fam161a disruption in mouse leads to specific CC inner scaffold loss and triggers microtubule doublet spreading, prior to outer segment collapse and photoreceptor degeneration, suggesting a molecular mechanism for a subtype of retinitis pigmentosa. Inherited retinal degeneration due to loss of photoreceptor cells is a leading cause of human blindness. Ultrastructure expansion microscopy on mouse retina reveals the presence of a novel structure inside the photoreceptor connecting cilium, the inner scaffold, that protects the outer segment against degeneration.
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Affiliation(s)
- Olivier Mercey
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Corinne Kostic
- Group for Retinal Disorder Research, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Eloïse Bertiaux
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Alexia Giroud
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Yashar Sadian
- CryoGenic Facility, University of Geneva, Geneva, Switzerland
| | - David C. A. Gaboriau
- Centre for Chromosome Biology, National University of Ireland Galway, Galway, Ireland
| | - Ciaran G. Morrison
- Centre for Chromosome Biology, National University of Ireland Galway, Galway, Ireland
| | - Ning Chang
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Yvan Arsenijevic
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (PG); (VH)
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (PG); (VH)
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7
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Casey MA, Hill JT, Hoshijima K, Bryan CD, Gribble SL, Brown JT, Chien CB, Yost HJ, Kwan KM. Shutdown corner, a large deletion mutant isolated from a haploid mutagenesis screen in zebrafish. G3 (BETHESDA, MD.) 2022; 12:jkab442. [PMID: 35079792 PMCID: PMC9210284 DOI: 10.1093/g3journal/jkab442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022]
Abstract
Morphogenesis, the formation of three-dimensional organ structures, requires precise coupling of genetic regulation and complex cell behaviors. The genetic networks governing many morphogenetic systems, including that of the embryonic eye, are poorly understood. In zebrafish, several forward genetic screens have sought to identify factors regulating eye development. These screens often look for eye defects at stages after the optic cup is formed and when retinal neurogenesis is under way. This approach can make it difficult to identify mutants specific for morphogenesis, as opposed to neurogenesis. To this end, we carried out a forward genetic, small-scale haploid mutagenesis screen in zebrafish (Danio rerio) to identify factors that govern optic cup morphogenesis. We screened ∼100 genomes and isolated shutdown corner (sco), a mutant that exhibits multiple tissue defects and harbors a ∼10-Mb deletion that encompasses 89 annotated genes. Using a combination of live imaging and antibody staining, we found cell proliferation, cell death, and tissue patterning defects in the sco optic cup. We also observed other phenotypes, including paralysis, neuromuscular defects, and ocular vasculature defects. To date, the largest deletion mutants reported in zebrafish are engineered using CRISPR-Cas9 and are less than 300 kb. Because of the number of genes within the deletion interval, shutdown corner [Df(Chr05:sco)z207] could be a useful resource to the zebrafish community, as it may be helpful for gene mapping, understanding genetic interactions, or studying many genes lost in the mutant.
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Affiliation(s)
- Macaulie A Casey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Jonathon T Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Kazuyuki Hoshijima
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Chase D Bryan
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA
| | - Suzanna L Gribble
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - J Thomas Brown
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
| | - Chi-Bin Chien
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
| | - H Joseph Yost
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Kristen M Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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8
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Wang X, Qu M, Liu Y, Schneider RF, Song Y, Chen Z, Zhang H, Zhang Y, Yu H, Zhang S, Li D, Qin G, Ma S, Zhong J, Yin J, Liu S, Fan G, Meyer A, Wang D, Lin Q. Genomic basis of evolutionary adaptation in a warm-blooded fish. Innovation (N Y) 2022; 3:100185. [PMID: 34984407 PMCID: PMC8693259 DOI: 10.1016/j.xinn.2021.100185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/07/2021] [Indexed: 11/16/2022] Open
Abstract
Few fishes have evolved elevated body temperatures compared with ambient temperatures, and only in opah (Lampris spp) is the entire body affected. To understand the molecular basis of endothermy, we analyzed the opah genome and identified 23 genes with convergent amino acid substitutions across fish, birds, and mammals, including slc8b1, which encodes the mitochondrial Na+/Ca2+ exchanger and is essential for heart function and metabolic heat production. Among endothermic fishes, 44 convergent genes with suggestive metabolic functions were identified, such as glrx3, encoding a crucial protein for hemoglobin maturation. Numerous genes involved in the production and retention of metabolic heat were also found to be under positive selection. Analyses of opah's unique inner-heat-producing pectoral muscle layer (PMI), an evolutionary key innovation, revealed that many proteins were co-opted from dorsal swimming muscles for thermogenesis and oxidative phosphorylation. Thus, the opah genome provides valuable resources and opportunities to uncover the genetic basis of thermal adaptations in fish.
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Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ralf F Schneider
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - Yue Song
- BGI-Qingdao, Qingdao 266555, China
| | - Zelin Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hao Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | | | - Dongxu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shaobo Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jia Zhong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shuaishuai Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Guangyi Fan
- BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,University of the Chinese Academy of Sciences, Beijing 100101, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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9
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Hong Y, Luo Y. Zebrafish Model in Ophthalmology to Study Disease Mechanism and Drug Discovery. Pharmaceuticals (Basel) 2021; 14:ph14080716. [PMID: 34451814 PMCID: PMC8400593 DOI: 10.3390/ph14080716] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Visual impairment and blindness are common and seriously affect people’s work and quality of life in the world. Therefore, the effective therapies for eye diseases are of high priority. Zebrafish (Danio rerio) is an alternative vertebrate model as a useful tool for the mechanism elucidation and drug discovery of various eye disorders, such as cataracts, glaucoma, diabetic retinopathy, age-related macular degeneration, photoreceptor degeneration, etc. The genetic and embryonic accessibility of zebrafish in combination with a behavioral assessment of visual function has made it a very popular model in ophthalmology. Zebrafish has also been widely used in ocular drug discovery, such as the screening of new anti-angiogenic compounds or neuroprotective drugs, and the oculotoxicity test. In this review, we summarized the applications of zebrafish as the models of eye disorders to study disease mechanism and investigate novel drug treatments.
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Affiliation(s)
| | - Yan Luo
- Correspondence: ; Tel.: +86-020-87335931
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10
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Abstract
Centrioles are microtubule-based cylindrical structures that assemble the centrosome and template the formation of cilia. The proximal part of centrioles is associated with the pericentriolar material, a protein scaffold from which microtubules are nucleated. This activity is mediated by the γ-tubulin ring complex (γTuRC) whose central role in centrosomal microtubule organization has been recognized for decades. However, accumulating evidence suggests that γTuRC activity at this organelle is neither restricted to the pericentriolar material nor limited to microtubule nucleation. Instead, γTuRC is found along the entire centriole cylinder, at subdistal appendages, and inside the centriole lumen, where its canonical function as a microtubule nucleator might be supplemented or replaced by a function in microtubule anchoring and centriole stabilization, respectively. In this Opinion, we discuss recent insights into the expanded repertoire of γTuRC activities at centrioles and how distinct subpopulations of γTuRC might act in concert to ensure centrosome and cilia biogenesis and function, ultimately supporting cell proliferation, differentiation and homeostasis. We propose that the classical view of centrosomal γTuRC as a pericentriolar material-associated microtubule nucleator needs to be revised.
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Affiliation(s)
- Nina Schweizer
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jens Lüders
- Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain
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11
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Reel PS, Reel S, Pearson E, Trucco E, Jefferson E. Using machine learning approaches for multi-omics data analysis: A review. Biotechnol Adv 2021; 49:107739. [PMID: 33794304 DOI: 10.1016/j.biotechadv.2021.107739] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/01/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
With the development of modern high-throughput omic measurement platforms, it has become essential for biomedical studies to undertake an integrative (combined) approach to fully utilise these data to gain insights into biological systems. Data from various omics sources such as genetics, proteomics, and metabolomics can be integrated to unravel the intricate working of systems biology using machine learning-based predictive algorithms. Machine learning methods offer novel techniques to integrate and analyse the various omics data enabling the discovery of new biomarkers. These biomarkers have the potential to help in accurate disease prediction, patient stratification and delivery of precision medicine. This review paper explores different integrative machine learning methods which have been used to provide an in-depth understanding of biological systems during normal physiological functioning and in the presence of a disease. It provides insight and recommendations for interdisciplinary professionals who envisage employing machine learning skills in multi-omics studies.
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Affiliation(s)
- Parminder S Reel
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Smarti Reel
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Ewan Pearson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Emanuele Trucco
- VAMPIRE project, Computing, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Emily Jefferson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, United Kingdom.
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12
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Mathieu H, Patten SA, Aragon-Martin JA, Ocaka L, Simpson M, Child A, Moldovan F. Genetic variant of TTLL11 gene and subsequent ciliary defects are associated with idiopathic scoliosis in a 5-generation UK family. Sci Rep 2021; 11:11026. [PMID: 34040021 PMCID: PMC8155187 DOI: 10.1038/s41598-021-90155-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Idiopathic scoliosis (IS) is a complex 3D deformation of the spine with a strong genetic component, most commonly found in adolescent girls. Adolescent idiopathic scoliosis (AIS) affects around 3% of the general population. In a 5-generation UK family, linkage analysis identified the locus 9q31.2-q34.2 as a candidate region for AIS; however, the causative gene remained unidentified. Here, using exome sequencing we identified a rare insertion c.1569_1570insTT in the tubulin tyrosine ligase like gene, member 11 (TTLL11) within that locus, as the IS causative gene in this British family. Two other TTLL11 mutations were also identified in two additional AIS cases in the same cohort. Analyses of primary cells of individuals carrying the c.1569_1570insTT (NM_194252) mutation reveal a defect at the primary cilia level, which is less present, smaller and less polyglutamylated compared to control. Further, in a zebrafish, the knock down of ttll11, and the mutated ttll11 confirmed its role in spine development and ciliary function in the fish retina. These findings provide evidence that mutations in TTLL11, a ciliary gene, contribute to the pathogenesis of IS.
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Affiliation(s)
- Hélène Mathieu
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, 2.17.026, Montreal, QC, H3T 1C5, Canada
| | - Shunmoogum A Patten
- INRS-Centre Armand-Frappier Santé et Biotechnologie, Laval, QC, H7V1B7, Canada
| | | | - Louise Ocaka
- Centre for Translational Omics-GOSgene, Department of Genetics and Genomic Medicine, UCL GOSH Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Michael Simpson
- Genetics and Molecular Medicine, King's College London, SE1 1UL, London, UK
| | - Anne Child
- Marfan Trust, NHLI, Imperial College, Guy Scadding Building, London, SW3 6LY, UK.
| | - Florina Moldovan
- CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, 2.17.026, Montreal, QC, H3T 1C5, Canada.
- Faculty of Dentistry, Université de Montréal, Montreal, QC, H3T 1J4, Canada.
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13
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Yang XR, Benson MD, MacDonald IM, Innes AM. A diagnostic approach to syndromic retinal dystrophies with intellectual disability. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:538-570. [PMID: 32918368 DOI: 10.1002/ajmg.c.31834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Inherited retinal dystrophies are a group of monogenic disorders that, as a whole, contribute significantly to the burden of ocular disease in both pediatric and adult patients. In their syndromic forms, retinal dystrophies can be observed in association with intellectual disability, frequently alongside other systemic manifestations. There are now over 80 genes implicated in syndromic retinal dystrophies with intellectual disability. Identifying and accurately characterizing these disorders allows the clinician to narrow the differential diagnosis, evaluate for relevant associated features, arrive at a timely and accurate diagnosis, and address both sight-threatening ocular manifestations and morbidity-causing systemic manifestations. The co-occurrence of retinal dystrophy and intellectual disability in an individual can be challenging to investigate, diagnose, and counsel given the considerable phenotypic and genotypic heterogeneity that exists within this broad group of disorders. We performed a review of the current literature and propose an algorithm to facilitate the evaluation, and clinical and mechanistic classification, of these individuals.
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Affiliation(s)
- Xiao-Ru Yang
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Matthew D Benson
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada
| | - Ian M MacDonald
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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14
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When phenotype does not match genotype: importance of "real-time" refining of phenotypic information for exome data interpretation. Genet Med 2020; 23:215-221. [PMID: 32801363 DOI: 10.1038/s41436-020-00938-5] [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: 06/08/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Clinical data provided to genetic testing laboratories are frequently scarce. Our purpose was to evaluate clinical scenarios where phenotypic refinement in proband's family members might impact exome data interpretation. METHODS Of 614 exomes, 209 were diagnostic and included in this study. Phenotypic information was gathered by the variant interpretation team from genetic counseling letters and images. If a discrepancy between reported clinical findings and presumably disease-causing variant segregation was observed, referring clinicians were contacted for phenotypic clarification. RESULTS In 16/209 (7.7%) cases, phenotypic refinement was important due to (1) lack of cosegregation of disease-causing variant with the reported phenotype; (2) identification of different disorders with overlapping symptoms in the same family; (3) similar features in proband and family members, but molecular cause identified in proband only; and (4) previously unrecognized maternal condition causative of child's phenotype. As a result of phenotypic clarification, in 12/16 (75%) cases definition of affected versus unaffected status in one of the family members has changed, and in one case variant classification has changed. CONCLUSION Detailed description of phenotypes in family members including differences in clinical presentations, even if subtle, are important in exome interpretation and should be communicated to the variant interpretation team.
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15
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Salmaninejad A, Motaee J, Farjami M, Alimardani M, Esmaeilie A, Pasdar A. Next-generation sequencing and its application in diagnosis of retinitis pigmentosa. Ophthalmic Genet 2020; 40:393-402. [PMID: 31755340 DOI: 10.1080/13816810.2019.1675178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Retinitis Pigmentosa (RP) is a major cause of heritable human blindness with a high genetic heterogeneity. It is characterized by the initial degeneration of rod photoreceptors followed by cone photoreceptors. RP is also a prominent reason of visual impairment, by a global prevalence of 1:4000. RP is usually specified with nyctalopia in puberty, followed by concentric visual field loss, that reflects the main impairment of rod photoreceptors; later in the life, as disease progresses, because of cone dysfunction, central vision loss also occurs. A precise molecular diagnosis is crucial for disease characterization and clinical prognosis. DNA sequencing is a powerful tool for deciphering various causes of different human diseases. The arrival of next-generation sequencing (NGS) technologies has diminished sequencing cost and considerably augmented the throughput, making whole-genome sequencing (WGS) a conceivable way for obtaining comprehensive genomic data and a more precise clinical decision. Nevertheless, the advantages gained from NGS technologies are among a number of challenges that must be sufficiently addressed before this technique can be altered from an investigation tools to a helpful method in routine clinical practices. This article aims to provide an overview about NGS technology and its related platforms. The challenges in the analysis and choosing an appropriate NGS method likewise their potential applications in clinical diagnosis are also discussed. The merit of such technique has been reflected in some recent studies where it is shown that using NGS and molecular information could help with clinical diagnosis, providing potential treatment options or changes, up-to-date family counseling and management.
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Affiliation(s)
- Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshid Motaee
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine,Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK
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16
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Heydeck W, Bayless BA, Stemm-Wolf AJ, O'Toole ET, Fabritius AS, Ozzello C, Nguyen M, Winey M. Tetrahymena Poc5 is a transient basal body component that is important for basal body maturation. J Cell Sci 2020; 133:jcs.240838. [PMID: 32350068 DOI: 10.1242/jcs.240838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 04/06/2020] [Indexed: 01/26/2023] Open
Abstract
Basal bodies (BBs) are microtubule-based organelles that act as a template for and stabilize cilia at the cell surface. Centrins ubiquitously associate with BBs and function in BB assembly, maturation and stability. Human POC5 (hPOC5) is a highly conserved centrin-binding protein that binds centrins through Sfi1p-like repeats and is required for building full-length, mature centrioles. Here, we use the BB-rich cytoskeleton of Tetrahymena thermophila to characterize Poc5 BB functions. Tetrahymena Poc5 (TtPoc5) uniquely incorporates into assembling BBs and is then removed from mature BBs prior to ciliogenesis. Complete genomic knockout of TtPOC5 leads to a significantly increased production of BBs, yet a markedly reduced ciliary density, both of which are rescued by reintroduction of TtPoc5. A second Tetrahymena POC5-like gene, SFR1, is similarly implicated in modulating BB production. When TtPOC5 and SFR1 are co-deleted, cell viability is compromised and BB overproduction is exacerbated. Overproduced BBs display defective transition zone formation and a diminished capacity for ciliogenesis. This study uncovers a requirement for Poc5 in building mature BBs, providing a possible functional link between hPOC5 mutations and impaired cilia.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Westley Heydeck
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Brian A Bayless
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Alexander J Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Eileen T O'Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Courtney Ozzello
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Marina Nguyen
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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17
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Yi Z, Ouyang J, Sun W, Li S, Xiao X, Zhang Q. Comparative exome sequencing reveals novel candidate genes for retinitis pigmentosa. EBioMedicine 2020; 56:102792. [PMID: 32454406 PMCID: PMC7248430 DOI: 10.1016/j.ebiom.2020.102792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/30/2020] [Accepted: 04/24/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Retinitis pigmentosa (RP) is the most common form of inherited retinal degeneration, but genetic defects in nearly half of families remain unresolved. This study aims to identify novel genes associated with RP based on whole exome sequencing (WES) data from 552 probands with RP. METHODS Biallelic loss-of-function (LoF) variants were selected from the WES data of 552 probands with RP and compared with that of 4728 in-house controls and the gnomAD database. Expression analysis and knockout mice model or knockdown zebrafish model were performed to confirm the association of a few candidate genes with RP. FINDINGS Unique biallelic LoF variants in ENSA, DACT2, DDR1, and CCDC188 were identified in four probands with RP, but were absent in 4728 in-house controls and were extremely rare in the gnomAD database. The expression of ENSA was enriched in the rod outer segments of human retina, and significant reduced responses of rods and cones were detected in Ensa knockout mice compared to wild-type mice by electroretinogram. The DACT2 transcript showed the highest expression in human retina and knockdown of dact2 in zebrafish resulted in photoreceptor disc membrane disarrangement. INTERPRETATION This study suggests that ENSA is likely a novel gene for RP and DACT2 is a potentially candidate gene for RP. Further studies are expected to evaluate the association between mutations in the other two genes and RP. To our knowledge, mutations in these genes have not been reported to be associated with RP before.
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Affiliation(s)
- Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou 510060, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou 510060, China.
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18
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Le Guennec M, Klena N, Gambarotto D, Laporte MH, Tassin AM, van den Hoek H, Erdmann PS, Schaffer M, Kovacik L, Borgers S, Goldie KN, Stahlberg H, Bornens M, Azimzadeh J, Engel BD, Hamel V, Guichard P. A helical inner scaffold provides a structural basis for centriole cohesion. SCIENCE ADVANCES 2020; 6:eaaz4137. [PMID: 32110738 PMCID: PMC7021493 DOI: 10.1126/sciadv.aaz4137] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/03/2019] [Indexed: 05/10/2023]
Abstract
The ninefold radial arrangement of microtubule triplets (MTTs) is the hallmark of the centriole, a conserved organelle crucial for the formation of centrosomes and cilia. Although strong cohesion between MTTs is critical to resist forces applied by ciliary beating and the mitotic spindle, how the centriole maintains its structural integrity is not known. Using cryo-electron tomography and subtomogram averaging of centrioles from four evolutionarily distant species, we found that MTTs are bound together by a helical inner scaffold covering ~70% of the centriole length that maintains MTTs cohesion under compressive forces. Ultrastructure Expansion Microscopy (U-ExM) indicated that POC5, POC1B, FAM161A, and Centrin-2 localize to the scaffold structure along the inner wall of the centriole MTTs. Moreover, we established that these four proteins interact with each other to form a complex that binds microtubules. Together, our results provide a structural and molecular basis for centriole cohesion and geometry.
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Affiliation(s)
- Maeva Le Guennec
- University of Geneva, Department of Cell Biology, Sciences III, Geneva, Switzerland
| | - Nikolai Klena
- University of Geneva, Department of Cell Biology, Sciences III, Geneva, Switzerland
| | - Davide Gambarotto
- University of Geneva, Department of Cell Biology, Sciences III, Geneva, Switzerland
| | - Marine H. Laporte
- University of Geneva, Department of Cell Biology, Sciences III, Geneva, Switzerland
| | - Anne-Marie Tassin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Hugo van den Hoek
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Philipp S. Erdmann
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lubomir Kovacik
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel CH-4058, Switzerland
| | - Susanne Borgers
- University of Geneva, Department of Cell Biology, Sciences III, Geneva, Switzerland
| | - Kenneth N. Goldie
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel CH-4058, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel CH-4058, Switzerland
| | - Michel Bornens
- Institut Curie, PSL Research University, CNRS-UMR 144, 75005 Paris, France
| | - Juliette Azimzadeh
- Université de Paris, Institut Jacques Monod, CNRS UMR7592, 75013 Paris, France
| | - Benjamin D. Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Corresponding author. (B.D.E.); (V.H.); (P.G.)
| | - Virginie Hamel
- University of Geneva, Department of Cell Biology, Sciences III, Geneva, Switzerland
- Corresponding author. (B.D.E.); (V.H.); (P.G.)
| | - Paul Guichard
- University of Geneva, Department of Cell Biology, Sciences III, Geneva, Switzerland
- Corresponding author. (B.D.E.); (V.H.); (P.G.)
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19
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Hassan A, Parent S, Mathieu H, Zaouter C, Molidperee S, Bagu ET, Barchi S, Villemure I, Patten SA, Moldovan F. Adolescent idiopathic scoliosis associated POC5 mutation impairs cell cycle, cilia length and centrosome protein interactions. PLoS One 2019; 14:e0213269. [PMID: 30845169 PMCID: PMC6405090 DOI: 10.1371/journal.pone.0213269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/19/2019] [Indexed: 01/11/2023] Open
Abstract
Adolescent Idiopathic Scoliosis (AIS) is a spinal deformity that affects approximately 3 percent of human adolescents. Although the etiology and molecular basis of AIS is unclear, several genes such as POC5 have been identified as possible causes of the condition. In order to understand the role of POC5 in the pathogenesis of AIS, we investigated the subcellular localization of POC5 in cilia of cells over-expressing either the wild type (wt) or an AIS-related POC5 variant POC5A429V. Mutation of POC5 was found to alter its subcellular localization and to induce ciliary retraction. Furthermore, we observed an impaired cell-cycle progression with the accumulation of cells in the S-phase in cells expressing POC5A429V. Using immunoprecipitation coupled to mass spectrometry, we identified specific protein interaction partners of POC5, most of which were components of cilia and cytoskeleton. Several of these interactions were altered upon mutation of POC5. Altogether, our results demonstrate major cellular alterations, disturbances in centrosome protein interactions and cilia retraction in cells expressing an AIS-related POC5 mutation. Our study suggests that defects in centrosomes and cilia may underlie AIS pathogenesis.
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Affiliation(s)
- Amani Hassan
- Faculty of Dentistry, Université de Montréal, Montréal, Québec, Canada
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | - Stefan Parent
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | - Hélène Mathieu
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | | | | | - Edward T. Bagu
- Department of Basic Biomedical Sciences, Sanford Medical School, University of South Dakota, Vermillion, SD, United States of America
| | - Soraya Barchi
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | | | - Shunmoogum A. Patten
- INRS–Institut Armand-Frappier, Université du Québec, Laval, Montréal, Québec, Canada
| | - Florina Moldovan
- Faculty of Dentistry, Université de Montréal, Montréal, Québec, Canada
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
- * E-mail:
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20
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Improved diagnostics by exome sequencing following raw data
reevaluation by clinical geneticists involved in the medical care of the individuals
tested. Genet Med 2018; 21:1443-1451. [DOI: 10.1038/s41436-018-0343-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
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21
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D'Argenio V. The High-Throughput Analyses Era: Are We Ready for the Data Struggle? High Throughput 2018; 7:E8. [PMID: 29498666 PMCID: PMC5876534 DOI: 10.3390/ht7010008] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/16/2018] [Accepted: 02/27/2018] [Indexed: 12/23/2022] Open
Abstract
Recent and rapid technological advances in molecular sciences have dramatically increased the ability to carry out high-throughput studies characterized by big data production. This, in turn, led to the consequent negative effect of highlighting the presence of a gap between data yield and their analysis. Indeed, big data management is becoming an increasingly important aspect of many fields of molecular research including the study of human diseases. Now, the challenge is to identify, within the huge amount of data obtained, that which is of clinical relevance. In this context, issues related to data interpretation, sharing and storage need to be assessed and standardized. Once this is achieved, the integration of data from different -omic approaches will improve the diagnosis, monitoring and therapy of diseases by allowing the identification of novel, potentially actionably biomarkers in view of personalized medicine.
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Affiliation(s)
- Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Pansini 5, 80131 Naples, Italy.
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