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Brody SL, Pan J, Huang T, Xu J, Xu H, Koenitizer J, Brennan SK, Nanjundappa R, Saba TG, Berical A, Hawkins FJ, Wang X, Zhang R, Mahjoub MR, Horani A, Dutcher SK. Loss of an extensive ciliary connectome induces proteostasis and cell fate switching in a severe motile ciliopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585965. [PMID: 38562900 PMCID: PMC10983967 DOI: 10.1101/2024.03.20.585965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Motile cilia have essential cellular functions in development, reproduction, and homeostasis. Genetic causes for motile ciliopathies have been identified, but the consequences on cellular functions beyond impaired motility remain unknown. Variants in CCDC39 and CCDC40 cause severe disease not explained by loss of motility. Using human cells with pathological variants in these genes, Chlamydomonas genetics, cryo-electron microscopy, single cell RNA transcriptomics, and proteomics, we identified perturbations in multiple cilia-independent pathways. Absence of the axonemal CCDC39/CCDC40 heterodimer results in loss of a connectome of over 90 proteins. The undocked connectome activates cell quality control pathways, switches multiciliated cell fate, impairs microtubule architecture, and creates a defective periciliary barrier. Both cilia-dependent and independent defects are likely responsible for the disease severity. Our findings provide a foundation for reconsidering the broad cellular impact of pathologic variants in ciliopathies and suggest new directions for therapies.
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Affiliation(s)
- Steven L Brody
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jiehong Pan
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Tao Huang
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jian Xu
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Huihui Xu
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jeffrey Koenitizer
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Steven K Brennan
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rashmi Nanjundappa
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Thomas G Saba
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48108, USA
| | - Andrew Berical
- Center for Regenerative Medicine, Boston University, Boston, MA, 02118, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine, Boston University, Boston, MA, 02118, USA
| | - Xiangli Wang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Moe R Mahjoub
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Amjad Horani
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48108, USA
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Susan K Dutcher
- Department of Cell Biology and Physisology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110, USA
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2
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Moran AL, Louzao-Martinez L, Norris DP, Peters DJM, Blacque OE. Transport and barrier mechanisms that regulate ciliary compartmentalization and ciliopathies. Nat Rev Nephrol 2024; 20:83-100. [PMID: 37872350 DOI: 10.1038/s41581-023-00773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
Primary cilia act as cell surface antennae, coordinating cellular responses to sensory inputs and signalling molecules that regulate developmental and homeostatic pathways. Cilia are therefore critical to physiological processes, and defects in ciliary components are associated with a large group of inherited pleiotropic disorders - known collectively as ciliopathies - that have a broad spectrum of phenotypes and affect many or most tissues, including the kidney. A central feature of the cilium is its compartmentalized structure, which imparts its unique molecular composition and signalling environment despite its membrane and cytosol being contiguous with those of the cell. Such compartmentalization is achieved via active transport pathways that bring protein cargoes to and from the cilium, as well as gating pathways at the ciliary base that establish diffusion barriers to protein exchange into and out of the organelle. Many ciliopathy-linked proteins, including those involved in kidney development and homeostasis, are components of the compartmentalizing machinery. New insights into the major compartmentalizing pathways at the cilium, namely, ciliary gating, intraflagellar transport, lipidated protein flagellar transport and ciliary extracellular vesicle release pathways, have improved our understanding of the mechanisms that underpin ciliary disease and associated renal disorders.
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Affiliation(s)
- Ailis L Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Laura Louzao-Martinez
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
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3
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Life-Saver or Undertaker: The Relationship between Primary Cilia and Cell Death in Vertebrate Embryonic Development. J Dev Biol 2022; 10:jdb10040052. [PMID: 36547474 PMCID: PMC9783631 DOI: 10.3390/jdb10040052] [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: 10/29/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The development of multicellular organisms requires a tightly coordinated network of cellular processes and intercellular signalling. For more than 20 years, it has been known that primary cilia are deeply involved in the mediation of intercellular signalling and that ciliary dysfunction results in severe developmental defects. Cilia-mediated signalling regulates cellular processes such as proliferation, differentiation, migration, etc. Another cellular process ensuring proper embryonic development is cell death. While the effect of cilia-mediated signalling on many cellular processes has been extensively studied, the relationship between primary cilia and cell death remains largely unknown. This article provides a short review on the current knowledge about this relationship.
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4
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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5
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Moreno-Leon L, Quezada-Ramirez MA, Bilsbury E, Kiss C, Guerin A, Khanna H. Prenatal phenotype analysis and mutation identification of a fetus with meckel gruber syndrome. Front Genet 2022; 13:982127. [PMID: 36061204 PMCID: PMC9437271 DOI: 10.3389/fgene.2022.982127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 12/05/2022] Open
Abstract
Ciliopathies are a class of inherited severe human disorders that occur due to defective formation or function of cilia. The RPGRIP1L (retinitis pigmentosa GTPase regulator-interacting protein1-like) gene encodes for a ciliary protein involved in regulating cilia formation and function. Mutations in RPGRIP1L cause ciliopathies associated with severe embryonic defects, such as Meckel-Gruber Syndrome (MKS). Here we report RPGRIP1L mutation analysis in a family diagnosed with MKS. The clinical manifestations of the fetus included thoraco-lumbar open neural tube defect with associated Chiari type II malformation and hydrocephalus, bilateral club feet, and single right kidney/ureter. Analysis of the parental DNA samples revealed that the father carried a previously reported mutation R1236C/+ whereas the mother had a novel splice site mutation IVS6+1 G > A/+ in RPGRIP1L. The splice site mutation resulted in the exclusion of in-frame exon 6 of RPGRIP1L (RPGRIP1L-∆Ex6) but expressed a stable protein in fibroblasts derived from the parents’ skin biopsies. The GFP-RPGRIP1L-∆Ex6 mutant protein exhibited relatively reduced ciliary localization in transiently-transfected cultured RPE-1 cells. Taken together, this study identifies a novel RPGRIP1L variant RPGRIP1L-∆Ex6, which in combination with RPGRIP1L-R1236C is associated with MKS. We also suggest that the deletion of exon 6 of RPGRIP1L leads to reduced ciliary localization of RPGRIP1L, indicating a plausible mechanism of associated disease.
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Affiliation(s)
- Laura Moreno-Leon
- Department of Ophthalmology and Visual Sciences, UMass Chan Medical School, Worcester, MA, United States
| | - Marco A. Quezada-Ramirez
- Department of Ophthalmology and Visual Sciences, UMass Chan Medical School, Worcester, MA, United States
| | - Evan Bilsbury
- Department of Ophthalmology and Visual Sciences, UMass Chan Medical School, Worcester, MA, United States
| | - Courtney Kiss
- Kingston Health Sciences Centre, Queen’s Medical School, Kingston, ON, Canada
| | - Andrea Guerin
- Kingston Health Sciences Centre, Queen’s Medical School, Kingston, ON, Canada
| | - Hemant Khanna
- Department of Ophthalmology and Visual Sciences, UMass Chan Medical School, Worcester, MA, United States
- *Correspondence: Hemant Khanna, ,
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6
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Pinello JF, Liu Y, Snell WJ. MAR1 links membrane adhesion to membrane merger during cell-cell fusion in Chlamydomonas. Dev Cell 2021; 56:3380-3392.e9. [PMID: 34813735 DOI: 10.1016/j.devcel.2021.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 09/22/2021] [Accepted: 10/28/2021] [Indexed: 01/17/2023]
Abstract
Union of two gametes to form a zygote is a defining event in the life of sexual eukaryotes, yet the mechanisms that underlie cell-cell fusion during fertilization remain poorly characterized. Here, in studies of fertilization in the green alga, Chlamydomonas, we report identification of a membrane protein on minus gametes, Minus Adhesion Receptor 1 (MAR1), that is essential for the membrane attachment with plus gametes that immediately precedes lipid bilayer merger. We show that MAR1 forms a receptor pair with previously identified receptor FUS1 on plus gametes, whose ectodomain architecture we find is identical to a sperm adhesion protein conserved throughout plant lineages. Strikingly, before fusion, MAR1 is biochemically and functionally associated with the ancient, evolutionarily conserved eukaryotic Class II fusion protein HAP2 on minus gametes. Thus, the integral membrane protein MAR1 provides a molecular link between membrane adhesion and bilayer merger during fertilization in Chlamydomonas.
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Affiliation(s)
- Jennifer F Pinello
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yanjie Liu
- Department of Cell Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9039, USA
| | - William J Snell
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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7
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The Major Ciliary Isoforms of RPGR Build Different Interaction Complexes with INPP5E and RPGRIP1L. Int J Mol Sci 2021; 22:ijms22073583. [PMID: 33808286 PMCID: PMC8037643 DOI: 10.3390/ijms22073583] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 01/24/2023] Open
Abstract
X-linked retinitis pigmentosa (XLRP) is frequently caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. A complex splicing process acts on the RPGR gene resulting in three major isoforms: RPGRex1-19, RPGRORF15 and RPGRskip14/15. We characterized the widely expressed, alternatively spliced transcript RPGRskip14/15 lacking exons 14 and 15. Using the CRISPR/eSpCas9 system, we generated HEK293T cell lines exclusively expressing the RPGRskip14/15 transcript from the endogenous RPGR gene. RPGRex1-19 and RPGRORF15 were knocked out. Immunocytochemistry demonstrated that the RPGRskip14/15 protein localizes along primary cilia, resembling the expression pattern of RPGRex1-19. The number of cilia-carrying cells was not affected by the absence of the RPGRex1-19 and RPGRORF15 isoforms. Co-immunoprecipitation assays demonstrated that both RPGRex1-19 and RPGRskip14/15 interact with PDE6D, further supporting that RPGRskip14/15 is associated with the protein networks along the primary cilium. Interestingly, interaction complexes with INPP5E or RPGRIP1L were only detectable with isoform RPGRex1-19, but not with RPGRskip14/15, demonstrating distinct functional properties of the major RPGR isoforms in spite of their similar subcellular localization. Our findings lead to the conclusion that protein binding sites within RPGR are mediated through alternative splicing. A tissue-specific expression ratio between RPGRskip14/15 and RPGRex1-19 seems required to regulate the ciliary concentration of RPGR interaction partners.
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8
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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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9
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Yoshioka H, Ramakrishnan SS, Suzuki A, Iwata J. Phenytoin Inhibits Cell Proliferation through microRNA-196a-5p in Mouse Lip Mesenchymal Cells. Int J Mol Sci 2021; 22:1746. [PMID: 33572377 PMCID: PMC7916186 DOI: 10.3390/ijms22041746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/22/2023] Open
Abstract
Cleft lip (CL) is one of the most common birth defects. It is caused by either genetic mutations or environmental factors. Recent studies suggest that environmental factors influence the expression of noncoding RNAs [e.g., microRNA (miRNA)], which can regulate the expression of genes crucial for cellular functions. In this study, we examined which miRNAs are associated with CL. Among 10 candidate miRNAs (miR-98-3p, miR-101a-3p, miR-101b-3p, miR-141-3p, miR-144-3p, miR-181a-5p, miR-196a-5p, miR-196b-5p, miR-200a-3p, and miR-710) identified through our bioinformatic analysis of CL-associated genes, overexpression of miR-181a-5p, miR-196a-5p, miR-196b-5p, and miR-710 inhibited cell proliferation through suppression of genes associated with CL in cultured mouse embryonic lip mesenchymal cells (MELM cells) and O9-1 cells, a mouse cranial neural crest cell line. In addition, we found that phenytoin, an inducer of CL, decreased cell proliferation through miR-196a-5p induction. Notably, treatment with a specific inhibitor for miR-196a-5p restored cell proliferation through normalization of expression of CL-associated genes in the cells treated with phenytoin. Taken together, our results suggest that phenytoin induces CL through miR-196a-5p induction, which suppresses the expression of CL-associated genes.
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Affiliation(s)
- Hiroki Yoshioka
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Sai Shankar Ramakrishnan
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (H.Y.); (S.S.R.); (A.S.)
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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10
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Ning K, Song E, Sendayen BE, Prosseda PP, Chang KC, Ghaffarieh A, Alvarado JA, Wang B, Haider KM, Berbari NF, Hu Y, Sun Y. Defective INPP5E distribution in NPHP1-related Senior-Loken syndrome. Mol Genet Genomic Med 2020; 9:e1566. [PMID: 33306870 PMCID: PMC7963418 DOI: 10.1002/mgg3.1566] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Background Senior–Loken syndrome is a rare genetic disorder that presents with nephronophthisis and retinal degeneration, leading to end‐stage renal disease and progressive blindness. The most frequent cause of juvenile nephronophthisis is a mutation in the nephronophthisis type 1 (NPHP1) gene. NPHP1 encodes the protein nephrocystin‐1, which functions at the transition zone (TZ) of primary cilia. Methods We report a 9‐year‐old Senior–Loken syndrome boy with NPHP1 deletion, who presents with bilateral vision decrease and cystic renal disease. Renal function deteriorated to require bilateral nephrectomy and renal transplant. We performed immunohistochemistry, H&E staining, and electron microscopy on the renal sample to determine the subcellular distribution of ciliary proteins in the absence of NPHP1. Results Immunohistochemistry and electron microscopy of the resected kidney showed disorganized cystic structures with loss of cilia in renal tubules. Phosphoinositides have been recently recognized as critical components of the ciliary membrane and immunostaining of kidney sections for phosphoinositide 5‐phosphatase, INPP5E, showed loss of staining compared to healthy control. Ophthalmic examination showed decreased electroretinogram consistent with early retinal degeneration. Conclusion The decreased expression of INPP5E specifically in the primary cilium, coupled with disorganized cilia morphology, suggests a novel role of NPHP1 that it is involved in regulating ciliary phosphoinositide composition in the ciliary membrane of renal tubular cells. In this study, we report a 9‐year‐old Senior‐Loken syndrome patient with NPHP1 deletion. We found the decreased expression of INPP5E specifically in the primary cilium, coupled with disorganized cilia morphology, suggests a novel role of NPHP1 in regulating ciliary phosphoinositide composition in the ciliary membrane of renal tubular cells.
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Affiliation(s)
- Ke Ning
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Emilie Song
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brent E Sendayen
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Philipp P Prosseda
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kun-Che Chang
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jorge A Alvarado
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Biao Wang
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn M Haider
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nicolas F Berbari
- Department of Biology, Indiana University Purdue University in Indianapolis, Indianapolis, IN, USA
| | - Yang Hu
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Sun
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA.,Palo Alto Veterans Administration Palo Alto, CA, USA
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11
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Bustamante-Marin XM, Horani A, Stoyanova M, Charng WL, Bottier M, Sears PR, Yin WN, Daniels LA, Bowen H, Conrad DF, Knowles MR, Ostrowski LE, Zariwala MA, Dutcher SK. Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia. PLoS Genet 2020; 16:e1008691. [PMID: 32764743 PMCID: PMC7444499 DOI: 10.1371/journal.pgen.1008691] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/19/2020] [Accepted: 02/22/2020] [Indexed: 01/10/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is characterized by chronic airway disease, reduced fertility, and randomization of the left/right body axis. It is caused by defects of motile cilia and sperm flagella. We screened a cohort of affected individuals that lack an obvious axonemal defect for pathogenic variants using whole exome capture, next generation sequencing, and bioinformatic analysis assuming an autosomal recessive trait. We identified one subject with an apparently homozygous nonsense variant [(c.1762C>T), p.(Arg588*)] in the uncharacterized CFAP57 gene. Interestingly, the variant results in the skipping of exon 11 (58 amino acids), which may be due to disruption of an exonic splicing enhancer. In normal human nasal epithelial cells, CFAP57 localizes throughout the ciliary axoneme. Nasal cells from the PCD patient express a shorter, mutant version of CFAP57 and the protein is not incorporated into the axoneme. The missing 58 amino acids include portions of WD repeats that may be important for loading onto the intraflagellar transport (IFT) complexes for transport or docking onto the axoneme. A reduced beat frequency and an alteration in ciliary waveform was observed. Knockdown of CFAP57 in human tracheobronchial epithelial cells (hTECs) recapitulates these findings. Phylogenetic analysis showed that CFAP57 is highly conserved in organisms that assemble motile cilia. CFAP57 is allelic with the BOP2/IDA8/FAP57 gene identified previously in Chlamydomonas reinhardtii. Two independent, insertional fap57 Chlamydomonas mutant strains show reduced swimming velocity and altered waveforms. Tandem mass tag (TMT) mass spectroscopy shows that FAP57 is missing, and the "g" inner dyneins (DHC7 and DHC3) and the "d" inner dynein (DHC2) are reduced, but the FAP57 paralog FBB7 is increased. Together, our data identify a homozygous variant in CFAP57 that causes PCD that is likely due to a defect in the inner dynein arm assembly process.
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Affiliation(s)
- Ximena M. Bustamante-Marin
- Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Mihaela Stoyanova
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wu-Lin Charng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Mathieu Bottier
- Department of Mechanical Engineering, Washington University, St. Louis, Missouri, United States of America
| | - Patrick R. Sears
- Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Wei-Ning Yin
- Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Leigh Anne Daniels
- Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Hailey Bowen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Donald F. Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Michael R. Knowles
- Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lawrence E. Ostrowski
- Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Maimoona A. Zariwala
- Department of Pathology and Laboratory Medicine and the Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
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12
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Dutcher SK. Asymmetries in the cilia of Chlamydomonas. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190153. [PMID: 31884924 PMCID: PMC7017335 DOI: 10.1098/rstb.2019.0153] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2019] [Indexed: 01/10/2023] Open
Abstract
The generation of ciliary waveforms requires the spatial and temporal regulation of dyneins. This review catalogues many of the asymmetric structures and proteins in the cilia of Chlamydomonas, a unicellular alga with two cilia that are used for motility in liquid medium. These asymmetries, which have been identified through mutant analysis, cryo-EM tomography and proteomics, provide a wealth of information to use for modelling how waveforms are generated and propagated. This article is part of the Theo Murphy meeting issue 'Unity and diversity of cilia in locomotion and transport'.
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Affiliation(s)
- Susan K. Dutcher
- Department of Genetics, Washington University in St Louis, Saint Louis, MO, USA
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13
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Bottier M, Thomas KA, Dutcher SK, Bayly PV. How Does Cilium Length Affect Beating? Biophys J 2019; 116:1292-1304. [PMID: 30878201 PMCID: PMC6451027 DOI: 10.1016/j.bpj.2019.02.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/23/2019] [Accepted: 02/13/2019] [Indexed: 12/21/2022] Open
Abstract
The effects of cilium length on the dynamics of cilia motion were investigated by high-speed video microscopy of uniciliated mutants of the swimming alga, Chlamydomonas reinhardtii. Cells with short cilia were obtained by deciliating cells via pH shock and allowing cilia to reassemble for limited times. The frequency of cilia beating was estimated from the motion of the cell body and of the cilium. Key features of the ciliary waveform were quantified from polynomial curves fitted to the cilium in each image frame. Most notably, periodic beating did not emerge until the cilium reached a critical length between 2 and 4 μm. Surprisingly, in cells that exhibited periodic beating, the frequency of beating was similar for all lengths with only a slight decrease in frequency as length increased from 4 μm to the normal length of 10-12 μm. The waveform average curvature (rad/μm) was also conserved as the cilium grew. The mechanical metrics of ciliary propulsion (force, torque, and power) all increased in proportion to length. The mechanical efficiency of beating appeared to be maximal at the normal wild-type length of 10-12 μm. These quantitative features of ciliary behavior illuminate the biophysics of cilia motion and, in future studies, may help distinguish competing hypotheses of the underlying mechanism of oscillation.
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Affiliation(s)
- Mathieu Bottier
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Kyle A Thomas
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Philip V Bayly
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri.
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14
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Picariello T, Brown JM, Hou Y, Swank G, Cochran DA, King OD, Lechtreck K, Pazour GJ, Witman GB. A global analysis of IFT-A function reveals specialization for transport of membrane-associated proteins into cilia. J Cell Sci 2019; 132:jcs220749. [PMID: 30659111 PMCID: PMC6382014 DOI: 10.1242/jcs.220749] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/02/2019] [Indexed: 12/28/2022] Open
Abstract
Intraflagellar transport (IFT), which is essential for the formation and function of cilia in most organisms, is the trafficking of IFT trains (i.e. assemblies of IFT particles) that carry cargo within the cilium. Defects in IFT cause several human diseases. IFT trains contain the complexes IFT-A and IFT-B. To dissect the functions of these complexes, we studied a Chlamydomonas mutant that is null for the IFT-A protein IFT140. The mutation had no effect on IFT-B but destabilized IFT-A, preventing flagella assembly. Therefore, IFT-A assembly requires IFT140. Truncated IFT140, which lacks the N-terminal WD repeats of the protein, partially rescued IFT and supported formation of half-length flagella that contained normal levels of IFT-B but greatly reduced amounts of IFT-A. The axonemes of these flagella had normal ultrastructure and, as investigated by SDS-PAGE, normal composition. However, composition of the flagellar 'membrane+matrix' was abnormal. Analysis of the latter fraction by mass spectrometry revealed decreases in small GTPases, lipid-anchored proteins and cell signaling proteins. Thus, IFT-A is specialized for the import of membrane-associated proteins. Abnormal levels of the latter are likely to account for the multiple phenotypes of patients with defects in IFT140.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Tyler Picariello
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jason M Brown
- Department of Biology, Salem State University, Salem, MA 01970, USA
| | - Yuqing Hou
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gregory Swank
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Deborah A Cochran
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - George B Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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