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Pir MS, Begar E, Yenisert F, Demirci HC, Korkmaz ME, Karaman A, Tsiropoulou S, Firat-Karalar EN, Blacque OE, Oner SS, Doluca O, Cevik S, Kaplan OI. CilioGenics: an integrated method and database for predicting novel ciliary genes. Nucleic Acids Res 2024:gkae554. [PMID: 38989623 DOI: 10.1093/nar/gkae554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024] Open
Abstract
Uncovering the full list of human ciliary genes holds enormous promise for the diagnosis of cilia-related human diseases, collectively known as ciliopathies. Currently, genetic diagnoses of many ciliopathies remain incomplete (1-3). While various independent approaches theoretically have the potential to reveal the entire list of ciliary genes, approximately 30% of the genes on the ciliary gene list still stand as ciliary candidates (4,5). These methods, however, have mainly relied on a single strategy to uncover ciliary candidate genes, making the categorization challenging due to variations in quality and distinct capabilities demonstrated by different methodologies. Here, we develop a method called CilioGenics that combines several methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF) network analysis, and text mining) to predict the ciliary capacity of each human gene. Our combined approach provides a CilioGenics score for every human gene that represents the probability that it will become a ciliary gene. Compared to methods that rely on a single method, CilioGenics performs better in its capacity to predict ciliary genes. Our top 500 gene list includes 258 new ciliary candidates, with 31 validated experimentally by us and others. Users may explore the whole list of human genes and CilioGenics scores on the CilioGenics database (https://ciliogenics.com/).
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Affiliation(s)
- Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Efe Begar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
| | - Ferhan Yenisert
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Hasan C Demirci
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Mustafa E Korkmaz
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Asli Karaman
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkiye
- School of Medicine, Koç University, Istanbul 34450, Turkiye
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sukru S Oner
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), 34700 Istanbul, Turkiye
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkiye
| | - Osman Doluca
- Izmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, Izmir, Turkiye
| | - Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkiye
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2
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Grimsrud MM, Forster M, Goeppert B, Hemmrich-Stanisak G, Sax I, Grzyb K, Braadland PR, Charbel A, Metzger C, Albrecht T, Steiert TA, Schlesner M, Manns MP, Vogel A, Yaqub S, Karlsen TH, Schirmacher P, Boberg KM, Franke A, Roessler S, Folseraas T. Whole-exome sequencing reveals novel cancer genes and actionable targets in biliary tract cancers in primary sclerosing cholangitis. Hepatol Commun 2024; 8:e0461. [PMID: 38967597 PMCID: PMC11227357 DOI: 10.1097/hc9.0000000000000461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/13/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND People with primary sclerosing cholangitis (PSC) have a 20% lifetime risk of biliary tract cancer (BTC). Using whole-exome sequencing, we characterized genomic alterations in tissue samples from BTC with underlying PSC. METHODS We extracted DNA from formalin-fixed, paraffin-embedded tumor and paired nontumor tissue from 52 resection or biopsy specimens from patients with PSC and BTC and performed whole-exome sequencing. Following copy number analysis, variant calling, and filtering, putative PSC-BTC-associated genes were assessed by pathway analyses and annotated to targeted cancer therapies. RESULTS We identified 53 candidate cancer genes with a total of 123 nonsynonymous alterations passing filtering thresholds in 2 or more samples. Of the identified genes, 19% had not previously been implicated in BTC, including CNGA3, KRT28, and EFCAB5. Another subset comprised genes previously implicated in hepato-pancreato-biliary cancer, such as ARID2, ELF3, and PTPRD. Finally, we identified a subset of genes implicated in a wide range of cancers such as the tumor suppressor genes TP53, CDKN2A, SMAD4, and RNF43 and the oncogenes KRAS, ERBB2, and BRAF. Focal copy number variations were found in 51.9% of the samples. Alterations in potential actionable genes, including ERBB2, MDM2, and FGFR3 were identified and alterations in the RTK/RAS (p = 0.036), TP53 (p = 0.04), and PI3K (p = 0.043) pathways were significantly associated with reduced overall survival. CONCLUSIONS In this exome-wide characterization of PSC-associated BTC, we delineated both PSC-specific and universal cancer genes. Our findings provide opportunities for a better understanding of the development of BTC in PSC and could be used as a platform to develop personalized treatment approaches.
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Affiliation(s)
- Marit M. Grimsrud
- Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
- Institute of Pathology, Hospital RKH Kliniken Ludwigsburg, Ludwigsburg, Germany
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | | | - Irmi Sax
- Biomedical Informatics, Data Mining and Data Analytics, University of Augsburg, Augsburg, Germany
| | - Krzysztof Grzyb
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Peder R. Braadland
- Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Alphonse Charbel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Carmen Metzger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas Albrecht
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Tim Alexander Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Matthias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, University of Augsburg, Augsburg, Germany
| | - Michael P. Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Sheraz Yaqub
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Hepatobiliary Surgery, Oslo University Hospital, Oslo, Norway
| | - Tom H. Karlsen
- Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section for Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Kirsten M. Boberg
- Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section for Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Trine Folseraas
- Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section for Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
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3
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King SM, Sakato-Antoku M, Patel-King RS, Balsbaugh JL. The methylome of motile cilia. Mol Biol Cell 2024; 35:ar89. [PMID: 38696262 PMCID: PMC11244166 DOI: 10.1091/mbc.e24-03-0130] [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: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/04/2024] Open
Abstract
Cilia are highly complex motile, sensory, and secretory organelles that contain perhaps 1000 or more distinct protein components, many of which are subject to various posttranslational modifications such as phosphorylation, N-terminal acetylation, and proteolytic processing. Another common modification is the addition of one or more methyl groups to the side chains of arginine and lysine residues. These tunable additions delocalize the side-chain charge, decrease hydrogen bond capacity, and increase both bulk and hydrophobicity. Methylation is usually mediated by S-adenosylmethionine (SAM)-dependent methyltransferases and reversed by demethylases. Previous studies have identified several ciliary proteins that are subject to methylation including axonemal dynein heavy chains that are modified by a cytosolic methyltransferase. Here, we have performed an extensive proteomic analysis of multiple independently derived cilia samples to assess the potential for SAM metabolism and the extent of methylation in these organelles. We find that cilia contain all the enzymes needed for generation of the SAM methyl donor and recycling of the S-adenosylhomocysteine and tetrahydrofolate byproducts. In addition, we find that at least 155 distinct ciliary proteins are methylated, in some cases at multiple sites. These data provide a comprehensive resource for studying the consequences of methyl marks on ciliary biology.
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Affiliation(s)
- Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Ramila S. Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT 06269
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4
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Gerniers A, Nijssen S, Dupont P. scCross: efficient search for rare subpopulations across multiple single-cell samples. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae371. [PMID: 38889273 DOI: 10.1093/bioinformatics/btae371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
MOTIVATION Identifying rare cell types is an important task to capture the heterogeneity of single-cell data, such as scRNA-seq. The widespread availability of such data enables to aggregate multiple samples, corresponding for example to different donors, into the same study. Yet, such aggregated data is often subject to batch effects between samples. Clustering it therefore generally requires the use of data integration methods, which can lead to overcorrection, making the identification of rare cells difficult. We present scCross, a biclustering method identifying rare subpopulations of cells present across multiple single-cell samples. It jointly identifies a group of cells with specific marker genes by relying on a global sum criterion, computed over entire subpopulation of cells, rather than pairwise comparisons between individual cells. This proves robust with respect to the high variability of scRNA-seq data, in particular batch effects. RESULTS We show through several case studies that scCross is able to identify rare subpopulations across multiple samples without performing prior data integration. Namely, it identifies a cilium subpopulation with potential new ciliary genes from lung cancer cells, which is not detected by typical alternatives. It also highlights rare subpopulations in human pancreas samples sequenced with different protocols, despite visible shifts in expression levels between batches. We further show that scCross outperforms typical alternatives at identifying a target rare cell type in a controlled experiment with artificially created batch effects. This shows the ability of scCross to efficiently identify rare cell subpopulations characterized by specific genes despite the presence of batch effects. AVAILABILITY AND IMPLEMENTATION The R and Scala implementation of scCross is freely available on GitHub, at https://github.com/agerniers/scCross/. A snapshot of the code and the data underlying this article are available on Zenodo, at https://zenodo.org/doi/10.5281/zenodo.10471063.
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Affiliation(s)
- Alexander Gerniers
- ICTEAM/INGI/Artificial Intelligence and Algorithms Group, UCLouvain, Louvain-la-Neuve 1348, Belgium
| | - Siegfried Nijssen
- ICTEAM/INGI/Artificial Intelligence and Algorithms Group, UCLouvain, Louvain-la-Neuve 1348, Belgium
| | - Pierre Dupont
- ICTEAM/INGI/Artificial Intelligence and Algorithms Group, UCLouvain, Louvain-la-Neuve 1348, Belgium
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5
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Fu G, Augspurger K, Sakizadeh J, Reck J, Bower R, Tritschler D, Gui L, Nicastro D, Porter ME. The MBO2/FAP58 heterodimer stabilizes assembly of inner arm dynein b and reveals axoneme asymmetries involved in ciliary waveform. Mol Biol Cell 2024; 35:ar72. [PMID: 38568782 PMCID: PMC11151096 DOI: 10.1091/mbc.e23-11-0439] [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: 11/17/2023] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Cilia generate three-dimensional waveforms required for cell motility and transport of fluid, mucus, and particles over the cell surface. This movement is driven by multiple dynein motors attached to nine outer doublet microtubules that form the axoneme. The outer and inner arm dyneins are organized into 96-nm repeats tandemly arrayed along the length of the doublets. Motility is regulated in part by projections from the two central pair microtubules that contact radial spokes located near the base of the inner dynein arms in each repeat. Although much is known about the structures and protein complexes within the axoneme, many questions remain about the regulatory mechanisms that allow the cilia to modify their waveforms in response to internal or external stimuli. Here, we used Chlamydomonas mbo (move backwards only) mutants with altered waveforms to identify at least two conserved proteins, MBO2/CCDC146 and FAP58/CCDC147, that form part of a L-shaped structure that varies between doublet microtubules. Comparative proteomics identified additional missing proteins that are altered in other motility mutants, revealing overlapping protein defects. Cryo-electron tomography and epitope tagging revealed that the L-shaped, MBO2/FAP58 structure interconnects inner dynein arms with multiple regulatory complexes, consistent with its function in modifying the ciliary waveform.
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Affiliation(s)
- Gang Fu
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Katherine Augspurger
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Jason Sakizadeh
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Jaimee Reck
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Raqual Bower
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
| | - Long Gui
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Mary E. Porter
- Department of Genetics, Cell Biology, and Genetics, University of Minnesota, Minneapolis, MN 55455
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Drygalski K, Higos R, Merabtene F, Mojsak P, Grubczak K, Ciborowski M, Razak H, Clément K, Dugail I. Extracellular matrix hyaluronan modulates fat cell differentiation and primary cilia dynamics. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159470. [PMID: 38423452 DOI: 10.1016/j.bbalip.2024.159470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Hyaluronan is an important extracellular matrix component, with poorly documented physiological role in the context of lipid-rich adipose tissue. We have investigated the global impact of hyaluronan removal from adipose tissue environment by in vitro exposure to exogenous hyaluronidase (or heat inactivated enzyme). Gene set expression analysis from RNA sequencing revealed downregulated adipogenesis as a main response to hyaluronan removal from human adipose tissue samples, which was confirmed by hyaluronidase-mediated inhibition of adipocyte differentiation in the 3T3L1 adipose cell line. Hyaluronidase exposure starting from the time of induction with the differentiation cocktail reduced lipid accumulation in mature adipocytes, limited the expression of terminal differentiation marker genes, and impaired the early induction of co-regulated Cebpa and Pparg mRNA. Reduction of Cebpa and Pparg expression by exogenous hyaluronidase was also observed in cultured primary preadipocytes from subcutaneous, visceral or brown adipose tissue of mice. Mechanistically, inhibition of adipogenesis by hyaluronan removal was not caused by changes in osmotic pressure or cell inflammatory status, could not be mimicked by exposure to threose, a metabolite generated by hyaluronan degradation, and was not linked to alteration in endogenous Wnt ligands expression. Rather, we observed that hyaluronan removal associated with disrupted primary cilia dynamics, with elongated cilium and higher proportions of preadipocytes that remained ciliated in hyaluronidase-treated conditions. Thus, our study points to a new link between ciliogenesis and hyaluronan impacting adipose tissue development.
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Affiliation(s)
- Krzysztof Drygalski
- INSERM, Sorbonne Université, NutriOmics team : Nutrition/Obesities- systemic approaches, Paris 75013, France; Department of Hypertension and Diabetology, Medical University of Gdansk, 80-210 Gdansk, Poland
| | - Romane Higos
- INSERM, Sorbonne Université, NutriOmics team : Nutrition/Obesities- systemic approaches, Paris 75013, France
| | - Fatiha Merabtene
- INSERM, Sorbonne Université, NutriOmics team : Nutrition/Obesities- systemic approaches, Paris 75013, France
| | - Patrycja Mojsak
- Clinical Research Centre, Medical University of Bialystok, 15-276 Białystok, Poland
| | - Kamil Grubczak
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Białystok, Poland
| | - Hady Razak
- Department of General and Endocrine Surgery, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Karine Clément
- INSERM, Sorbonne Université, NutriOmics team : Nutrition/Obesities- systemic approaches, Paris 75013, France; Assistance Publique-Hopitaux de Paris, Nutrition department, Pitié-Salpetrière Hospital, 75013 Paris, France
| | - Isabelle Dugail
- INSERM, Sorbonne Université, NutriOmics team : Nutrition/Obesities- systemic approaches, Paris 75013, France.
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7
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Leggere JC, Hibbard JV, Papoulas O, Lee C, Pearson CG, Marcotte EM, Wallingford JB. Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants. Mol Biol Cell 2024; 35:ar39. [PMID: 38170584 PMCID: PMC10916875 DOI: 10.1091/mbc.e23-03-0084] [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: 03/10/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
DIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome of Tetrahymena thermophila. A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging in Xenopus multiciliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.
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Affiliation(s)
- Janelle C. Leggere
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Jaime V.K. Hibbard
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Ophelia Papoulas
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - Chad G. Pearson
- Anschutz Medical Campus, Department of Cell and Developmental Biology, University of Colorado, Aurora, CO 80045
| | - Edward M. Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
| | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, TX 78712
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8
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Kalot R, Sentell Z, Kitzler TM, Torban E. Primary cilia and actin regulatory pathways in renal ciliopathies. FRONTIERS IN NEPHROLOGY 2024; 3:1331847. [PMID: 38292052 PMCID: PMC10824913 DOI: 10.3389/fneph.2023.1331847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
Ciliopathies are a group of rare genetic disorders caused by defects to the structure or function of the primary cilium. They often affect multiple organs, leading to brain malformations, congenital heart defects, and anomalies of the retina or skeletal system. Kidney abnormalities are among the most frequent ciliopathic phenotypes manifesting as smaller, dysplastic, and cystic kidneys that are often accompanied by renal fibrosis. Many renal ciliopathies cause chronic kidney disease and often progress to end-stage renal disease, necessitating replacing therapies. There are more than 35 known ciliopathies; each is a rare hereditary condition, yet collectively they account for a significant proportion of chronic kidney disease worldwide. The primary cilium is a tiny microtubule-based organelle at the apex of almost all vertebrate cells. It serves as a "cellular antenna" surveying environment outside the cell and transducing this information inside the cell to trigger multiple signaling responses crucial for tissue morphogenesis and homeostasis. Hundreds of proteins and unique cellular mechanisms are involved in cilia formation. Recent evidence suggests that actin remodeling and regulation at the base of the primary cilium strongly impacts ciliogenesis. In this review, we provide an overview of the structure and function of the primary cilium, focusing on the role of actin cytoskeleton and its regulators in ciliogenesis. We then describe the key clinical, genetic, and molecular aspects of renal ciliopathies. We highlight what is known about actin regulation in the pathogenesis of these diseases with the aim to consider these recent molecular findings as potential therapeutic targets for renal ciliopathies.
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Affiliation(s)
- Rita Kalot
- Department of Medicine and Department of Physiology, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Zachary Sentell
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas M. Kitzler
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Health Center, Montreal, QC, Canada
| | - Elena Torban
- Department of Medicine and Department of Physiology, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, Canada
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9
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Wu JY, Cho SJ, Descant K, Li PH, Shapson-Coe A, Januszewski M, Berger DR, Meyer C, Casingal C, Huda A, Liu J, Ghashghaei T, Brenman M, Jiang M, Scarborough J, Pope A, Jain V, Stein JL, Guo J, Yasuda R, Lichtman JW, Anton ES. Mapping of neuronal and glial primary cilia contactome and connectome in the human cerebral cortex. Neuron 2024; 112:41-55.e3. [PMID: 37898123 PMCID: PMC10841524 DOI: 10.1016/j.neuron.2023.09.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 07/25/2023] [Accepted: 09/22/2023] [Indexed: 10/30/2023]
Abstract
Primary cilia act as antenna receivers of environmental signals and enable effective neuronal or glial responses. Disruption of their function is associated with circuit disorders. To understand the signals these cilia receive, we comprehensively mapped cilia's contacts within the human cortical connectome using serial-section EM reconstruction of a 1 mm3 cortical volume, spanning the entire cortical thickness. We mapped the "contactome" of cilia emerging from neurons and astrocytes in every cortical layer. Depending on the layer and cell type, cilia make distinct patterns of contact. Primary cilia display cell-type- and layer-specific variations in size, shape, and microtubule axoneme core, which may affect their signaling competencies. Neuronal cilia are intrinsic components of a subset of cortical synapses and thus a part of the connectome. This diversity in the structure, contactome, and connectome of primary cilia endows each neuron or glial cell with a unique barcode of access to the surrounding neural circuitry.
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Affiliation(s)
- Jun Yao Wu
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Su-Ji Cho
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Katherine Descant
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Peter H Li
- Google Research, Mountain View, CA 94043, USA
| | - Alexander Shapson-Coe
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Daniel R Berger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cailyn Meyer
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Cristine Casingal
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ariba Huda
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jiaqi Liu
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tina Ghashghaei
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mikayla Brenman
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Michelle Jiang
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Joseph Scarborough
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Art Pope
- Google Research, Mountain View, CA 94043, USA
| | - Viren Jain
- Google Research, Mountain View, CA 94043, USA
| | - Jason L Stein
- UNC Neuroscience Center and the Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jiami Guo
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA.
| | - Jeff W Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - E S Anton
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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10
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Chae S, Park TJ, Kwon T. Convergent differentiation of multiciliated cells. Sci Rep 2023; 13:23028. [PMID: 38155158 PMCID: PMC10754865 DOI: 10.1038/s41598-023-50077-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Multiciliated cells (MCCs) are epithelial cells that control body fluid flow and contribute to the clearance of pathogenic microbes and other particles from the airways, egg transport in oviducts, and circulation of cerebrospinal fluid in the central nervous system. Although MCCs have shared functions to control fluid flow via coordinated motility of multiple ciliary structures, they are found in multiple mammalian tissues originating from distinct germ layers and differentiate via distinct developmental pathways. To understand the similarities and differences of MCCs in multiple tissues, we investigated single-cell transcriptome data of nasal epithelial cells, bronchial tubes, fallopian tubes, and ependymal cells in the subventricular zone from humans and mice by cross-species data integration. Expression of cilia-associated genes was indistinguishable between these MCCs, although cell populations had unique properties by the species and tissue, demonstrating that they share the same final differentiation status for ciliary functions. We further analyzed the final differentiation step of MCCs from their distinctive progenitors and confirmed their convergent gene set expression for ciliogenesis at the final step. These results may provide new insight into understanding ciliogenesis during the developmental process.
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Affiliation(s)
- Shinhyeok Chae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tae Joo Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
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11
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Walker JT, Saunders DC, Rai V, Chen HH, Orchard P, Dai C, Pettway YD, Hopkirk AL, Reihsmann CV, Tao Y, Fan S, Shrestha S, Varshney A, Petty LE, Wright JJ, Ventresca C, Agarwala S, Aramandla R, Poffenberger G, Jenkins R, Mei S, Hart NJ, Phillips S, Kang H, Greiner DL, Shultz LD, Bottino R, Liu J, Below JE, Parker SCJ, Powers AC, Brissova M. Genetic risk converges on regulatory networks mediating early type 2 diabetes. Nature 2023; 624:621-629. [PMID: 38049589 DOI: 10.1038/s41586-023-06693-2] [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: 12/02/2021] [Accepted: 09/28/2023] [Indexed: 12/06/2023]
Abstract
Type 2 diabetes mellitus (T2D), a major cause of worldwide morbidity and mortality, is characterized by dysfunction of insulin-producing pancreatic islet β cells1,2. T2D genome-wide association studies (GWAS) have identified hundreds of signals in non-coding and β cell regulatory genomic regions, but deciphering their biological mechanisms remains challenging3-5. Here, to identify early disease-driving events, we performed traditional and multiplexed pancreatic tissue imaging, sorted-islet cell transcriptomics and islet functional analysis of early-stage T2D and control donors. By integrating diverse modalities, we show that early-stage T2D is characterized by β cell-intrinsic defects that can be proportioned into gene regulatory modules with enrichment in signals of genetic risk. After identifying the β cell hub gene and transcription factor RFX6 within one such module, we demonstrated multiple layers of genetic risk that converge on an RFX6-mediated network to reduce insulin secretion by β cells. RFX6 perturbation in primary human islet cells alters β cell chromatin architecture at regions enriched for T2D GWAS signals, and population-scale genetic analyses causally link genetically predicted reduced RFX6 expression with increased T2D risk. Understanding the molecular mechanisms of complex, systemic diseases necessitates integration of signals from multiple molecules, cells, organs and individuals, and thus we anticipate that this approach will be a useful template to identify and validate key regulatory networks and master hub genes for other diseases or traits using GWAS data.
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Affiliation(s)
- John T Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vivek Rai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Hung-Hsin Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chunhua Dai
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yasminye D Pettway
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander L Hopkirk
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Conrad V Reihsmann
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yicheng Tao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Simin Fan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Shristi Shrestha
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jordan J Wright
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christa Ventresca
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Samir Agarwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Radhika Aramandla
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Greg Poffenberger
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Regina Jenkins
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shaojun Mei
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nathaniel J Hart
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sharon Phillips
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hakmook Kang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dale L Greiner
- Department of Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Rita Bottino
- Imagine Pharma, Devon, PA, USA
- Institute of Cellular Therapeutics, Allegheny-Singer Research Institute, Allegheny Health Network, Pittsburgh, PA, USA
| | - Jie Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
| | - Alvin C Powers
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- VA Tennessee Valley Healthcare System, Nashville, TN, USA.
| | - Marcela Brissova
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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12
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Freke GM, Martins T, Davies RJ, Beyer T, Seda M, Peskett E, Haq N, Prasai A, Otto G, Jeyabalan Srikaran J, Hernandez V, Diwan GD, Russell RB, Ueffing M, Huranova M, Boldt K, Beales PL, Jenkins D. De-Suppression of Mesenchymal Cell Identities and Variable Phenotypic Outcomes Associated with Knockout of Bbs1. Cells 2023; 12:2662. [PMID: 37998397 PMCID: PMC10670506 DOI: 10.3390/cells12222662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue-specific, as well as gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane-trafficking and intraflagellar transport (IFT) adaptor protein complex formed by eight BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis, we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations in Bbs1, as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach, we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically defined clones. Our results suggest that BBS1 is required for the suppression of mesenchymal cell identities as the IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, as well as BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively, this work suggests that the dynamic stability of the BBSome is essential for the suppression of mesenchymal cell identities as epithelial cells differentiate.
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Affiliation(s)
- Grace Mercedes Freke
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tiago Martins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Rosalind Jane Davies
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tina Beyer
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Marian Seda
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Emma Peskett
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Naila Haq
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Avishek Prasai
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Georg Otto
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Jeshmi Jeyabalan Srikaran
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Victor Hernandez
- Life Sciences Department, CHMLS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK;
| | - Gaurav D. Diwan
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Robert B. Russell
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Karsten Boldt
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Philip L. Beales
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Dagan Jenkins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
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13
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Yeo S, Jang J, Jung HJ, Lee H, Choe Y. Primary cilia-mediated regulation of microglial secretion in Alzheimer's disease. Front Mol Biosci 2023; 10:1250335. [PMID: 37942288 PMCID: PMC10627801 DOI: 10.3389/fmolb.2023.1250335] [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: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
Alzheimer's disease (AD) is a brain disorder manifested by a gradual decline in cognitive function due to the accumulation of extracellular amyloid plaques, disruptions in neuronal substance transport, and the degeneration of neurons. In affected neurons, incomplete clearance of toxic proteins by neighboring microglia leads to irreversible brain inflammation, for which cellular signaling is poorly understood. Through single-cell transcriptomic analysis, we discovered distinct regional differences in the ability of microglia to clear damaged neurites. Specifically, microglia in the septal region of wild type mice exhibited a transcriptomic signature resembling disease-associated microglia (DAM). These lateral septum (LS)-enriched microglia were associated with dense axonal bundles originating from the hippocampus. Further transcriptomic and proteomic approaches revealed that primary cilia, small hair-like structures found on cells, played a role in the regulation of microglial secretory function. Notably, primary cilia were transiently observed in microglia, and their presence was significantly reduced in microglia from AD mice. We observed significant changes in the secretion and proteomic profiles of the secretome after inhibiting the primary cilia gene intraflagellar transport particle 88 (Ift88) in microglia. Intriguingly, inhibiting primary cilia in the septal microglia of AD mice resulted in the expansion of extracellular amyloid plaques and damage to adjacent neurites. These results indicate that DAM-like microglia are present in the LS, a critical target region for hippocampal nerve bundles, and that the primary ciliary signaling system regulates microglial secretion, affecting extracellular proteostasis. Age-related primary ciliopathy probably contributes to the selective sensitivity of microglia, thereby exacerbating AD. Targeting the primary ciliary signaling system could therefore be a viable strategy for modulating neuroimmune responses in AD treatments.
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Affiliation(s)
- Seungeun Yeo
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jaemyung Jang
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyun Jin Jung
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyeyoung Lee
- Division of Applied Bioengineering, Dong-eui University, Busan, Republic of Korea
| | - Youngshik Choe
- Korea Brain Research Institute, Daegu, Republic of Korea
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14
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Chen J, Wang Y, Wu B, Shi H, Wang L. Experimental and molecular support for Cfap70 as a causative gene of 'multiple morphological abnormalities of the flagella' with male infertility†. Biol Reprod 2023; 109:450-460. [PMID: 37458246 DOI: 10.1093/biolre/ioad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 10/17/2023] Open
Abstract
Multiple morphological abnormalities of the flagella, a severe form of asthenozoospermia, can lead to male infertility. Recent studies have implicated an association between human CFAP70 deficiency and multiple morphological abnormalities of the flagella; however, the underlying biological mechanism and supporting experimental evidence in animal models remain unclear. To address this gap, we used CRISPR/Cas9 technology to generate Cfap70-deficient mice to investigate the relationship between Cfap70 deficiency and multiple morphological abnormalities of the flagella. Our findings show that the loss of CFAP70 leads to multiple morphological abnormalities of the flagella and spermiogenesis defects. Specifically, the lack of CFAP70 impairs sperm flagellum biogenesis and head shaping during spermiogenesis. Late-step spermatids from Cfap70-deficient mouse testis exhibited club-shaped sperm heads and abnormal disassembly of the manchette. Furthermore, we found that CFAP70 interacts with DNAI1 and DNAI2; Cfap70 deficiency also reduces the level of AKAP3 in sperm flagella, indicating that CFAP70 may participate in the flagellum assembly and transport of flagellar components. These findings provide compelling evidence implicating Cfap70 as a causative gene of multiple morphological abnormalities of the flagella and highlight the consequences of CFAP70 loss on flagellum biogenesis.
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Affiliation(s)
- Jingwen Chen
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, School of Pharmacy, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
| | - Yaling Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Bangguo Wu
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, School of Pharmacy, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Huijuan Shi
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, School of Pharmacy, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
| | - Lingbo Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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15
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Gnanasekaran H, Chandrasekhar SP, Kandeeban S, Periyasamy P, Bhende M, Khetan V, Gupta N, Kabra M, Namboothri S, Sen P, Sripriya S. Mutation profile of Bardet-Biedl syndrome patients from India: Implicative role of multiallelic rare variants and oligogenic inheritance pattern. Clin Genet 2023; 104:443-460. [PMID: 37431782 DOI: 10.1111/cge.14398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/12/2023]
Abstract
Bardet-Biedl syndrome (BBS), a rare primary form of ciliopathy, with heterogeneous clinical and genetic presentation is characterized by rod cone dystrophy, obesity, polydactyly, urogenital abnormalities, and cognitive impairment. Here, we delineate the genetic profile in a cohort of 108 BBS patients from India by targeted gene sequencing-based approach for a panel of ciliopathy (including BBS) and other inherited retinal disease genes. We report here a higher frequency of BBS10 and BBS1 gene variations. A different spectrum of variations including a putatively novel gene TSPOAP1, for BBS was identified. Increased percentage frequency of digenic variants (36%) in the disease cohort, role of modifiers in familial cases are some of the salient observations in this work. This study appends the knowledge of BBS genetics pertaining to patients from India. We observed a different molecular epidemiology of BBS patients in this study cohort compared to other reports, which emphasizes the need for molecular testing in affected patients.
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Affiliation(s)
- Harshavardhini Gnanasekaran
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, Tamilnadu, India
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamilnadu, India
| | - Sathya Priya Chandrasekhar
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, Tamilnadu, India
| | - Suganya Kandeeban
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, Tamilnadu, India
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamilnadu, India
| | - Porkodi Periyasamy
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, Tamilnadu, India
| | - Muna Bhende
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Vikas Khetan
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Neerja Gupta
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Madhulika Kabra
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Sheela Namboothri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Kochi, Kerala, India
| | - Parveen Sen
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Sarangapani Sripriya
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, Tamilnadu, India
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16
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Otto M, Hoyer-Fender S. ODF2 Negatively Regulates CP110 Levels at the Centrioles/Basal Bodies to Control the Biogenesis of Primary Cilia. Cells 2023; 12:2194. [PMID: 37681926 PMCID: PMC10486571 DOI: 10.3390/cells12172194] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
Primary cilia are essential sensory organelles that develop when an inhibitory cap consisting of CP110 and other proteins is eliminated. The degradation of CP110 by the ubiquitin-dependent proteasome pathway mediated by NEURL4 and HYLS1 removes the inhibitory cap. Here, we investigated the suitability of rapamycin-mediated dimerization for centriolar recruitment and asked whether the induced recruitment of NEURL4 or HYLS1 to the centriole promotes primary cilia development and CP110 degradation. We used rapamycin-mediated dimerization with ODF2 to induce their targeted recruitment to the centriole. We found decreased CP110 levels in the transfected cells, but independent of rapamycin-mediated dimerization. By knocking down ODF2, we showed that ODF2 controls CP110 levels. The overexpression of ODF2 is not sufficient to promote the formation of primary cilia, but the overexpression of NEURL4 or HYLS1 is. The co-expression of ODF2 and HYLS1 resulted in the formation of tube-like structures, indicating an interaction. Thus, ODF2 controls primary cilia formation by negatively regulating the concentration of CP110 levels. Our data suggest that ODF2 most likely acts as a scaffold for the binding of proteins such as NEURL4 or HYLS1 to mediate CP110 degradation.
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Affiliation(s)
| | - Sigrid Hoyer-Fender
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology—Developmental Biology, GZMB, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
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17
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Clearman KR, Haycraft CJ, Croyle MJ, Collawn JF, Yoder BK. Functions of the primary cilium in the kidney and its connection with renal diseases. Curr Top Dev Biol 2023; 155:39-94. [PMID: 38043952 DOI: 10.1016/bs.ctdb.2023.07.001] [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
The nonmotile primary cilium is a sensory structure found on most mammalian cell types that integrates multiple signaling pathways involved in tissue development and postnatal function. As such, mutations disrupting cilia activities cause a group of disorders referred to as ciliopathies. These disorders exhibit a wide spectrum of phenotypes impacting nearly every tissue. In the kidney, primary cilia dysfunction caused by mutations in polycystin 1 (Pkd1), polycystin 2 (Pkd2), or polycystic kidney and hepatic disease 1 (Pkhd1), result in polycystic kidney disease (PKD), a progressive disorder causing renal functional decline and end-stage renal disease. PKD affects nearly 1 in 1000 individuals and as there is no cure for PKD, patients frequently require dialysis or renal transplantation. Pkd1, Pkd2, and Pkhd1 encode membrane proteins that all localize in the cilium. Pkd1 and Pkd2 function as a nonselective cation channel complex while Pkhd1 protein function remains uncertain. Data indicate that the cilium may act as a mechanosensor to detect fluid movement through renal tubules. Other functions proposed for the cilium and PKD proteins in cyst development involve regulation of cell cycle and oriented division, regulation of renal inflammation and repair processes, maintenance of epithelial cell differentiation, and regulation of mitochondrial structure and metabolism. However, how loss of cilia or cilia function leads to cyst development remains elusive. Studies directed at understanding the roles of Pkd1, Pkd2, and Pkhd1 in the cilium and other locations within the cell will be important for developing therapeutic strategies to slow cyst progression.
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Affiliation(s)
- Kelsey R Clearman
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney J Haycraft
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mandy J Croyle
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bradley K Yoder
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States.
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18
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Cevik S, Peng X, Beyer T, Pir MS, Yenisert F, Woerz F, Hoffmann F, Altunkaynak B, Pir B, Boldt K, Karaman A, Cakiroglu M, Oner SS, Cao Y, Ueffing M, Kaplan OI. WDR31 displays functional redundancy with GTPase-activating proteins (GAPs) ELMOD and RP2 in regulating IFT complex and recruiting the BBSome to cilium. Life Sci Alliance 2023; 6:e202201844. [PMID: 37208194 PMCID: PMC10200814 DOI: 10.26508/lsa.202201844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023] Open
Abstract
The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caenorhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumulations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into the cilia and exit from the cilia are impacted. Furthermore, anterograde IFT in the middle segment travels at increased speed in wdr-31;rpi-2;elmd-1 Remarkably, a non-ciliary protein leaks into the cilia of wdr-31;rpi-2;elmd-1, possibly because of IFT defects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.
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Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Xiaoyu Peng
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Tina Beyer
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Mustafa S Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Ferhan Yenisert
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Franziska Woerz
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Felix Hoffmann
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Betul Altunkaynak
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Betul Pir
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Karsten Boldt
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Asli Karaman
- Science and Advanced Technology Application and Research Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - Miray Cakiroglu
- Science and Advanced Technology Application and Research Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - S Sadik Oner
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
- Science and Advanced Technology Application and Research Center, Istanbul Medeniyet University, Istanbul, Turkey
| | - Ying Cao
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Marius Ueffing
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
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19
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Turan MG, Orhan ME, Cevik S, Kaplan OI. CiliaMiner: an integrated database for ciliopathy genes and ciliopathies. Database (Oxford) 2023; 2023:baad047. [PMID: 37542408 PMCID: PMC10403755 DOI: 10.1093/database/baad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 06/05/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023]
Abstract
Cilia are found in eukaryotic species ranging from single-celled organisms, such as Chlamydomonas reinhardtii, to humans, but not in plants. The ability to respond to repellents and/or attractants, regulate cell proliferation and differentiation and provide cellular mobility are just a few examples of how crucial cilia are to cells and organisms. Over 30 distinct rare disorders generally known as ciliopathy are caused by abnormalities or functional impairments in cilia and cilia-related compartments. Because of the complexity of ciliopathies and the rising number of ciliopathies and ciliopathy genes, a ciliopathy-oriented and up-to-date database is required. Here, we present CiliaMiner, a manually curated ciliopathy database that includes ciliopathy lists collected from articles and databases. Analysis reveals that there are 55 distinct disorders likely related to ciliopathy, with over 4000 clinical manifestations. Based on comparative symptom analysis and subcellular localization data, diseases are classified as primary, secondary or atypical ciliopathies. CiliaMiner provides easy access to all of these diseases and disease genes, as well as clinical features and gene-specific clinical features, as well as subcellular localization of each protein. Additionally, the orthologs of disease genes are also provided for mice, zebrafish, Xenopus, Drosophila, Caenorhabditis elegans and Chlamydomonas reinhardtii. CiliaMiner (https://kaplanlab.shinyapps.io/ciliaminer) aims to serve the cilia community with its comprehensive content and highly enriched interactive heatmaps, and will be continually updated. Database URL: https://kaplanlab.shinyapps.io/ciliaminer/.
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Affiliation(s)
- Merve Gül Turan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Sumer Kampusu, Kayseri 38080, Turkey
- Department of Bioengineering, School of Life and Natural Sciences, Abdullah Gul University, Sumer Kampusu, Kayseri 38080, Turkey
| | - Mehmet Emin Orhan
- Department of Bioengineering, School of Life and Natural Sciences, Abdullah Gul University, Sumer Kampusu, Kayseri 38080, Turkey
| | - Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Sumer Kampusu, Kayseri 38080, Turkey
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Sumer Kampusu, Kayseri 38080, Turkey
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20
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Carotenuto P, Gradilone SA, Franco B. Cilia and Cancer: From Molecular Genetics to Therapeutic Strategies. Genes (Basel) 2023; 14:1428. [PMID: 37510333 PMCID: PMC10379587 DOI: 10.3390/genes14071428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Cilia are microtubule-based organelles that project from the cell surface with motility or sensory functions. Primary cilia work as antennae to sense and transduce extracellular signals. Cilia critically control proliferation by mediating cell-extrinsic signals and by regulating cell cycle entry. Recent studies have shown that primary cilia and their associated proteins also function in autophagy and genome stability, which are important players in oncogenesis. Abnormal functions of primary cilia may contribute to oncogenesis. Indeed, defective cilia can either promote or suppress cancers, depending on the cancer-initiating mutation, and the presence or absence of primary cilia is associated with specific cancer types. Together, these findings suggest that primary cilia play important, but distinct roles in different cancer types, opening up a completely new avenue of research to understand the biology and treatment of cancers. In this review, we discuss the roles of primary cilia in promoting or inhibiting oncogenesis based on the known or predicted functions of cilia and cilia-associated proteins in several key processes and related clinical implications.
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Affiliation(s)
- Pietro Carotenuto
- Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy
- TIGEM, Telethon Institute of Genetics and Medicine, 80078 Naples, Italy
| | - Sergio A. Gradilone
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA;
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brunella Franco
- Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy
- TIGEM, Telethon Institute of Genetics and Medicine, 80078 Naples, Italy
- School of Advanced Studies, Genomic and Experimental medicine Program (Scuola Superiore Meridionale), 80138 Naples, Italy
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21
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Elliott KH, Balchand SK, Bonatto Paese CL, Chang CF, Yang Y, Brown KM, Rasicci DT, He H, Thorner K, Chaturvedi P, Murray SA, Chen J, Porollo A, Peterson KA, Brugmann SA. Identification of a heterogeneous and dynamic ciliome during embryonic development and cell differentiation. Development 2023; 150:dev201237. [PMID: 36971348 PMCID: PMC10163354 DOI: 10.1242/dev.201237] [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: 08/24/2022] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
Primary cilia are nearly ubiquitous organelles that transduce molecular and mechanical signals. Although the basic structure of the cilium and the cadre of genes that contribute to ciliary formation and function (the ciliome) are believed to be evolutionarily conserved, the presentation of ciliopathies with narrow, tissue-specific phenotypes and distinct molecular readouts suggests that an unappreciated heterogeneity exists within this organelle. Here, we provide a searchable transcriptomic resource for a curated primary ciliome, detailing various subgroups of differentially expressed genes within the ciliome that display tissue and temporal specificity. Genes within the differentially expressed ciliome exhibited a lower level of functional constraint across species, suggesting organism and cell-specific function adaptation. The biological relevance of ciliary heterogeneity was functionally validated by using Cas9 gene-editing to disrupt ciliary genes that displayed dynamic gene expression profiles during osteogenic differentiation of multipotent neural crest cells. Collectively, this novel primary cilia-focused resource will allow researchers to explore longstanding questions related to how tissue and cell-type specific functions and ciliary heterogeneity may contribute to the range of phenotypes associated with ciliopathies.
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Affiliation(s)
- Kelsey H. Elliott
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Sai K. Balchand
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Christian Louis Bonatto Paese
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Ching-Fang Chang
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Yanfen Yang
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | - Kari M. Brown
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
| | | | - Hao He
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Konrad Thorner
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | - Praneet Chaturvedi
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | | | - Jing Chen
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | - Aleksey Porollo
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
| | | | - Samantha A. Brugmann
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical, Cincinnati, OH 45229, USA
- University of Cincinnati, College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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22
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Lewis M, Terré B, Knobel PA, Cheng T, Lu H, Attolini CSO, Smak J, Coyaud E, Garcia-Cao I, Sharma S, Vineethakumari C, Querol J, Gil-Gómez G, Piergiovanni G, Costanzo V, Peiró S, Raught B, Zhao H, Salvatella X, Roy S, Mahjoub MR, Stracker TH. GEMC1 and MCIDAS interactions with SWI/SNF complexes regulate the multiciliated cell-specific transcriptional program. Cell Death Dis 2023; 14:201. [PMID: 36932059 PMCID: PMC10023806 DOI: 10.1038/s41419-023-05720-4] [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: 10/07/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Multiciliated cells (MCCs) project dozens to hundreds of motile cilia from their apical surface to promote the movement of fluids or gametes in the mammalian brain, airway or reproductive organs. Differentiation of MCCs requires the sequential action of the Geminin family transcriptional activators, GEMC1 and MCIDAS, that both interact with E2F4/5-DP1. How these factors activate transcription and the extent to which they play redundant functions remains poorly understood. Here, we demonstrate that the transcriptional targets and proximal proteomes of GEMC1 and MCIDAS are highly similar. However, we identified distinct interactions with SWI/SNF subcomplexes; GEMC1 interacts primarily with the ARID1A containing BAF complex while MCIDAS interacts primarily with BRD9 containing ncBAF complexes. Treatment with a BRD9 inhibitor impaired MCIDAS-mediated activation of several target genes and compromised the MCC differentiation program in multiple cell based models. Our data suggest that the differential engagement of distinct SWI/SNF subcomplexes by GEMC1 and MCIDAS is required for MCC-specific transcriptional regulation and mediated by their distinct C-terminal domains.
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Affiliation(s)
- Michael Lewis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Berta Terré
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
- MRC Clinical Trials Unit at UCL, London, UK
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
- CDR-Life AG, Zurich, 8592, Switzerland
| | - Tao Cheng
- Washington University in St Louis, Departments of Medicine (Nephrology), Cell Biology and Physiology, St. Louis, MO, 20814, USA
| | - Hao Lu
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Jordann Smak
- National Cancer Institute, Radiation Oncology Branch, Bethesda, MD, 20892, USA
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Isabel Garcia-Cao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Shalu Sharma
- National Cancer Institute, Radiation Oncology Branch, Bethesda, MD, 20892, USA
| | - Chithran Vineethakumari
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
| | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, 08035, Spain
| | - Gabriel Gil-Gómez
- Apoptosis Signalling Group, IMIM (Institut Hospital del Mar d'Investigacions Mediques), Barcelona, 08003, Spain
| | - Gabriele Piergiovanni
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, 20139, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, 20139, Italy
| | - Vincenzo Costanzo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, 20139, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, 20139, Italy
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, 08035, Spain
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Haotian Zhao
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, NY, 11568, USA
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Singapore
- Department of Pediatrics, National University of Singapore, 119288, Singapore, Singapore
| | - Moe R Mahjoub
- Washington University in St Louis, Departments of Medicine (Nephrology), Cell Biology and Physiology, St. Louis, MO, 20814, USA
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, Barcelona, 08028, Spain.
- National Cancer Institute, Radiation Oncology Branch, Bethesda, MD, 20892, USA.
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23
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Yuan G, Yang ST, Yang S. Regulator of G protein signaling 12 drives inflammatory arthritis by activating synovial fibroblasts through MYCBP2/KIF2A signaling. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:197-210. [PMID: 36700049 PMCID: PMC9843488 DOI: 10.1016/j.omtn.2022.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Synovial fibroblasts are the active and aggressive drivers in the progression of arthritis, but the cellular and molecular mechanisms remain unknown. Here, our results showed that regulator of G protein signaling 12 (RGS12) maintained ciliogenesis in synovial fibroblasts, which is critical for the development of inflammatory arthritis. Deletion of RGS12 led to a significant decrease in ciliogenesis, adhesion, migration, and secretion of synovial fibroblasts. Mechanistically, RGS12 overexpression in synovial fibroblasts increased the length and number of cilia but decreased the protein level of kinesin family member 2A (KIF2A). The results of LC-MS analyses showed that RGS12 interacted with MYC binding protein 2 to enhance its ubiquitination activity, through which the KIF2A protein was degraded in synovial fibroblasts. Moreover, overexpression of KIF2A blocked the increases in cilia length and number. Mice with RGS12 deficiency or treatment of RGS12 shRNA nanoparticles significantly decreased the clinical score, paw swelling, synovitis, and cartilage destruction during inflammatory arthritis by inhibiting the activation of synovial fibroblasts. Therefore, this study provides evidence that RGS12 activates synovial fibroblasts' pathological function via promoting MCYBP2-mediated degradation of KIF2A and ciliogenesis. Our data suggest that RGS12 may be a potential drug target for the treatment of inflammatory arthritis.
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Affiliation(s)
- Gongsheng Yuan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shu-ting Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shuying Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Penn Center for Musculoskeletal Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Innovation & Precision Dentistry, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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24
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Leggere JC, Hibbard JVK, Papoulas O, Lee C, Pearson CG, Marcotte EM, Wallingford JB. Label-free proteomic comparison reveals ciliary and non-ciliary phenotypes of IFT-A mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531778. [PMID: 36945534 PMCID: PMC10028850 DOI: 10.1101/2023.03.08.531778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
DIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome of Tetrahymena thermophila . A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging in Xenopus multiciliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.
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25
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Khatri D, Putoux A, Cologne A, Kaltenbach S, Besson A, Bertiaux E, Guguin J, Fendler A, Dupont MA, Benoit-Pilven C, Qebibo L, Ahmed-Elie S, Audebert-Bellanger S, Blanc P, Rambaud T, Castelle M, Cornen G, Grotto S, Guët A, Guibaud L, Michot C, Odent S, Ruaud L, Sacaze E, Hamel V, Bordonné R, Leutenegger AL, Edery P, Burglen L, Attié-Bitach T, Mazoyer S, Delous M. Deficiency of the minor spliceosome component U4atac snRNA secondarily results in ciliary defects in human and zebrafish. Proc Natl Acad Sci U S A 2023; 120:e2102569120. [PMID: 36802443 PMCID: PMC9992838 DOI: 10.1073/pnas.2102569120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 12/12/2022] [Indexed: 02/23/2023] Open
Abstract
In the human genome, about 750 genes contain one intron excised by the minor spliceosome. This spliceosome comprises its own set of snRNAs, among which U4atac. Its noncoding gene, RNU4ATAC, has been found mutated in Taybi-Linder (TALS/microcephalic osteodysplastic primordial dwarfism type 1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes. These rare developmental disorders, whose physiopathological mechanisms remain unsolved, associate ante- and post-natal growth retardation, microcephaly, skeletal dysplasia, intellectual disability, retinal dystrophy, and immunodeficiency. Here, we report bi-allelic RNU4ATAC mutations in five patients presenting with traits suggestive of the Joubert syndrome (JBTS), a well-characterized ciliopathy. These patients also present with traits typical of TALS/RFMN/LWS, thus widening the clinical spectrum of RNU4ATAC-associated disorders and indicating ciliary dysfunction as a mechanism downstream of minor splicing defects. Intriguingly, all five patients carry the n.16G>A mutation, in the Stem II domain, either at the homozygous or compound heterozygous state. A gene ontology term enrichment analysis on minor intron-containing genes reveals that the cilium assembly process is over-represented, with no less than 86 cilium-related genes containing at least one minor intron, among which there are 23 ciliopathy-related genes. The link between RNU4ATAC mutations and ciliopathy traits is supported by alterations of primary cilium function in TALS and JBTS-like patient fibroblasts, as well as by u4atac zebrafish model, which exhibits ciliopathy-related phenotypes and ciliary defects. These phenotypes could be rescued by WT but not by pathogenic variants-carrying human U4atac. Altogether, our data indicate that alteration of cilium biogenesis is part of the physiopathological mechanisms of TALS/RFMN/LWS, secondarily to defects of minor intron splicing.
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Affiliation(s)
- Deepak Khatri
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Audric Cologne
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Sophie Kaltenbach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Eloïse Bertiaux
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Justine Guguin
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Adèle Fendler
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marie A. Dupont
- Laboratory of hereditary kidney diseases, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Clara Benoit-Pilven
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Leila Qebibo
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Samira Ahmed-Elie
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Clinical Genetics Unit, Centre de Compétence Anomalies du Développement et Syndromes Polymalformatifs, Centre Hospitalier Universitaire Morvan, 29200Brest, France
| | | | | | - Martin Castelle
- Hematology-Immunology Unit, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
| | - Gaëlle Cornen
- Pediatric service, Centre Hospitalier Morlaix, 29600Morlaix, France
| | - Sarah Grotto
- Clinical Genetics Unit, Maternité Port-Royal, Assistance Publique - Hôpitaux de Paris, Cochin Broca Hôtel-Dieu Hospitals75014Paris, France
| | - Agnès Guët
- Neonatal and Pediatric Units, Louis-Mourier Hospital, 92700Colombes, France
| | - Laurent Guibaud
- Pediatric and Fetal Imaging, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Caroline Michot
- Clinical Genetics Department, Centre de Référence Maladies Rares–Maladies Osseuses Constitutionnelles, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Hospitalier Universitaire Rennes, Centre de référence Anomalies du développement et syndromes malformatifs, Univ Rennes, CNRS, INSERM, Institut de Génétique et Développement de Rennes UMR 6290/ Equipe de Recherche Labellisée 1305, 35000Rennes, France
| | - Lyse Ruaud
- NeuroDiderot, UMR1141, University of Paris, 75019Paris, France
- Departement of Genetics, Assistance Publique - Hôpitaux de Paris, Robert Debré Hospital, 75019Paris, France
| | - Elise Sacaze
- Pediatric Service, Centre Hospitalier Régional Universitaire Brest, 29200Brest, France
| | - Virginie Hamel
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Rémy Bordonné
- Institute of Molecular Genetics of Montpellier, UMR5535 CNRS, University of Montpellier, 34000Montpellier, France
| | | | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Lydie Burglen
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Tania Attié-Bitach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
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Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ, Bosch F, Braun RE, Brown SDM, Chin HJG, Dickinson ME, Hsu CW, Dobbie M, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Mammano F, Nutter LMJ, Parkinson H, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, Brooks B, McKerlie C, Lloyd KCK, Westerberg H, Moshiri A. Genome-wide screening reveals the genetic basis of mammalian embryonic eye development. BMC Biol 2023; 21:22. [PMID: 36737727 PMCID: PMC9898963 DOI: 10.1186/s12915-022-01475-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/23/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.
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Affiliation(s)
- Justine M Chee
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Dave Clary
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Kendall Higgins
- University of Miami: Miller School of Medicine, Miami, FL, USA
| | - Lynette Bower
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Ann Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Ruolin Guo
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fatima Bosch
- Centre of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Steve D M Brown
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - H-J Genie Chin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), Taipei City, Taiwan
| | - Mary E Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chih-Wei Hsu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael Dobbie
- Phenomics Australia, The John Curtin School of Medical Research, Canberra, Australia
| | - Xiang Gao
- Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Sanjeev Galande
- Indian Institutes of Science Education and Research, Pune, India
| | - Anne Grobler
- Faculty of Health Sciences, PCDDP North-West University, Potchefstroom, South Africa
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Monterotondo Scalo, Italy
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Parkinson
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Chuan Qin
- National Laboratory Animal Center, National Applied Research Laboratories, Beijing, China
| | | | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - J-K Seong
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Ying Xu
- CAM-SU Genomic Resource Center, Soochow University, Suzhou, China
| | - Brian Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Colin McKerlie
- The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, CA, USA
| | - Henrik Westerberg
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, University of California Davis, Sacramento, CA, USA.
- UC Davis Eye Center, 4860 Y St., Ste. 2400, Sacramento, CA, 95817, USA.
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27
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Kwon KY, Jeong H, Jang DG, Kwon T, Park TJ. Ckb and Ybx2 interact with Ribc2 and are necessary for the ciliary beating of multi-cilia. Genes Genomics 2023; 45:157-167. [PMID: 36508087 DOI: 10.1007/s13258-022-01350-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Motile cilia in a vertebrate are important to sustaining activities of life. Fluid flow on the apical surface of several tissues, including bronchial epithelium, ependymal epithelium, and fallopian tubules is generated by the ciliary beating of motile cilia. Multi-ciliated cells in ependymal tissue are responsible for the circulation of cerebrospinal fluid (CSF), which is essential for the development and homeostasis of the central nervous system, and airway tissues are protected from external contaminants by cilia-driven mucosal flow over the top of the airway epithelium. OBJECTIVE A previous study reported that reduction of Ribc2 protein leads to disruption of ciliary beating in multi-ciliated cells. However, knowledge regarding the molecular function of Ribc2 is limited, thus currently available information is also limited. Therefore, we evaluated the importance of proteins involved in the interaction with Ribc2 in the process of ciliary beating. METHODS Immunoprecipitation and mass spectrometry analysis was performed for the discovery of proteins involved in the interaction with Ribc2. Expression of the target gene was inhibited by injection of antisense morpholinos and measurement of the fluid flow on the embryonic epidermis of Xenopus was performed using fluorescent beads for examination of the ciliary beating of multi cilia. In addition, the flag-tagged protein was expressed by injection of mRNA and the changes in protein localization in the cilia were measured by immunostaining and western blot analysis for analysis of the molecular interaction between Ribc2 and Ribc2 binding proteins in multi-cilia. RESULTS The IP/MS analysis identified Ckb and Ybx2 as Ribc2 binding proteins and our results showed that localization of both Ckb and Ybx2 occurs at the axoneme of multi-cilia on the embryonic epithelium of Xenopus laevis. In addition, our findings confirmed that knock-down of Ckb or Ybx2 resulted in abnormal ciliary beating and reduction of cilia-driven fluid flow on multi-cilia of Xenopus laevis. In addition, significantly decreased localization of Ckb or Ybx2 in the ciliary axoneme was observed in Ribc2-depleted multi-cilia. CONCLUSION Ckb and Ybx2 are involved in the interaction with Ribc2 and are necessary for the ciliary beating of multi-cilia.
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Affiliation(s)
- Keun Yeong Kwon
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hyeongsun Jeong
- Department of Biological Medical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Dong Gil Jang
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Taejoon Kwon
- Department of Biological Medical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Tae Joo Park
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
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28
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Boschen KE, Steensen MC, Simon JM, Parnell SE. Short-term transcriptomic changes in the mouse neural tube induced by an acute alcohol exposure. Alcohol 2023; 106:1-9. [PMID: 36202274 PMCID: PMC11096843 DOI: 10.1016/j.alcohol.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 01/28/2023]
Abstract
Alcohol exposure during the formation and closure of the neural tube, or neurulation (embryonic day [E] 8-10 in mice; ∼4th week of human pregnancy), perturbs development of midline brain structures and significantly disrupts gene expression in the rostroventral neural tube (RVNT). Previously, alcohol exposure during neurulation was found to alter gene pathways related to cell proliferation, p53 signaling, ribosome biogenesis, immune signaling, organogenesis, and cell migration 6 or 24 h after administration. Our current study expands upon this work by investigating short-term gene expression changes in the RVNT following a single binge-like alcohol exposure during neurulation. Female C57BL/6J mice were administered a single dose of 2.9 g/kg alcohol or vehicle on E9.0 to target mid-neurulation. The RVNTs of stage-matched embryos were collected 2 or 4 h after exposure and processed for RNA-seq. Functional profiling was performed with g:Profiler, as well as with the CiliaCarta and DisGeNet databases. Two hours following E9.0 alcohol exposure, 650 genes in the RVNT were differentially expressed. Functional enrichment analysis revealed that pathways related to cellular metabolism, gene expression, cell cycle, organogenesis, and Hedgehog signaling were down-regulated, and pathways related to cellular stress response, p53 signaling, and hypoxia were up-regulated by alcohol. Four hours after alcohol exposure, 225 genes were differentially expressed. Biological processes related to metabolism, RNA binding, ribosome biogenesis, and methylation were down-regulated, while protein localization and binding, autophagy, and intracellular signaling pathways were up-regulated. Two hours after alcohol exposure, the differentially expressed genes were associated with disease terms related to eye and craniofacial development and anoxia. These data provide further information regarding the biological functions targeted by alcohol exposure during neurulation in regions of the neural tube that give rise to alcohol-sensitive midline brain structures. Disruption of these gene pathways contributes to the craniofacial and brain malformations associated with prenatal alcohol exposure.
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Affiliation(s)
- Karen E Boschen
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Melina C Steensen
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy M Simon
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Scott E Parnell
- Bowles Center for Alcohol Studies, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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29
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Impact of 5-HT 6 Receptor Subcellular Localization on Its Signaling and Its Pathophysiological Roles. Cells 2023; 12:cells12030426. [PMID: 36766768 PMCID: PMC9913600 DOI: 10.3390/cells12030426] [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: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
The serotonin (5-HT)6 receptor still raises particular interest given its unique spatio-temporal pattern of expression among the serotonin receptor subtypes. It is the only serotonin receptor specifically expressed in the central nervous system, where it is detected very early in embryonic life and modulates key neurodevelopmental processes, from neuronal migration to brain circuit refinement. Its predominant localization in the primary cilium of neurons and astrocytes is also unique among the serotonin receptor subtypes. Consistent with the high expression levels of the 5-HT6 receptor in brain regions involved in the control of cognitive processes, it is now well-established that the pharmacological inhibition of the receptor induces pro-cognitive effects in several paradigms of cognitive impairment in rodents, including models of neurodevelopmental psychiatric disorders and neurodegenerative diseases. The 5-HT6 receptor can engage several signaling pathways in addition to the canonical Gs signaling, but there is still uncertainty surrounding the signaling pathways that underly its modulation of cognition, as well as how the receptor's coupling is dependent on its cellular compartmentation. Here, we describe recent findings showing how the proper subcellular localization of the receptor is achieved, how this peculiar localization determines signaling pathways engaged by the receptor, and their pathophysiological influence.
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30
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Aslanyan MG, Doornbos C, Diwan GD, Anvarian Z, Beyer T, Junger K, van Beersum SEC, Russell RB, Ueffing M, Ludwig A, Boldt K, Pedersen LB, Roepman R. A targeted multi-proteomics approach generates a blueprint of the ciliary ubiquitinome. Front Cell Dev Biol 2023; 11:1113656. [PMID: 36776558 PMCID: PMC9908615 DOI: 10.3389/fcell.2023.1113656] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
Establishment and maintenance of the primary cilium as a signaling-competent organelle requires a high degree of fine tuning, which is at least in part achieved by a variety of post-translational modifications. One such modification is ubiquitination. The small and highly conserved ubiquitin protein possesses a unique versatility in regulating protein function via its ability to build mono and polyubiquitin chains onto target proteins. We aimed to take an unbiased approach to generate a comprehensive blueprint of the ciliary ubiquitinome by deploying a multi-proteomics approach using both ciliary-targeted ubiquitin affinity proteomics, as well as ubiquitin-binding domain-based proximity labelling in two different mammalian cell lines. This resulted in the identification of several key proteins involved in signaling, cytoskeletal remodeling and membrane and protein trafficking. Interestingly, using two different approaches in IMCD3 and RPE1 cells, respectively, we uncovered several novel mechanisms that regulate cilia function. In our IMCD3 proximity labeling cell line model, we found a highly enriched group of ESCRT-dependent clathrin-mediated endocytosis-related proteins, suggesting an important and novel role for this pathway in the regulation of ciliary homeostasis and function. In contrast, in RPE1 cells we found that several structural components of caveolae (CAV1, CAVIN1, and EHD2) were highly enriched in our cilia affinity proteomics screen. Consistently, the presence of caveolae at the ciliary pocket and ubiquitination of CAV1 specifically, were found likely to play a role in the regulation of ciliary length in these cells. Cilia length measurements demonstrated increased ciliary length in RPE1 cells stably expressing a ubiquitination impaired CAV1 mutant protein. Furthermore, live cell imaging in the same cells revealed decreased CAV1 protein turnover at the cilium as the possible cause for this phenotype. In conclusion, we have generated a comprehensive list of cilia-specific proteins that are subject to regulation via ubiquitination which can serve to further our understanding of cilia biology in health and disease.
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Affiliation(s)
- Mariam G. Aslanyan
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Cenna Doornbos
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Gaurav D. Diwan
- BioQuant, Heidelberg University, Heidelberg, Germany,Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Zeinab Anvarian
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tina Beyer
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Sylvia E. C. van Beersum
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Robert B. Russell
- BioQuant, Heidelberg University, Heidelberg, Germany,Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Alexander Ludwig
- School of Biological Sciences, NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Lotte B. Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Ronald Roepman,
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31
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Munch TN, Hedley PL, Hagen CM, Bækvad-Hansen M, Geller F, Bybjerg-Grauholm J, Nordentoft M, Børglum AD, Werge TM, Melbye M, Hougaard DM, Larsen LA, Christensen ST, Christiansen M. The genetic background of hydrocephalus in a population-based cohort: implication of ciliary involvement. Brain Commun 2023; 5:fcad004. [PMID: 36694575 PMCID: PMC9866251 DOI: 10.1093/braincomms/fcad004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/04/2022] [Accepted: 01/08/2023] [Indexed: 01/11/2023] Open
Abstract
Hydrocephalus is one of the most common congenital disorders of the central nervous system and often displays psychiatric co-morbidities, in particular autism spectrum disorder. The disease mechanisms behind hydrocephalus are complex and not well understood, but some association with dysfunctional cilia in the brain ventricles and subarachnoid space has been indicated. A better understanding of the genetic aetiology of hydrocephalus, including the role of ciliopathies, may bring insights into a potentially shared genetic aetiology. In this population-based case-cohort study, we, for the first time, investigated variants of postulated hydrocephalus candidate genes. Using these data, we aimed to investigate potential involvement of the ciliome in hydrocephalus and describe genotype-phenotype associations with an autism spectrum disorder. One-hundred and twenty-one hydrocephalus candidate genes were screened in a whole-exome-sequenced sub-cohort of the Lundbeck Foundation Initiative for Integrative Psychiatric Research study, comprising 72 hydrocephalus patients and 4181 background population controls. Candidate genes containing high-impact variants of interest were systematically evaluated for their involvement in ciliary function and an autism spectrum disorder. The median age at diagnosis for the hydrocephalus patients was 0 years (range 0-27 years), the median age at analysis was 22 years (11-35 years), and 70.5% were males. The median age for controls was 18 years (range 11-26 years) and 53.3% were males. Fifty-two putative hydrocephalus-associated variants in 34 genes were identified in 42 patients (58.3%). In hydrocephalus cases, we found increased, but not significant, enrichment of high-impact protein altering variants (odds ratio 1.51, 95% confidence interval 0.92-2.51, P = 0.096), which was driven by a significant enrichment of rare protein truncating variants (odds ratio 2.71, 95% confidence interval 1.17-5.58, P = 0.011). Fourteen of the genes with high-impact variants are part of the ciliome, whereas another six genes affect cilia-dependent processes during neurogenesis. Furthermore, 15 of the 34 genes with high-impact variants and three of eight genes with protein truncating variants were associated with an autism spectrum disorder. Because symptoms of other diseases may be neglected or masked by the hydrocephalus-associated symptoms, we suggest that patients with congenital hydrocephalus undergo clinical genetic assessment with respect to ciliopathies and an autism spectrum disorder. Our results point to the significance of hydrocephalus as a ciliary disease in some cases. Future studies in brain ciliopathies may not only reveal new insights into hydrocephalus but also, brain disease in the broadest sense, given the essential role of cilia in neurodevelopment.
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Affiliation(s)
- Tina N Munch
- Correspondence to: Tina Nørgaard Munch, MD Associate Professor, Department of Neurosurgery 6031 Copenhagen University Hospital, Inge Lehmanns Vej 6 DK-2100 Copenhagen Ø, Denmark E-mail:
| | - Paula L Hedley
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Brazen Bio, Los Angeles, 90502 CA, USA
| | - Christian M Hagen
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Merete Nordentoft
- Department of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Mental Health Centre, Capital Region of Denmark, 2900 Hellerup, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Center for Genomics and Personalized Medicine, Aarhus University, DK-8000 Aarhus, Denmark,Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark
| | - Thomas M Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Mental Health Centre, Capital Region of Denmark, 2900 Hellerup, Denmark
| | - Mads Melbye
- Department of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark,Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo 0473, Norway,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark
| | - Lars A Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Søren T Christensen
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, DK-8000 Aarhus, Denmark,Department of Biomedical Science, University of Copenhagen, DK-2100 Copenhagen, Denmark
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32
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Delvallée C, Dollfus H. Retinal Degeneration Animal Models in Bardet-Biedl Syndrome and Related Ciliopathies. Cold Spring Harb Perspect Med 2023; 13:13/1/a041303. [PMID: 36596648 PMCID: PMC9808547 DOI: 10.1101/cshperspect.a041303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Retinal degeneration due to photoreceptor ciliary-related proteins dysfunction accounts for more than 25% of all inherited retinal dystrophies. The cilium, being an evolutionarily conserved and ubiquitous organelle implied in many cellular functions, can be investigated by way of many models from invertebrate models to nonhuman primates, all these models have massively contributed to the pathogenesis understanding of human ciliopathies. Taking the Bardet-Biedl syndrome (BBS) as an emblematic example as well as other related syndromic ciliopathies, the contribution of a wide range of models has enabled to characterize the role of the BBS proteins in the archetypical cilium but also at the level of the connecting cilium of the photoreceptors. There are more than 24 BBS genes encoding for proteins that form different complexes such as the BBSome and the chaperone proteins complex. But how they lead to retinal degeneration remains a matter of debate with the possible accumulation of proteins in the inner segment and/or accumulation of unwanted proteins in the outer segment that cannot return in the inner segment machinery. Many BBS proteins (but not the chaperonins for instance) can be modeled in primitive organisms such as Paramecium, Chlamydomonas reinardtii, Trypanosoma brucei, and Caenorhabditis elegans These models have enabled clarifying the role of a subset of BBS proteins in the primary cilium as well as their relations with other modules such as the intraflagellar transport (IFT) module, the nephronophthisis (NPHP) module, or the Meckel-Gruber syndrome (MKS)/Joubert syndrome (JBTS) module mostly involved with the transition zone of the primary cilia. Assessing the role of the primary cilia structure of the connecting cilium of the photoreceptor cells has been very much studied by way of zebrafish modeling (Danio rerio) as well as by a plethora of mouse models. More recently, large animal models have been described for three BBS genes and one nonhuman primate model in rhesus macaque for BBS7 In completion to animal models, human cell models can now be used notably thanks to gene editing and the use of induced pluripotent stem cells (iPSCs). All these models are not only important for pathogenesis understanding but also very useful for studying therapeutic avenues, their pros and cons, especially for gene replacement therapy as well as pharmacological triggers.
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Affiliation(s)
- Clarisse Delvallée
- Laboratoire de Génétique Médicale UMRS1112, Centre de Recherche Biomédicale de Strasbourg, CRBS, Institut de Génétique Médicale d'Alsace, IGMA, Strasbourg 67000, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale UMRS1112, Centre de Recherche Biomédicale de Strasbourg, CRBS, Institut de Génétique Médicale d'Alsace, IGMA, Strasbourg 67000, France
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33
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Czerny CC, Borschel A, Cai M, Otto M, Hoyer-Fender S. FOXA1 is a transcriptional activator of Odf2/Cenexin and regulates primary ciliation. Sci Rep 2022; 12:21468. [PMID: 36509813 PMCID: PMC9744847 DOI: 10.1038/s41598-022-25966-w] [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: 06/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Primary cilia are sensory organelles essential for embryonic and postnatal development, and tissue homeostasis in adulthood. They are generated in a cell cycle-dependent manner and found on most cells of the body. Although cilia formation is intensively investigated virtually nothing is known about the transcriptional regulation of primary ciliation. We used here Odf2/Cenexin, encoding a protein of the mother centriole and the basal body that is mandatory for primary cilia formation, as the target gene for the identification of transcriptional activators. We identified a consensus binding site for Fox transcription factors (TFs) in its promoter region and focused here on the Fox family. We found transcriptional activation of Odf2 neither by FOXO TFs nor by the core TF for multiciliation, FOXJ1. However, we identified FOXA1 as a transcriptional activator of Odf2 by reporter gene assays and qRT-PCR, and showed by qWB that Foxa1 knockdown caused a decrease in ODF2 and CP110 proteins. We verified the binding sequence of FOXA1 in the Odf2 promoter by ChIP. Finally, we demonstrated that knockdown of FOXA1 affected primary cilia formation. We, thus, showed for the first time, that FOXA1 regulates primary ciliation by transcriptional activation of ciliary genes.
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Affiliation(s)
- Christian Carl Czerny
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Anett Borschel
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Mingfang Cai
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
| | - Madeline Otto
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany ,grid.424957.90000 0004 0624 9165Present Address: Thermo Fisher Scientific GENEART, Regensburg, Germany
| | - Sigrid Hoyer-Fender
- grid.7450.60000 0001 2364 4210Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology – Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität, Justus-von-Liebig-Weg 11, Göttingen, Germany
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34
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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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35
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Wang J, Thomas HR, Thompson RG, Waldrep SC, Fogerty J, Song P, Li Z, Ma Y, Santra P, Hoover JD, Yeo NC, Drummond IA, Yoder BK, Amack JD, Perkins B, Parant JM. Variable phenotypes and penetrance between and within different zebrafish ciliary transition zone mutants. Dis Model Mech 2022; 15:dmm049568. [PMID: 36533556 PMCID: PMC9844136 DOI: 10.1242/dmm.049568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022] Open
Abstract
Meckel syndrome, nephronophthisis, Joubert syndrome and Bardet-Biedl syndrome are caused by mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest that these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes, suggesting that the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants, including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1 and nphp4, as well as mutants in ift88 and ift172. Our data indicate that variations in phenotypes exist between different TZ mutants, supporting different tissue-specific functions of these TZ genes. Further, we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants, the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We also demonstrated that multiple-guide-derived CRISPR/Cas9 F0 'crispant' embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12 and cfap52).
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Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Joseph Fogerty
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Zhang Li
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Yongjie Ma
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Peu Santra
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jonathan D. Hoover
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Iain A. Drummond
- Davis Center for Aging and Regeneration, Mount Desert Island Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA
| | - Bradley K. Yoder
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Jeffrey D. Amack
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Brian Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
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36
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Ignatenko O, Malinen S, Rybas S, Vihinen H, Nikkanen J, Kononov A, Jokitalo ES, Ince-Dunn G, Suomalainen A. Mitochondrial dysfunction compromises ciliary homeostasis in astrocytes. J Biophys Biochem Cytol 2022; 222:213692. [PMID: 36383135 PMCID: PMC9674092 DOI: 10.1083/jcb.202203019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/19/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Astrocytes, often considered as secondary responders to neurodegeneration, are emerging as primary drivers of brain disease. Here we show that mitochondrial DNA depletion in astrocytes affects their primary cilium, the signaling organelle of a cell. The progressive oxidative phosphorylation deficiency in astrocytes induces FOXJ1 and RFX transcription factors, known as master regulators of motile ciliogenesis. Consequently, a robust gene expression program involving motile cilia components and multiciliated cell differentiation factors are induced. While the affected astrocytes still retain a single cilium, these organelles elongate and become remarkably distorted. The data suggest that chronic activation of the mitochondrial integrated stress response (ISRmt) in astrocytes drives anabolic metabolism and promotes ciliary elongation. Collectively, our evidence indicates that an active signaling axis involving mitochondria and primary cilia exists and that ciliary signaling is part of ISRmt in astrocytes. We propose that metabolic ciliopathy is a novel pathomechanism for mitochondria-related neurodegenerative diseases.
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Affiliation(s)
- Olesia Ignatenko
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Satu Malinen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sofiia Rybas
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Joni Nikkanen
- Cardiovascular Research Institute, University of California, San Francisco, CA
| | | | - Eija S. Jokitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Gulayse Ince-Dunn
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anu Suomalainen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,HUS Diagnostics, Helsinki University Hospital, Helsinki, Finland
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37
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Walczak-Sztulpa J, Wawrocka A, Sikora W, Pawlak M, Bukowska-Olech E, Kopaczewski B, Urzykowska A, Arts HH, Gotz-Więckowska A, Grenda R, Latos-Bieleńska A, Glazar R. WDR35 variants in a cranioectodermal dysplasia patient with early onset end-stage renal disease and retinal dystrophy. Am J Med Genet A 2022; 188:3071-3077. [PMID: 35875935 DOI: 10.1002/ajmg.a.62903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/31/2023]
Abstract
Cranioectodermal dysplasia (CED) is rare heterogeneous condition. It belongs to a group of disorders defined as ciliopathies and is associated with defective cilia function and structure. To date six genes have been associated with CED. Here we describe a 4-year-old male CED patient whose features include dolichocephaly, multi-suture craniosynostosis, epicanthus, frontal bossing, narrow thorax, limb shortening, and brachydactyly. The patient presented early-onset chronic kidney disease and was transplanted at the age of 2 years and 5 months. At the age of 3.5 years a retinal degeneration was diagnosed. Targeted sequencing by NGS revealed the presence of compound heterozygous variants in the WDR35 gene. The variants are a novel missense change in exon 9 p.(Gly303Arg) and a previously described nonsense variant in exon 18 p.(Leu641*). Our findings suggest that patients with WDR35 defects may be at risk to develop early-onset retinal degeneration. Therefore, CED patients with pathogenic variation in this gene should be assessed at least once by the ophthalmologist before the age of 4 years to detect early signs of retinal degeneration.
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Affiliation(s)
| | - Anna Wawrocka
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Weronika Sikora
- Students' Scientific Society of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Pawlak
- Department of Ophthalmology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Bartłomiej Kopaczewski
- Department of Neurosurgery, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Poznan, Poland
| | - Agnieszka Urzykowska
- Department of Nephrology, Kidney Transplantation and Hypertension, The Children's Memorial Health Institute, Warsaw, Poland
| | - Heleen H Arts
- Department of Pathology and Laboratory Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.,IWK Health Centre, Clinical Genomics Laboratory, Halifax, Nova Scotia, Canada
| | - Anna Gotz-Więckowska
- Department of Ophthalmology, Poznan University of Medical Sciences, Poznan, Poland
| | - Ryszard Grenda
- Department of Nephrology, Kidney Transplantation and Hypertension, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Renata Glazar
- Centers for Medical Genetics GENESIS, Poznan, Poland
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38
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Cho JH, Li ZA, Zhu L, Muegge BD, Roseman HF, Lee EY, Utterback T, Woodhams LG, Bayly PV, Hughes JW. Islet primary cilia motility controls insulin secretion. SCIENCE ADVANCES 2022; 8:eabq8486. [PMID: 36149960 PMCID: PMC9506710 DOI: 10.1126/sciadv.abq8486] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 06/16/2023]
Abstract
Primary cilia are specialized cell-surface organelles that mediate sensory perception and, in contrast to motile cilia and flagella, are thought to lack motility function. Here, we show that primary cilia in human and mouse pancreatic islets exhibit movement that is required for glucose-dependent insulin secretion. Islet primary cilia contain motor proteins conserved from those found in classic motile cilia, and their three-dimensional motion is dynein-driven and dependent on adenosine 5'-triphosphate and glucose metabolism. Inhibition of cilia motion blocks beta cell calcium influx and insulin secretion. Human beta cells have enriched ciliary gene expression, and motile cilia genes are altered in type 2 diabetes. Our findings redefine primary cilia as dynamic structures having both sensory and motile function and establish that pancreatic islet cilia movement plays a regulatory role in insulin secretion.
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Affiliation(s)
- Jung Hoon Cho
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO, USA
| | - Zipeng A. Li
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO, USA
| | - Lifei Zhu
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO, USA
| | - Brian D. Muegge
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO, USA
- Department of Medicine, VA Medical Center, 915 North Grand Blvd, St. Louis, MO, USA
| | - Henry F. Roseman
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO, USA
| | - Eun Young Lee
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO, USA
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Toby Utterback
- Department of Mechanical Engineering and Materials Science, Washington University McKelvey School of Engineering, 1 Brookings Drive, St. Louis, MO, USA
| | - Louis G. Woodhams
- Department of Mechanical Engineering and Materials Science, Washington University McKelvey School of Engineering, 1 Brookings Drive, St. Louis, MO, USA
| | - Philip V. Bayly
- Department of Mechanical Engineering and Materials Science, Washington University McKelvey School of Engineering, 1 Brookings Drive, St. Louis, MO, USA
| | - Jing W. Hughes
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO, USA
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39
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The interaction between LC8 and LCA5 reveals a novel oligomerization function of LC8 in the ciliary-centrosome system. Sci Rep 2022; 12:15623. [PMID: 36114230 PMCID: PMC9481538 DOI: 10.1038/s41598-022-19454-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Dynein light chain LC8 is a small dimeric hub protein that recognizes its partners through short linear motifs and is commonly assumed to drive their dimerization. It has more than 100 known binding partners involved in a wide range of cellular processes. Recent large-scale interaction studies suggested that LC8 could also play a role in the ciliary/centrosome system. However, the cellular function of LC8 in this system remains elusive. In this work, we characterized the interaction of LC8 with the centrosomal protein lebercilin (LCA5), which is associated with a specific form of ciliopathy. We showed that LCA5 binds LC8 through two linear motifs. In contrast to the commonly accepted model, LCA5 forms dimers through extensive coiled coil formation in a LC8-independent manner. However, LC8 enhances the oligomerization ability of LCA5 that requires a finely balanced interplay of coiled coil segments and both binding motifs. Based on our results, we propose that LC8 acts as an oligomerization engine that is responsible for the higher order oligomer formation of LCA5. As LCA5 shares several common features with other centrosomal proteins, the presented LC8 driven oligomerization could be widespread among centrosomal proteins, highlighting an important novel cellular function of LC8.
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40
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Wing PAC, Prange-Barczynska M, Cross A, Crotta S, Orbegozo Rubio C, Cheng X, Harris JM, Zhuang X, Johnson RL, Ryan KA, Hall Y, Carroll MW, Issa F, Balfe P, Wack A, Bishop T, Salguero FJ, McKeating JA. Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model. PLoS Pathog 2022; 18:e1010807. [PMID: 36067210 PMCID: PMC9481176 DOI: 10.1371/journal.ppat.1010807] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/16/2022] [Accepted: 08/10/2022] [Indexed: 12/03/2022] Open
Abstract
Understanding the host pathways that define susceptibility to Severe-acute-respiratory-syndrome-coronavirus-2 (SARS-CoV-2) infection and disease are essential for the design of new therapies. Oxygen levels in the microenvironment define the transcriptional landscape, however the influence of hypoxia on virus replication and disease in animal models is not well understood. In this study, we identify a role for the hypoxic inducible factor (HIF) signalling axis to inhibit SARS-CoV-2 infection, epithelial damage and respiratory symptoms in the Syrian hamster model. Pharmacological activation of HIF with the prolyl-hydroxylase inhibitor FG-4592 significantly reduced infectious virus in the upper and lower respiratory tract. Nasal and lung epithelia showed a reduction in SARS-CoV-2 RNA and nucleocapsid expression in treated animals. Transcriptomic and pathological analysis showed reduced epithelial damage and increased expression of ciliated cells. Our study provides new insights on the intrinsic antiviral properties of the HIF signalling pathway in SARS-CoV-2 replication that may be applicable to other respiratory pathogens and identifies new therapeutic opportunities.
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Affiliation(s)
- Peter A. C. Wing
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Maria Prange-Barczynska
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Amy Cross
- Radcliffe Department of Surgery, University of Oxford, United Kingdom
| | - Stefania Crotta
- Immunoregulation Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Xiaotong Cheng
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - James M. Harris
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Rachel L. Johnson
- United Kingdom Health Security Agency (UKHSA), Porton Down, Salisbury, United Kingdom
| | - Kathryn A. Ryan
- United Kingdom Health Security Agency (UKHSA), Porton Down, Salisbury, United Kingdom
| | - Yper Hall
- United Kingdom Health Security Agency (UKHSA), Porton Down, Salisbury, United Kingdom
| | - Miles W. Carroll
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Fadi Issa
- Radcliffe Department of Surgery, University of Oxford, United Kingdom
| | - Peter Balfe
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tammie Bishop
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Francisco J. Salguero
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- United Kingdom Health Security Agency (UKHSA), Porton Down, Salisbury, United Kingdom
| | - Jane A. McKeating
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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41
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Regulated processing and secretion of a peptide precursor in cilia. Proc Natl Acad Sci U S A 2022; 119:e2206098119. [PMID: 35878031 PMCID: PMC9351486 DOI: 10.1073/pnas.2206098119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cilia are sensory and secretory organelles that both receive information from the environment and transmit signals. Cilia-derived vesicles (ectosomes), formed by outward budding of the ciliary membrane, carry enzymes and other bioactive products; this process represents an ancient mode of regulated secretion. Peptidergic intercellular communication controls a wide range of physiological and behavioral responses and occurs throughout eukaryotes. The Chlamydomonas reinhardtii genome encodes what appear to be numerous prepropeptides and enzymes homologous to those used to convert metazoan prepropeptides into bioactive peptide products. Since C. reinhardtii, a green alga, lack the dense core vesicles in which metazoan peptides are processed and stored, we explored the hypothesis that propeptide processing and secretion occur through the regulated release of ciliary ectosomes. A synthetic peptide (GATI-amide) that could be generated from a 91-kDa peptide precursor (proGATI) serves as a chemotactic modulator, attracting minus gametes while repelling plus gametes. Here we dissect the processing pathway that leads to formation of an amidated peptidergic sexual signal specifically on the ciliary ectosomes of plus gametes. Unlike metazoan propeptides, modeling studies identified stable domains in proGATI. Mass spectrometric analysis of a potential prohormone convertase and the amidated proGATI-derived products found in cilia and mating ectosomes link endoproteolytic cleavage to ectosome entry. Extensive posttranslational modification of proGATI confers stability to its amidated product. Analysis of this pathway affords insight into the evolution of peptidergic signaling; this will facilitate studies of the secretory functions of metazoan cilia.
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Best S, Lord J, Roche M, Watson CM, Poulter JA, Bevers RPJ, Stuckey A, Szymanska K, Ellingford JM, Carmichael J, Brittain H, Toomes C, Inglehearn C, Johnson CA, Wheway G. Molecular diagnoses in the congenital malformations caused by ciliopathies cohort of the 100,000 Genomes Project. J Med Genet 2022; 59:737-747. [PMID: 34716235 PMCID: PMC9340050 DOI: 10.1136/jmedgenet-2021-108065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/27/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Primary ciliopathies represent a group of inherited disorders due to defects in the primary cilium, the 'cell's antenna'. The 100,000 Genomes Project was launched in 2012 by Genomics England (GEL), recruiting National Health Service (NHS) patients with eligible rare diseases and cancer. Sequence data were linked to Human Phenotype Ontology (HPO) terms entered by recruiting clinicians. METHODS Eighty-three prescreened probands were recruited to the 100,000 Genomes Project suspected to have congenital malformations caused by ciliopathies in the following disease categories: Bardet-Biedl syndrome (n=45), Joubert syndrome (n=14) and 'Rare Multisystem Ciliopathy Disorders' (n=24). We implemented a bespoke variant filtering and analysis strategy to improve molecular diagnostic rates for these participants. RESULTS We determined a research molecular diagnosis for n=43/83 (51.8%) probands. This is 19.3% higher than previously reported by GEL (n=27/83 (32.5%)). A high proportion of diagnoses are due to variants in non-ciliopathy disease genes (n=19/43, 44.2%) which may reflect difficulties in clinical recognition of ciliopathies. n=11/83 probands (13.3%) had at least one causative variant outside the tiers 1 and 2 variant prioritisation categories (GEL's automated triaging procedure), which would not be reviewed in standard 100,000 Genomes Project diagnostic strategies. These include four structural variants and three predicted to cause non-canonical splicing defects. Two unrelated participants have biallelic likely pathogenic variants in LRRC45, a putative novel ciliopathy disease gene. CONCLUSION These data illustrate the power of linking large-scale genome sequence to phenotype information. They demonstrate the value of research collaborations in order to maximise interpretation of genomic data.
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Affiliation(s)
- Sunayna Best
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
- Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Jenny Lord
- Department of Human Development and Health, University of Southampton Faculty of Medicine, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Christopher M Watson
- Department of Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, West Yorkshire, UK
- School of Medicine, University of Leeds, Leeds, UK
| | - James A Poulter
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Roel P J Bevers
- Genomics England, Queen Mary University of London, London, UK
| | - Alex Stuckey
- Genomics England, Queen Mary University of London, London, UK
| | - Katarzyna Szymanska
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester, UK
| | - Jenny Carmichael
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Helen Brittain
- Genomics England, Queen Mary University of London, London, UK
| | - Carmel Toomes
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Chris Inglehearn
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Colin A Johnson
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Gabrielle Wheway
- Department of Human Development and Health, University of Southampton Faculty of Medicine, Southampton, UK
- Southampton University Hospitals NHS Trust, Southampton, UK
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Tiryaki F, Deretic J, Firat-Karalar EN. ENKD1 is a centrosomal and ciliary microtubule-associated protein important for primary cilium content regulation. FEBS J 2022; 289:3789-3812. [PMID: 35072334 DOI: 10.1111/febs.16367] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/08/2021] [Accepted: 01/20/2022] [Indexed: 12/19/2022]
Abstract
Centrioles and cilia are conserved, microtubule-based structures critical for cell function and development. Their dysfunction causes cancer and developmental disorders. How microtubules are organized into ordered structures by microtubule-associated proteins (MAPs) and tubulin modifications is best understood during mitosis but is largely unexplored for the centrioles and the ciliary axoneme, which are composed of stable microtubules that maintain their length at a steady-state. In particular, we know little about the identity of the centriolar and ciliary MAPs and how they work together during the assembly and maintenance of the cilium and centriole. Here, we identified the Enkurin domain containing 1 (ENKD1) as a component of the centriole wall and the axoneme in mammalian cells and showed that it has extensive proximity interactions with these compartments and MAPs. Using in vitro and cellular assays, we found that ENKD1 is a new MAP that regulates microtubule organization and stability. Consistently, we observed an increase in tubulin polymerization and microtubule stability, as well as disrupted microtubule organization in ENKD1 overexpression. Cells depleted for ENKD1 were defective in ciliary length and content regulation and failed to respond to Hedgehog pathway activation. Together, our results advance our understanding of the functional and regulatory relationship between MAPs and the primary cilium.
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Affiliation(s)
- Fatmanur Tiryaki
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Jovana Deretic
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - 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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44
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Tereshko L, Turrigiano GG, Sengupta P. Primary cilia in the postnatal brain: Subcellular compartments for organizing neuromodulatory signaling. Curr Opin Neurobiol 2022; 74:102533. [PMID: 35405626 PMCID: PMC9167775 DOI: 10.1016/j.conb.2022.102533] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/22/2022] [Accepted: 03/06/2022] [Indexed: 11/03/2022]
Abstract
Primary cilia have well characterized roles in early brain development, relaying signals critical for neurogenesis and brain formation during embryonic stages. Less understood are the contributions of cilia-mediated signaling to postnatal brain function. Several cilia-localized receptors that bind neuropeptides and neurotransmitters endogenous to the brain have been identified in adult neurons, but the functional significance of signaling through these cilia-localized receptors is largely unexplored. Ciliopathic disorders in humans often manifest with neurodevelopmental abnormalities and cognitive deficits. Intriguingly, recent research has also linked several neuropsychiatric disorders and neurodegenerative diseases to ciliary dysfunction. This review summarizes recent evidence suggesting that cilia signaling may dynamically regulate postnatal neuronal physiology and connectivity, and highlights possible links among cilia, neuronal circuitry, neuron survival, and neurological disorders.
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Affiliation(s)
- Lauren Tereshko
- Department of Biology, Brandeis University, Waltham, MA 02454,Current address: Biogen, Cambridge, MA 02142
| | - Gina G. Turrigiano
- Department of Biology, Brandeis University, Waltham, MA 02454,Corresponding authors: ;
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA.
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45
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Lange KI, Best S, Tsiropoulou S, Berry I, Johnson CA, Blacque OE. Interpreting ciliopathy-associated missense variants of uncertain significance (VUS) in Caenorhabditis elegans. Hum Mol Genet 2022; 31:1574-1587. [PMID: 34964473 PMCID: PMC9122650 DOI: 10.1093/hmg/ddab344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Better methods are required to interpret the pathogenicity of disease-associated variants of uncertain significance (VUS), which cannot be actioned clinically. In this study, we explore the use of an animal model (Caenorhabditis elegans) for in vivo interpretation of missense VUS alleles of TMEM67, a cilia gene associated with ciliopathies. CRISPR/Cas9 gene editing was used to generate homozygous knock-in C. elegans worm strains carrying TMEM67 patient variants engineered into the orthologous gene (mks-3). Quantitative phenotypic assays of sensory cilia structure and function (neuronal dye filling, roaming and chemotaxis assays) measured how the variants impacted mks-3 gene function. Effects of the variants on mks-3 function were further investigated by looking at MKS-3::GFP localization and cilia ultrastructure. The quantitative assays in C. elegans accurately distinguished between known benign (Asp359Glu, Thr360Ala) and known pathogenic (Glu361Ter, Gln376Pro) variants. Analysis of eight missense VUS generated evidence that three are benign (Cys173Arg, Thr176Ile and Gly979Arg) and five are pathogenic (Cys170Tyr, His782Arg, Gly786Glu, His790Arg and Ser961Tyr). Results from worms were validated by a genetic complementation assay in a human TMEM67 knock-out hTERT-RPE1 cell line that tests a TMEM67 signalling function. We conclude that efficient genome editing and quantitative functional assays in C. elegans make it a tractable in vivo animal model for rapid, cost-effective interpretation of ciliopathy-associated missense VUS alleles.
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Affiliation(s)
- Karen I Lange
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sunayna Best
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, West Yorkshire, UK
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ian Berry
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol BS10 5NB, UK
| | - Colin A Johnson
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, West Yorkshire, UK
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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Lalioti V, González-Sanz S, Lois-Bermejo I, González-Jiménez P, Viedma-Poyatos Á, Merino A, Pajares MA, Pérez-Sala D. Cell surface detection of vimentin, ACE2 and SARS-CoV-2 Spike proteins reveals selective colocalization at primary cilia. Sci Rep 2022; 12:7063. [PMID: 35487944 PMCID: PMC9052736 DOI: 10.1038/s41598-022-11248-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/04/2022] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 Spike protein mediates docking of the virus onto cells prior to viral invasion. Several cellular receptors facilitate SARS-CoV-2 Spike docking at the cell surface, of which ACE2 plays a key role in many cell types. The intermediate filament protein vimentin has been reported to be present at the surface of certain cells and act as a co-receptor for several viruses; furthermore, its potential involvement in interactions with Spike proteins has been proposed. Nevertheless, the potential colocalization of vimentin with Spike and its receptors on the cell surface has not been explored. Here we have assessed the binding of Spike protein constructs to several cell types. Incubation of cells with tagged Spike S or Spike S1 subunit led to discrete dotted patterns at the cell surface, which consistently colocalized with endogenous ACE2, but sparsely with a lipid raft marker. Vimentin immunoreactivity mostly appeared as spots or patches unevenly distributed at the surface of diverse cell types. Of note, vimentin could also be detected in extracellular particles and in the cytoplasm underlying areas of compromised plasma membrane. Interestingly, although overall colocalization of vimentin-positive spots with ACE2 or Spike was moderate, a selective enrichment of the three proteins was detected at elongated structures, positive for acetylated tubulin and ARL13B. These structures, consistent with primary cilia, concentrated Spike binding at the top of the cells. Our results suggest that a vimentin-Spike interaction could occur at selective locations of the cell surface, including ciliated structures, which can act as platforms for SARS-CoV-2 docking.
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Affiliation(s)
- Vasiliki Lalioti
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Silvia González-Sanz
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Irene Lois-Bermejo
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Patricia González-Jiménez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Álvaro Viedma-Poyatos
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Andrea Merino
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - María A Pajares
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain.
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47
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Ahn S, Yang H, Son S, Lee HS, Park D, Yim H, Choi HJ, Swoboda P, Lee J. The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Rep 2022; 39:110661. [PMID: 35417689 DOI: 10.1016/j.celrep.2022.110661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Cilia are important for the interaction with environments and the proper function of tissues. While the basic structure of cilia is well conserved, ciliated cells have various functions. To understand the distinctive identities of ciliated cells, the identification of cell-specific proteins and its regulation is essential. Here, we report the mechanism that confers a specific identity on IL2 neurons in Caenorhabditis elegans, neurons important for the dauer larva-specific nictation behavior. We show that DAF-19M, an isoform of the sole C. elegans RFX transcription factor DAF-19, heads a regulatory subroutine, regulating target genes through an X-box motif variant under the control of terminal selector proteins UNC-86 and CFI-1 in IL2 neurons. Considering the conservation of DAF-19M module in IL2 neurons for nictation and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature "recognizing the environment."
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Affiliation(s)
- Soungyub Ahn
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Sangwon Son
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyun Sik Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dongjun Park
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
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48
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Sakato-Antoku M, King SM. Developmental Changes in Ciliary Composition during Gametogenesis in Chlamydomonas. Mol Biol Cell 2022; 33:br10. [PMID: 35389765 PMCID: PMC9561859 DOI: 10.1091/mbc.e22-02-0033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chlamydomonas reinhardtii transitions from mitotically dividing vegetative cells to sexually competent gametes of two distinct mating types following nutrient deprivation. Gametes of opposite mating type interact via their cilia, initiating an intraciliary signaling cascade and ultimately fuse forming diploid zygotes. The process of gametogenesis is genetically encode, and a previous study revealed numerous significant changes in mRNA abundance during this life-cycle transition. Here we describe a proteomic analysis of cilia derived from vegetative and gametic cells of both mating types in an effort to assess the global changes that occur within the organelle during this process. We identify numerous membrane- and/or matrix-associated proteins in gametic cilia that were not detected in cilia from vegetative cells. This includes the pro-protein from which the GATI-amide gametic chemotactic modulator derives, as well as receptors, a dynamin-related protein, ammonium transporters, two proteins potentially involved in the intraciliary signaling cascade-driven increase in cAMP, and multiple proteins with a variety of interaction domains. These changes in ciliary composition likely directly affect the functional properties of this organelle as the cell transitions between life-cycle stages.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
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49
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Djenoune L, Berg K, Brueckner M, Yuan S. A change of heart: new roles for cilia in cardiac development and disease. Nat Rev Cardiol 2022; 19:211-227. [PMID: 34862511 PMCID: PMC10161238 DOI: 10.1038/s41569-021-00635-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/27/2022]
Abstract
Although cardiac abnormalities have been observed in a growing class of human disorders caused by defective primary cilia, the function of cilia in the heart remains an underexplored area. The primary function of cilia in the heart was long thought to be restricted to left-right axis patterning during embryogenesis. However, new findings have revealed broad roles for cilia in congenital heart disease, valvulogenesis, myocardial fibrosis and regeneration, and mechanosensation. In this Review, we describe advances in our understanding of the mechanisms by which cilia function contributes to cardiac left-right axis development and discuss the latest findings that highlight a broader role for cilia in cardiac development. Specifically, we examine the growing line of evidence connecting cilia function to the pathogenesis of congenital heart disease. Furthermore, we also highlight research from the past 10 years demonstrating the role of cilia function in common cardiac valve disorders, including mitral valve prolapse and aortic valve disease, and describe findings that implicate cardiac cilia in mechanosensation potentially linking haemodynamic and contractile forces with genetic regulation of cardiac development and function. Finally, given the presence of cilia on cardiac fibroblasts, we also explore the potential role of cilia in fibrotic growth and summarize the evidence implicating cardiac cilia in heart regeneration.
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Affiliation(s)
- Lydia Djenoune
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kathryn Berg
- Department of Paediatrics, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Martina Brueckner
- Department of Paediatrics, Yale University School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Shiaulou Yuan
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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50
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ALKBH3-dependent m1A demethylation of Aurora A mRNA inhibits ciliogenesis. Cell Discov 2022; 8:25. [PMID: 35277482 PMCID: PMC8917145 DOI: 10.1038/s41421-022-00385-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
Primary cilia are antenna-like subcellular structures to act as signaling platforms to regulate many cellular processes and embryonic development. m1A RNA modification plays key roles in RNA metabolism and gene expression; however, the physiological function of m1A modification remains largely unknown. Here we find that the m1A demethylase ALKBH3 significantly inhibits ciliogenesis in mammalian cells by its demethylation activity. Mechanistically, ALKBH3 removes m1A sites on mRNA of Aurora A, a master suppressor of ciliogenesis. Depletion of ALKBH3 enhances Aurora A mRNA decay and inhibits its translation. Moreover, alkbh3 morphants exhibit ciliary defects, including curved body, pericardial edema, abnormal otoliths, and dilation in pronephric ducts in zebrafish embryos, which are significantly rescued by wild-type alkbh3, but not by its catalytically inactive mutant. The ciliary defects caused by ALKBH3 depletion in both vertebrate cells and embryos are also significantly reversed by ectopic expression of Aurora A mRNA. Together, our data indicate that ALKBH3-dependent m1A demethylation has a crucial role in the regulation of Aurora A mRNA, which is essential for ciliogenesis and cilia-associated developmental events in vertebrates.
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