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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024:e0000624. [PMID: 38995044 DOI: 10.1128/mmbr.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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2
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Auman HJ, Fernandes IH, Berríos-Otero CA, Colombo S, Yelon D. Zebrafish smarcc1a mutants reveal requirements for BAF chromatin remodeling complexes in distinguishing the atrioventricular canal from the cardiac chambers. Dev Dyn 2024; 253:157-172. [PMID: 37083132 PMCID: PMC10589389 DOI: 10.1002/dvdy.595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/13/2023] [Accepted: 04/08/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Essential patterning processes transform the heart tube into a compartmentalized organ with distinct chambers separated by an atrioventricular canal (AVC). This transition involves the refinement of expression of genes that are first found broadly throughout the heart tube and then become restricted to the AVC. Despite the importance of cardiac patterning, we do not fully understand the mechanisms that limit gene expression to the AVC. RESULTS We show that the zebrafish gene smarcc1a, encoding a BAF chromatin remodeling complex subunit homologous to mammalian BAF155, is critical for cardiac patterning. In smarcc1a mutants, myocardial differentiation and heart tube assembly appear to proceed normally. Subsequently, the smarcc1a mutant heart fails to exhibit refinement of gene expression patterns to the AVC, and the persistence of broad gene expression is accompanied by failure of chamber expansion. In addition to their cardiac defects, smarcc1a mutants lack pectoral fins, indicating similarity to tbx5a mutants. However, comparison of smarcc1a and tbx5a mutants suggests that perturbation of tbx5a function is not sufficient to cause the smarcc1a mutant phenotype. CONCLUSIONS Our data indicate an important role for Smarcc1a-containing chromatin remodeling complexes in regulating the changes in gene expression and morphology that distinguish the AVC from the cardiac chambers.
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Affiliation(s)
- Heidi J. Auman
- Skirball Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Ivy H. Fernandes
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Sophie Colombo
- Skirball Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Deborah Yelon
- Skirball Institute, New York University School of Medicine, New York, NY, 10016, USA
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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3
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Kretschmer V, Schneider S, Matthiessen PA, Reichert D, Hotaling N, Glasßer G, Lieberwirth I, Bharti K, De Cegli R, Conte I, Nandrot EF, May-Simera HL. Deletion of IFT20 exclusively in the RPE ablates primary cilia and leads to retinal degeneration. PLoS Biol 2023; 21:e3002402. [PMID: 38048369 PMCID: PMC10721183 DOI: 10.1371/journal.pbio.3002402] [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: 12/06/2022] [Revised: 12/14/2023] [Accepted: 10/26/2023] [Indexed: 12/06/2023] Open
Abstract
Vision impairment places a serious burden on the aging society, affecting the lives of millions of people. Many retinal diseases are of genetic origin, of which over 50% are due to mutations in cilia-associated genes. Most research on retinal degeneration has focused on the ciliated photoreceptor cells of the retina. However, the contribution of primary cilia in other ocular cell types has largely been ignored. The retinal pigment epithelium (RPE) is a monolayer epithelium at the back of the eye intricately associated with photoreceptors and essential for visual function. It is already known that primary cilia in the RPE are critical for its development and maturation; however, it remains unclear whether this affects RPE function and retinal tissue homeostasis. We generated a conditional knockout mouse model, in which IFT20 is exclusively deleted in the RPE, ablating primary cilia. This leads to defective RPE function, followed by photoreceptor degeneration and, ultimately, vision impairment. Transcriptomic analysis offers insights into mechanisms underlying pathogenic changes, which include transcripts related to epithelial homeostasis, the visual cycle, and phagocytosis. Due to the loss of cilia exclusively in the RPE, this mouse model enables us to tease out the functional role of RPE cilia and their contribution to retinal degeneration, providing a powerful tool for basic and translational research in syndromic and non-syndromic retinal degeneration. Non-ciliary mechanisms of IFT20 in the RPE may also contribute to pathogenesis and cannot be excluded, especially considering the increasing evidence of non-ciliary functions of ciliary proteins.
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Affiliation(s)
- Viola Kretschmer
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Sandra Schneider
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Peter Andreas Matthiessen
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Dominik Reichert
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nathan Hotaling
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gunnar Glasßer
- Max Planck Institute for Polymer Research, Mainz, Germany
| | | | - Kapil Bharti
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rossella De Cegli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- University of Naples “Federico II”, Naples, Italy
| | | | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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4
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Walton NA, Nguyen HH, Procknow SS, Johnson D, Anzelmi A, Jay PY. Repurposing Normal Chromosomal Microarray Data to Harbor Genetic Insights into Congenital Heart Disease. BIOLOGY 2023; 12:1290. [PMID: 37887000 PMCID: PMC10604103 DOI: 10.3390/biology12101290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/28/2023]
Abstract
About 15% of congenital heart disease (CHD) patients have a known pathogenic copy number variant. The majority of their chromosomal microarray (CMA) tests are deemed normal. Diagnostic interpretation typically ignores microdeletions smaller than 100 kb. We hypothesized that unreported microdeletions are enriched for CHD genes. We analyzed "normal" CMAs of 1762 patients who were evaluated at a pediatric referral center, of which 319 (18%) had CHD. Using CMAs from monozygotic twins or replicates from the same individual, we established a size threshold based on probe count for the reproducible detection of small microdeletions. Genes in the microdeletions were sequentially filtered by their nominal association with a CHD diagnosis, the expression level in the fetal heart, and the deleteriousness of a loss-of-function mutation. The subsequent enrichment for CHD genes was assessed using the presence of known or potentially novel genes implicated by a large whole-exome sequencing study of CHD. The unreported microdeletions were modestly enriched for both known CHD genes and those of unknown significance identified using their de novo mutation in CHD patients. Our results show that readily available "normal" CMA data can be a fruitful resource for genetic discovery and that smaller deletions should receive more attention in clinical evaluation.
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Affiliation(s)
- Nephi A. Walton
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hoang H. Nguyen
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Sara S. Procknow
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Darren Johnson
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA
| | - Alexander Anzelmi
- Department of Medicine, Thomas Jefferson University Hospitals, Philadelphia, PA 19107, USA
| | - Patrick Y. Jay
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
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5
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Yan J, Ding Y, Peng Z, Qin L, Gu J, Wan C. Systematic Proteomics Study on the Embryonic Development of Danio rerio. J Proteome Res 2023; 22:2814-2826. [PMID: 37500539 DOI: 10.1021/acs.jproteome.3c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The early development of zebrafish (Danio rerio) is a complex and dynamic physiological process involving cell division, differentiation, and movement. Currently, the genome and transcriptome techniques have been widely used to study the embryonic development of zebrafish. However, the research of proteomics based on proteins that directly execute functions is relatively vacant. In this work, we apply label-free quantitative proteomics to explore protein profiling during zebrafish's embryogenesis, and a total of 5961 proteins were identified at 10 stages of zebrafish's early development. The identified proteins were divided into 11 modules according to weighted gene coexpression network analysis (WGCNA), and the characteristics between modules were significantly different. For example, mitochondria-related functions enriched the early development of zebrafish. Primordial germ cell-related proteins were identified at the 4-cell stage, while the eye development event is dominated at 5 days post fertilization (dpf). By combining with published transcriptomics data, we discovered some proteins that may be involved in activating zygotic genes. Meanwhile, 137 novel proteins were identified. This study comprehensively analyzed the dynamic processes in the embryonic development of zebrafish from the perspective of proteomics. It provided solid data support for further understanding of the molecular mechanism of its development.
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Affiliation(s)
- Jiahao Yan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Yuhe Ding
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Zhao Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Lu Qin
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Jingyu Gu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
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6
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Brücker L, Becker SK, Maissl V, Harms G, Parsons M, May-Simera HL. The actin-bundling protein Fascin-1 modulates ciliary signalling. J Mol Cell Biol 2023; 15:mjad022. [PMID: 37015875 PMCID: PMC10485897 DOI: 10.1093/jmcb/mjad022] [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: 02/17/2022] [Revised: 12/22/2022] [Accepted: 01/25/2023] [Indexed: 04/06/2023] Open
Abstract
Primary cilia are microtubule-based cell organelles important for cellular communication. Since they are involved in the regulation of numerous signalling pathways, defects in cilia development or function are associated with genetic disorders, collectively called ciliopathies. Besides their ciliary functions, recent research has shown that several ciliary proteins are involved in the coordination of the actin cytoskeleton. Although ciliary and actin phenotypes are related, the exact nature of their interconnection remains incompletely understood. Here, we show that the protein BBS6, associated with the ciliopathy Bardet-Biedl syndrome, cooperates with the actin-bundling protein Fascin-1 in regulating filopodia and ciliary signalling. We found that loss of Bbs6 affects filopodia length potentially via attenuated interaction with Fascin-1. Conversely, loss of Fascin-1 leads to a ciliary phenotype, subsequently affecting ciliary Wnt signalling, possibly in collaboration with BBS6. Our data shed light on how ciliary proteins are involved in actin regulations and provide new insight into the involvement of the actin regulator Fascin-1 in ciliogenesis and cilia-associated signalling. Advancing our knowledge of the complex regulations between primary cilia and actin dynamics is important to understand the pathogenic consequences of ciliopathies.
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Affiliation(s)
- Lena Brücker
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Stefanie Kornelia Becker
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Vanessa Maissl
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Gregory Harms
- Imaging Core Facility, Cell Biology Unit, University Medical Centre, Johannes Gutenberg University Mainz, 55101 Mainz, Germany
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Helen Louise May-Simera
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
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7
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Ewerling A, Maissl V, Wickstead B, May-Simera HL. Neofunctionalization of ciliary BBS proteins to nuclear roles is likely a frequent innovation across eukaryotes. iScience 2023; 26:106410. [PMID: 37034981 PMCID: PMC10074162 DOI: 10.1016/j.isci.2023.106410] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/20/2022] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The eukaryotic BBSome is a transport complex within cilia and assembled by chaperonin-like BBS proteins. Recent work indicates nuclear functions for BBS proteins in mammals, but it is unclear how common these are in extant proteins or when they evolved. We screened for BBS orthologues across a diverse set of eukaryotes, consolidated nuclear association via signal sequence predictions and permutation analysis, and validated nuclear localization in mammalian cells via fractionation and immunocytochemistry. BBS proteins are-with exceptions-conserved as a set in ciliated species. Predictions highlight five most likely nuclear proteins and suggest that nuclear roles evolved independently of nuclear access during mitosis. Nuclear localization was confirmed in human cells. These findings suggest that nuclear BBS functions are potentially not restricted to mammals, but may be a common frequently co-opted eukaryotic feature. Understanding the functional spectrum of BBS proteins will help elucidating their role in gene regulation, development, and disease.
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Affiliation(s)
- Alexander Ewerling
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Vanessa Maissl
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Helen Louise May-Simera
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
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8
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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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9
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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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10
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Gupta N, D'Acierno M, Zona E, Capasso G, Zacchia M. Bardet-Biedl syndrome: The pleiotropic role of the chaperonin-like BBS6, 10, and 12 proteins. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:9-19. [PMID: 35373910 PMCID: PMC9325507 DOI: 10.1002/ajmg.c.31970] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/08/2022] [Accepted: 03/27/2022] [Indexed: 12/11/2022]
Abstract
Bardet–Biedl syndrome (BBS) is a rare pleiotropic disorder known as a ciliopathy. Despite significant genetic heterogeneity, BBS1 and BBS10 are responsible for major diagnosis in western countries. It is well established that eight BBS proteins, namely BBS1, 2, 4, 5, 7, 8, 9, and 18, form the BBSome, a multiprotein complex serving as a regulator of ciliary membrane protein composition. Less information is available for BBS6, BBS10, and BBS12, three proteins showing sequence homology with the CCT/TRiC family of group II chaperonins. Even though their chaperonin function is debated, scientific evidence demonstrated that they are required for initial BBSome assembly in vitro. Recent studies suggest that genotype may partially predict clinical outcomes. Indeed, patients carrying truncating mutations in any gene show the most severe phenotype; moreover, mutations in chaperonin‐like BBS proteins correlated with severe kidney impairment. This study is a critical review of the literature on genetics, expression level, cellular localization and function of BBS proteins, focusing primarily on the chaperonin‐like BBS proteins, and aiming to provide some clues to understand the pathomechanisms of disease in this setting.
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Affiliation(s)
- Neha Gupta
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy.,BioGem S.C.A.R.L., Benevento, Benevento Province, Italy
| | - Mariavittoria D'Acierno
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy.,BioGem S.C.A.R.L., Benevento, Benevento Province, Italy
| | - Enrica Zona
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy
| | | | - Miriam Zacchia
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania L. Vanvitelli, Naples, Italy
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11
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Abstract
The BBSome is an octameric protein complex involved in Bardet-Biedl syndrome (BBS), a human pleiotropic, autosomal recessive condition. Patients with BBS display various clinical features including obesity, hypertension, and renal abnormalities. Association studies have also linked the BBS genes to hypertension and other cardiovascular risks in the general population. The BBSome was originally associated with the function of cilia, a highly specialized organelle that extend from the cell membrane of most vertebrate cells. However, subsequent studies have implicated the BBSome in the control of a myriad of other cellular processes not related to cilia including cell membrane localization of receptors and gene expression. The development of animal models of BBS such as mouse lines lacking various components of the BBSome and associated proteins has facilitated studying their role in the control of cardiovascular function and deciphering the pathophysiological mechanisms responsible for the cardiovascular aberrations associated with BBS. These studies revealed the importance of the neuronal, renal, vascular, and cardiac BBSome in the regulation of blood pressure, renal function, vascular reactivity, and cardiac development. The BBSome has also emerged as a critical regulator of key systems involved in cardiovascular control including the renin-angiotensin system. Better understanding of the influence of the BBSome on the molecular and physiological processes relevant to cardiovascular health and disease has the potential of identifying novel mechanisms underlying hypertension and other cardiovascular risks.
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Affiliation(s)
- Yuying Zhao
- Department of Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA, USA,Human Toxicology Graduate Program, University of Iowa Graduate College, Iowa City, IA, USA
| | - Kamal Rahmouni
- Department of Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA, USA,Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA,Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, IA, USA,Obesity Research and Educational Initiative, University of Iowa Carver College of Medicine, Iowa City, IA, USA,Iowa City VA Health Care System, Iowa City, IA, USA,Corresponding author: Kamal Rahmouni, Ph.D., Department of Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA, , Tel: 319 353 5256, Fax: 319 353 5350
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12
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Vasquez SSV, van Dam J, Wheway G. An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. Mol Biol Cell 2021; 32:br13. [PMID: 34613793 PMCID: PMC8694072 DOI: 10.1091/mbc.e21-05-0226] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cilia are microtubule-based organelles with important functions in motility and sensation. They contribute to a broad spectrum of developmental disorders called ciliopathies and have recently been linked to common conditions such as cancers and congenital heart disease. There has been increasing interest in the biology of cilia and their contribution to disease over the past two decades. In 2013 we published a "Gold Standard" list of genes confirmed to be associated with cilia. This was published as part of the SYSCILIA consortium for systems biology study dissecting the contribution of cilia to human health and disease, and was named the Syscilia Gold Standard (SCGS). Since this publication, interest in cilia and understanding of their functions have continued to grow, and we now present an updated SCGS version 2. This includes an additional 383 genes, more than doubling the size of SCGSv1. We use this dataset to conduct a review of advances in understanding of cilia biology 2013- 2021 and offer perspectives on the future of cilia research. We hope that this continues to be a useful resource for the cilia community.
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Affiliation(s)
| | - John van Dam
- Theoretical Biology and Bioinformatics, Department of Biology, Science Faculty, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom
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13
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Eintracht J, Forsythe E, May-Simera H, Moosajee M. Translational readthrough of ciliopathy genes BBS2 and ALMS1 restores protein, ciliogenesis and function in patient fibroblasts. EBioMedicine 2021; 70:103515. [PMID: 34365092 PMCID: PMC8353411 DOI: 10.1016/j.ebiom.2021.103515] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Ciliary dysfunction underlies a range of genetic disorders collectively termed ciliopathies, for which there are no treatments available. Bardet-Biedl syndrome (BBS) is characterised by multisystemic involvement, including rod-cone dystrophy and renal abnormalities. Together with Alström syndrome (AS), they are known as the 'obesity ciliopathies' due to their common phenotype. Nonsense mutations are responsible for approximately 11% and 40% of BBS and AS cases, respectively. Translational readthrough inducing drugs (TRIDs) can restore full-length protein bypassing in-frame premature termination codons, and are a potential therapeutic approach for nonsense-mediated ciliopathies. METHODS Patient fibroblasts harbouring nonsense mutations from two different ciliopathies (Bardet-Biedl Syndrome and Alström Syndrome) were treated with PTC124 (ataluren) or amlexanox. Following treatment, gene expression, protein levels and ciliogenesis were evaluated. The expression of intraflagellar transport protein IFT88 and G-protein coupled receptor SSTR3 was investigated as a readout of ciliary function. FINDINGS mRNA expression was significantly increased in amlexanox-treated patient fibroblasts, and full-length BBS2 or ALMS1 protein expression was restored in PTC124- and amlexanox-treated fibroblasts. Treatment with TRIDs significantly improved ciliogenesis defects in BBS2Y24*/R275* fibroblasts. Treatment recovered IFT88 expression and corrected SSTR3 mislocalisation in BBS2Y24*/R275* and ALMS1S1645*/S1645* fibroblasts, suggesting rescue of ciliary function. INTERPRETATION The recovery of full-length BBS2 and ALMS1 expression and correction of anatomical and functional ciliary defects in BBS2Y24*/R275* and ALMS1S1645*/S1645* fibroblasts suggest TRIDs are a potential therapeutic option for the treatment of nonsense-mediated ciliopathies. FUNDING Wellcome Trust 205174/Z/16/Z, National Centre for the Replacement, Refinement & Reduction of Animals in Research. Deutsche Forschungsgemeinschaft SPP2127 (DFG Grant MA 6139/3-1).
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Affiliation(s)
| | - Elizabeth Forsythe
- Clinical Genetics Unit, Great Ormond Street Hospital; Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health
| | - Helen May-Simera
- Institute of Molecular Physiology, Johannes Gutenburg University, Mainz
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, United Kingdom; The Francis Crick Institute, London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom; Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
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14
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Lu B, Wang X, Fu J, Shi J, Wu Y, Qi Y. Genetic Adaptations of an Island Pit-Viper to a Unique Sedentary Life with Extreme Seasonal Food Availability. G3 (BETHESDA, MD.) 2020; 10:1639-1646. [PMID: 32184370 PMCID: PMC7202027 DOI: 10.1534/g3.120.401101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/02/2020] [Indexed: 12/05/2022]
Abstract
The Shedao pit-viper (Gloydius shedaoensis) exhibits an extreme sedentary lifestyle. The island species exclusively feeds on migratory birds during migratory seasons and experiences prolonged hibernation and aestivation period each year (up to eight months). The sedentary strategy reduces energy expenditure, but may trigger a series of adverse effects and the snakes have likely evolved genetic modifications to alleviate these effects. To investigate the genetic adaptations, we sequenced and compared the transcriptomes of the Shedao pit-viper and its closest mainland relative, the black eyebrow pit-viper (G. intermedius). The Shedao pit-viper revealed a low rate of molecular evolution compared to its mainland relative, which is possibly associated with metabolic suppression. Signals of positive selection were detected in two genes related to antithrombin (SERPINC1) and muscle atrophy (AARS). Those genes exert significant functions in thrombosis, inhibiting oxidation and prolonged fasting. Convergent and parallel substitutions of amino acid with two other sedentary vertebrates, which often suggest adaptation, were found in a fatty acid beta-oxidation related gene (ACATA1) and a circadian link gene (KLF10), which regulate lipogenesis, gluconeogenesis, and glycolysis. Furthermore, a circadian clock gene (CRY2) exhibited two amino acid substitutions specific to the Shedao pit-viper and one variant was predicted to affect protein function. Modifications of these genes and their related functions may have contributed to the survival of this island snake species with a sedentary lifestyle and extreme seasonal food availability. Our study demonstrated several important clues for future research on physiological and other phenotypic adaptation.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiaoping Wang
- Nature Conservation of Snake Island and Laotieshan Mountain, Dalian 116041, China
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jingsong Shi
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Science, Beijing 100044, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yayong Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- College of life sciences and food engineering, Yibin University, Yibin 644007, China
| | - Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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15
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Ciliary Genes in Renal Cystic Diseases. Cells 2020; 9:cells9040907. [PMID: 32276433 PMCID: PMC7226761 DOI: 10.3390/cells9040907] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/27/2020] [Accepted: 04/05/2020] [Indexed: 12/28/2022] Open
Abstract
Cilia are microtubule-based organelles, protruding from the apical cell surface and anchoring to the cytoskeleton. Primary (nonmotile) cilia of the kidney act as mechanosensors of nephron cells, responding to fluid movements by triggering signal transduction. The impaired functioning of primary cilia leads to formation of cysts which in turn contribute to development of diverse renal diseases, including kidney ciliopathies and renal cancer. Here, we review current knowledge on the role of ciliary genes in kidney ciliopathies and renal cell carcinoma (RCC). Special focus is given on the impact of mutations and altered expression of ciliary genes (e.g., encoding polycystins, nephrocystins, Bardet-Biedl syndrome (BBS) proteins, ALS1, Oral-facial-digital syndrome 1 (OFD1) and others) in polycystic kidney disease and nephronophthisis, as well as rare genetic disorders, including syndromes of Joubert, Meckel-Gruber, Bardet-Biedl, Senior-Loken, Alström, Orofaciodigital syndrome type I and cranioectodermal dysplasia. We also show that RCC and classic kidney ciliopathies share commonly disturbed genes affecting cilia function, including VHL (von Hippel-Lindau tumor suppressor), PKD1 (polycystin 1, transient receptor potential channel interacting) and PKD2 (polycystin 2, transient receptor potential cation channel). Finally, we discuss the significance of ciliary genes as diagnostic and prognostic markers, as well as therapeutic targets in ciliopathies and cancer.
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16
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Abstract
The BBSome, a complex of 8 BBS (Bardet-Biedl syndrome) proteins known for its role in the control of cilia function and other cellular processes, has been implicated in blood pressure control, but the underlying mechanisms are not fully understood. Here, we show that neuronal BBSome plays an important role in blood pressure regulation. Targeted inactivation of the BBSome in the nervous system through Bbs1 gene deletion causes sympathetically mediated increase in blood pressure in mice. This phenotype is reproduced by selective ablation of the Bbs1 gene from the LRb (leptin receptor)-expressing neurons. Strikingly, the well-known role of the BBSome in the regulation of cilia formation and function is unlikely to account for the prohypertensive effect of BBSome inactivation as disruption of the IFT (intraflagellar transport) machinery required for ciliogenesis by deleting the Ift88 gene in LRb neurons had no effect on arterial pressure and sympathetic nerve activity. Furthermore, we found that Bbs1 gene deletion from AgRP (agouti-related protein) neurons or POMC (proopiomelanocortin) neurons increased renal and splanchnic sympathetic nerve activity without altering blood pressure. This lack of blood pressure increase despite the sympathetic overdrive may be explained by vascular adrenergic desensitization as indicated by the reduced vascular contractile response evoked by phenylephrine and the decreased expression of adrenergic receptors. Our results identify the neuronal BBSome as a new player in hemodynamic, sympathetic, and vascular regulation, in a manner independent of cilia.
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Affiliation(s)
- Deng-Fu Guo
- From the Department of Neuroscience and Pharmacology (D.-F.G., J.J.R., D.A.M., K.R.), University of Iowa Carver College of Medicine, Iowa City
| | - John J Reho
- From the Department of Neuroscience and Pharmacology (D.-F.G., J.J.R., D.A.M., K.R.), University of Iowa Carver College of Medicine, Iowa City
| | - Donald A Morgan
- From the Department of Neuroscience and Pharmacology (D.-F.G., J.J.R., D.A.M., K.R.), University of Iowa Carver College of Medicine, Iowa City
| | - Kamal Rahmouni
- From the Department of Neuroscience and Pharmacology (D.-F.G., J.J.R., D.A.M., K.R.), University of Iowa Carver College of Medicine, Iowa City.,Department of Internal Medicine (K.R.), University of Iowa Carver College of Medicine, Iowa City.,Obesity Research and Education Initiative (K.R.), University of Iowa Carver College of Medicine, Iowa City.,Fraternal Order of Eagles Diabetes Research Center (K.R.), University of Iowa Carver College of Medicine, Iowa City.,Iowa Neuroscience Institute (K.R.), University of Iowa Carver College of Medicine, Iowa City.,Veterans Affairs Health Care System, Iowa City (K.R.)
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17
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Patnaik SR, Farag A, Brücker L, Volz AK, Schneider S, Kretschmer V, May-Simera HL. Tissue-dependent differences in Bardet-Biedl syndrome gene expression. Biol Cell 2020; 112:39-52. [PMID: 31845361 DOI: 10.1111/boc.201900077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/20/2019] [Accepted: 11/28/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND INFORMATION Primary cilia are highly conserved multifunctional cell organelles that extend from the cell membrane. A range of genetic disorders, collectively termed ciliopathies, is attributed to primary cilia dysfunction. The archetypical ciliopathy is the Bardet-Biedl syndrome (BBS), patients of which display virtually all symptoms associated with dysfunctional cilia. The primary cilium acts as a sensory organelle transmitting intra- and extracellular signals thereby transducing various signalling pathways facilitated by the BBS proteins. Growing evidence suggests that cilia proteins also have alternative functions in ciliary independent mechanisms, which might be contributing to disease etiology. RESULTS In an attempt to gain more insight into possible differences in organ specific roles, we examined whether relative gene expression for individual Bbs genes was constant across different tissues in mouse, in order to distinguish possible differences in organ specific roles. All tested tissues show differentially expressed Bbs transcripts with some tissues showing a more similar stoichiometric composition of transcripts than others do. However, loss of Bbs6 or Bbs8 affects expression of other Bbs transcripts in a tissue-dependent way. CONCLUSIONS AND SIGNIFICANCE Our data support the hypothesis that in some organs, BBS proteins not only function in a complex but might also have alternative functions in a ciliary independent context. This significantly alters our understanding of disease pathogenesis and development of possible treatment strategies.
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Affiliation(s)
- Sarita Rani Patnaik
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, 55128, Germany
| | - Aalaa Farag
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, 55128, Germany
| | - Lena Brücker
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, 55128, Germany
| | - Ann-Kathrin Volz
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, 55128, Germany
| | - Sandra Schneider
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, 55128, Germany
| | - Viola Kretschmer
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, 55128, Germany
| | - Helen Louise May-Simera
- Cilia Cell Biology, Institute of Molecular Physiology, Johannes-Gutenberg University, Mainz, 55128, Germany
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18
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Liu CF, Tang WW. Epigenetics in Cardiac Hypertrophy and Heart Failure. JACC Basic Transl Sci 2019; 4:976-993. [PMID: 31909304 PMCID: PMC6938823 DOI: 10.1016/j.jacbts.2019.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
Abstract
Heart failure (HF) is a complex syndrome affecting millions of people around the world. Over the past decade, the therapeutic potential of targeting epigenetic regulators in HF has been discussed extensively. Recent advances in next-generation sequencing techniques have contributed substantial progress in our understanding of the role of DNA methylation, post-translational modifications of histones, adenosine triphosphate (ATP)-dependent chromatin conformation and remodeling, and non-coding RNAs in HF pathophysiology. In this review, we summarize epigenomic studies on human and animal models in HF.
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Key Words
- BET, bromodomain
- EZH2, Enhancer of zeste homolog 2
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- HDM, histone demethylase
- HF, heart failure
- HMT, histone methyltransferase
- PRC2, polycomb repressor complex 2
- PTMs, post-translational modifications
- TAD, topologically associating domains
- TMAO, trimethylamine N-oxide
- cardiac hypertrophy
- epigenetics
- heart failure
- lnc-RNAs, long ncRNAs
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Affiliation(s)
- Chia-Feng Liu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - W.H. Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic, Cleveland, Ohio
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19
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Functional analysis of new human Bardet-Biedl syndrome loci specific variants in the zebrafish model. Sci Rep 2019; 9:12936. [PMID: 31506453 PMCID: PMC6736949 DOI: 10.1038/s41598-019-49217-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 08/16/2019] [Indexed: 11/09/2022] Open
Abstract
The multiple genetic approaches available for molecular diagnosis of human diseases have made possible to identify an increasing number of pathogenic genetic changes, particularly with the advent of next generation sequencing (NGS) technologies. However, the main challenge lies in the interpretation of their functional impact, which has resulted in the widespread use of animal models. We describe here the functional modelling of seven BBS loci variants, most of them novel, in zebrafish embryos to validate their in silico prediction of pathogenicity. We show that target knockdown (KD) of known BBS (BBS1, BB5 or BBS6) loci leads to developmental defects commonly associated with ciliopathies, as previously described. These KD pleiotropic phenotypes were rescued by co-injecting human wild type (WT) loci sequence but not with the equivalent mutated mRNAs, providing evidence of the pathogenic effect of these BBS changes. Furthermore, direct assessment of cilia located in Kupffer's vesicle (KV) showed a reduction of ciliary length associated with all the studied variants, thus confirming a deleterious effect. Taken together, our results seem to prove the pathogenicity of the already classified and unclassified new BBS variants, as well as highlight the usefulness of zebrafish as an animal model for in vivo assays in human ciliopathies.
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20
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Guo DF, Rahmouni K. The Bardet-Biedl syndrome protein complex regulates cell migration and tissue repair through a Cullin-3/RhoA pathway. Am J Physiol Cell Physiol 2019; 317:C457-C465. [PMID: 31216194 DOI: 10.1152/ajpcell.00498.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cell motility and migration play critical roles in various physiological processes and disease states. Here, we show that the BBBsome, a macromolecule composed of eight Bardet-Biedl syndrome (BBS) proteins including BBS1, is a critical determinant of cell migration and wound healing. Fibroblast cells derived from mice or humans harboring a homozygous missense mutation (BBS1M390R/M390R) that disrupt the BBSome exhibit defects in migration and wound healing. Furthermore, we demonstrate that BBS1M390R/M390R mice have significantly delayed wound closure. In line with this, we provide data suggesting that BBS1M390R/M390R fibroblasts have impaired platelet-derived growth factor-AA (PDGF) receptor-α signaling, a key regulator of directional cell migration acting as a chemoattractant during postnatal migration responses such as wound healing. In addition, we show that BBS1M390R/M390R fibroblasts have upregulated RhoA expression and activity. The relevance of RhoA upregulation is demonstrated by the ability of RhoA-kinase inhibitor Y27632 to partially rescue the migration defect of BBS1M390R/M390R fibroblasts cells. We also show that accumulation of RhoA protein in BBS1M390R/M390R fibroblasts cells is associated with reduction and inactivation of the ubiquitin ligase Cullin-3. Consistent with this, Cullin-3 inhibition with MLN4924 is sufficient to reduce migration of normal fibroblasts. These data implicate the BBSome in cell motility and tissue repair through a mechanism that involves PDGF receptor signaling and Cullin-3-mediated control of RhoA.
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Affiliation(s)
- Deng-Fu Guo
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Kamal Rahmouni
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa.,Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa.,Obesity Education and Research Initiative, University of Iowa Carver College of Medicine, Iowa City, Iowa.,Fraternal Order of Eagles Diabetes Research, University of Iowa Carver College of Medicine, Iowa City, Iowa.,Veterans Affairs Health Care System, Iowa City, Iowa
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21
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Kinesin 1 regulates cilia length through an interaction with the Bardet-Biedl syndrome related protein CCDC28B. Sci Rep 2018; 8:3019. [PMID: 29445114 PMCID: PMC5813027 DOI: 10.1038/s41598-018-21329-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/02/2018] [Indexed: 01/12/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinal degeneration, obesity, polydactyly, renal disease and mental retardation. CCDC28B is a BBS-associated protein that we have previously shown plays a role in cilia length regulation whereby its depletion results in shortened cilia both in cells and Danio rerio (zebrafish). At least part of that role is achieved by its interaction with the mTORC2 component SIN1, but the mechanistic details of this interaction and/or additional functions that CCDC28B might play in the context of cilia remain poorly understood. Here we uncover a novel interaction between CCDC28B and the kinesin 1 molecular motor that is relevant to cilia. CCDC28B interacts with kinesin light chain 1 (KLC1) and the heavy chain KIF5B. Notably, depletion of these kinesin 1 components results in abnormally elongated cilia. Furthermore, through genetic interaction studies we demonstrate that kinesin 1 regulates ciliogenesis through CCDC28B. We show that kinesin 1 regulates the subcellular distribution of CCDC28B, unexpectedly, inhibiting its nuclear accumulation, and a ccdc28b mutant missing a nuclear localization motif fails to rescue the phenotype in zebrafish morphant embryos. Therefore, we uncover a previously unknown role of kinesin 1 in cilia length regulation that relies on the BBS related protein CCDC28B.
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