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Nagata N, Kurosaka H, Higashi K, Yamaguchi M, Yamamoto S, Inubushi T, Nagata M, Ishihara Y, Yonei A, Miyashita Y, Asano Y, Sakai N, Sakata Y, Kawabata S, Yamashiro T. Characteristic craniofacial defects associated with a novel USP9X truncation mutation. Hum Genome Var 2024; 11:21. [PMID: 38755172 PMCID: PMC11099082 DOI: 10.1038/s41439-024-00277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Germline loss-of-function mutations in USP9X have been reported to cause a wide spectrum of congenital anomalies. Here, we report a Japanese girl with a novel heterozygous nonsense mutation in USP9X who exhibited intellectual disability with characteristic craniofacial abnormalities, including hypotelorism, brachycephaly, hypodontia, micrognathia, severe dental crowding, and an isolated submucous cleft palate. Our findings provide further evidence that disruptions in USP9X contribute to a broad range of congenital craniofacial abnormalities.
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Affiliation(s)
- Namiki Nagata
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Hiroshi Kurosaka
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan.
| | - Kotaro Higashi
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
- Department of Removable Prosthodontics and Gerodontology, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Masaya Yamaguchi
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
- Bioinformatics Research Unit, Osaka University Graduate School of Dentistry, Suita, Japan
- Bioinformatics Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Suita, Japan
| | - Sayuri Yamamoto
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ayumi Yonei
- Department of Genetic Counseling, Osaka University Hospital, Osaka, Japan
| | - Yohei Miyashita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Norio Sakai
- Child Healthcare and Genetic Science Laboratory, Division of Health Sciences, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shigetada Kawabata
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Suita, Japan
| | - Takashi Yamashiro
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
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2
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Cideciyan AV, Jacobson SG, Ho AC, Swider M, Sumaroka A, Roman AJ, Wu V, Russell RC, Viarbitskaya I, Garafalo AV, Schwartz MR, Girach A. Durable vision improvement after a single intravitreal treatment with antisense oligonucleotide in CEP290-LCA: Replication in two eyes. Am J Ophthalmol Case Rep 2023; 32:101873. [PMID: 37388818 PMCID: PMC10302566 DOI: 10.1016/j.ajoc.2023.101873] [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] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 06/11/2023] [Indexed: 07/01/2023] Open
Abstract
Purpose An intravitreally injected antisense oligonucleotide, sepofarsen, was designed to modulate splicing within retinas of patients with severe vision loss due to deep intronic c.2991 + 1655A > G variant in the CEP290 gene. A previous report showed vision improvements following a single injection in one eye with unexpected durability lasting at least 15 months. The current study evaluated durability of efficacy beyond 15 months in the previously treated left eye. In addition, peak efficacy and durability were evaluated in the treatment-naive right eye, and re-injection of the left eye 4 years after the first injection. Observations Visual function was evaluated with best corrected standard and low-luminance visual acuities, microperimetry, dark-adapted chromatic perimetry, and full-field sensitivity testing. Retinal structure was evaluated with OCT imaging. At the fovea, all visual function measures and IS/OS intensity of the OCT showed transient improvements peaking at 3-6 months, remaining better than baseline at ∼2 years, and returning to baseline by 3-4 years after each single injection. Conclusions and Importance These results suggest that sepofarsen reinjection intervals may need to be longer than 2 years.
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Affiliation(s)
- Artur V. Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel G. Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen C. Ho
- Wills Eye Hospital, Thomas Jefferson University, Philadelphia, USA
| | - Malgorzata Swider
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander Sumaroka
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro J. Roman
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivian Wu
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert C. Russell
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iryna Viarbitskaya
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandra V. Garafalo
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Shi X, Wu W, Feng Z, Fan P, Shi R, Zhang X. MARCH7-mediated ubiquitination decreases the solubility of ATG14 to inhibit autophagy. Cell Rep 2023; 42:113045. [PMID: 37632749 DOI: 10.1016/j.celrep.2023.113045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023] Open
Abstract
Autophagy is a fundamental biological process critical to all eukaryotic cellular life. Although autophagy has been increasingly studied, how its process is precisely coordinated remains an open question. ATG14 (ATG14L/Barkor) is known to play a crucial role in both autophagosome formation and autophagosome-lysosome fusion. However, how ATG14 is regulated, especially at the post-translation level, is still not clear. Here, we report that MARCH7 (membrane-associated ring-CH-type finger 7), an E3 ubiquitin ligase, inhibits autophagy by ubiquitinating ATG14. MARCH7 significantly promotes K6-, K11-, and K63-linked mixed polyubiquitination on ATG14, triggering the aggregation of ATG14 and reducing its solubility in cells. Functionally, we find that MARCH7 depletion decreases the number of aggresome-like induced structures (ALISs). Mechanistically, we show that ubiquitinated ATG14 has fewer interactions with STX17, leading to the inhibition of autophagy flux. Collectively, our study reveals a mechanism in regulating autophagy and suggests a potential strategy for the treatment of autophagy-related diseases.
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Affiliation(s)
- Xue Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfeng Wu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China
| | - Zhenhuan Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyang Fan
- SanQuan College, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China.
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4
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Saito M, Otsu W, Miyadera K, Nishimura Y. Recent advances in the understanding of cilia mechanisms and their applications as therapeutic targets. Front Mol Biosci 2023; 10:1232188. [PMID: 37780208 PMCID: PMC10538646 DOI: 10.3389/fmolb.2023.1232188] [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: 05/31/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
The primary cilium is a single immotile microtubule-based organelle that protrudes into the extracellular space. Malformations and dysfunctions of the cilia have been associated with various forms of syndromic and non-syndromic diseases, termed ciliopathies. The primary cilium is therefore gaining attention due to its potential as a therapeutic target. In this review, we examine ciliary receptors, ciliogenesis, and ciliary trafficking as possible therapeutic targets. We first discuss the mechanisms of selective distribution, signal transduction, and physiological roles of ciliary receptors. Next, pathways that regulate ciliogenesis, specifically the Aurora A kinase, mammalian target of rapamycin, and ubiquitin-proteasome pathways are examined as therapeutic targets to regulate ciliogenesis. Then, in the photoreceptors, the mechanism of ciliary trafficking which takes place at the transition zone involving the ciliary membrane proteins is reviewed. Finally, some of the current therapeutic advancements highlighting the role of large animal models of photoreceptor ciliopathy are discussed.
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Affiliation(s)
- Masaki Saito
- Department of Molecular Physiology and Pathology, School of Pharma-Sciences, Teikyo University, Tokyo, Japan
| | - Wataru Otsu
- Department of Biomedical Research Laboratory, Gifu Pharmaceutical University, Gifu, Japan
| | - Keiko Miyadera
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
- Mie University Research Center for Cilia and Diseases, Tsu, Mie, Japan
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5
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Tsai M, Rayner RE, Chafin L, Farkas D, Adair J, Mishan C, Mallampalli RK, Kim SH, Cormet-Boyaka E, Londino JD. Influenza virus reduces ubiquitin E3 ligase MARCH10 expression to decrease ciliary beat frequency. Am J Physiol Lung Cell Mol Physiol 2023; 324:L666-L676. [PMID: 36852930 PMCID: PMC10151042 DOI: 10.1152/ajplung.00191.2022] [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: 06/20/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
Respiratory viruses, such as influenza, decrease airway cilia function and expression, which leads to reduced mucociliary clearance and inhibited overall immune defense. Ubiquitination is a posttranslational modification using E3 ligases, which plays a role in the assembly and disassembly of cilia. We examined the role of membrane-associated RING-CH (MARCH) family of E3 ligases during influenza infection and determined that MARCH10, specifically expressed in ciliated epithelial cells, is significantly decreased during influenza infection in mice, human lung epithelial cells, and human lung tissue. Cellular depletion of MARCH10 in differentiated human bronchial epithelial cells (HBECs) using CRISPR/Cas9 showed a decrease in ciliary beat frequency. Furthermore, MARCH10 cellular knockdown in combination with influenza infection selectively decreased immunoreactive levels of the ciliary component, dynein axonemal intermediate chain 1. Cellular overexpression of MARCH10 significantly decreased influenza hemagglutinin protein levels in the differentiated HBECs and knockdown of MARCH10 increased IL-1β cytokine expression, whereas overexpression had the reciprocal effect. These findings suggest that MARCH10 may have a protective role in airway pulmonary host defense and innate immunity during influenza infection.
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Affiliation(s)
- MuChun Tsai
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Rachael E Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States
| | - Lexie Chafin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Daniela Farkas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Jessica Adair
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Chelsea Mishan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Rama K Mallampalli
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States
| | - Sun Hee Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States
| | - James D Londino
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States
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6
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Chiuso F, Delle Donne R, Giamundo G, Rinaldi L, Borzacchiello D, Moraca F, Intartaglia D, Iannucci R, Senatore E, Lignitto L, Garbi C, Conflitti P, Catalanotti B, Conte I, Feliciello A. Ubiquitylation of BBSome is required for ciliary assembly and signaling. EMBO Rep 2023; 24:e55571. [PMID: 36744302 PMCID: PMC10074118 DOI: 10.15252/embr.202255571] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/27/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinal degeneration, obesity, renal abnormalities, postaxial polydactyly, and developmental defects. Genes mutated in BBS encode for components and regulators of the BBSome, an octameric complex that controls the trafficking of cargos and receptors within the primary cilium. Although both structure and function of the BBSome have been extensively studied, the impact of ubiquitin signaling on BBSome is largely unknown. We identify the E3 ubiquitin ligase PJA2 as a novel resident of the ciliary compartment and regulator of the BBSome. Upon GPCR-cAMP stimulation, PJA2 ubiquitylates BBSome subunits. We demonstrate that ubiquitylation of BBS1 at lysine 143 increases the stability of the BBSome and promotes its binding to BBS3, an Arf-like GTPase protein controlling the targeting of the BBSome to the ciliary membrane. Downregulation of PJA2 or expression of a ubiquitylation-defective BBS1 mutant (BBS1K143R ) affects the trafficking of G-protein-coupled receptors (GPCRs) and Shh-dependent gene transcription. Expression of BBS1K143R in vivo impairs cilium formation, embryonic development, and photoreceptors' morphogenesis, thus recapitulating the BBS phenotype in the medaka fish model.
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Affiliation(s)
- Francesco Chiuso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Rossella Delle Donne
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Giuliana Giamundo
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Biology, University of Naples Federico II, Naples, Italy
| | - Laura Rinaldi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Domenica Borzacchiello
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Federica Moraca
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy.,Net4Science srl, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | | | - Rosa Iannucci
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Emanuela Senatore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Luca Lignitto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy.,Cancer Research Center of Marseille (CRCM), CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Corrado Garbi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Paolo Conflitti
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Bruno Catalanotti
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Biology, University of Naples Federico II, Naples, Italy
| | - Antonio Feliciello
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
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7
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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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8
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Strong A, Behr M, Lott C, Clark AJ, Mentch F, Da Silva RP, Rux DR, Campbell R, Skraban C, Wang X, Anari JB, Sinder B, Cahill PJ, Sleiman P, Hakonarson H. Molecular diagnosis and novel genes and phenotypes in a pediatric thoracic insufficiency cohort. Sci Rep 2023; 13:991. [PMID: 36653407 PMCID: PMC9849333 DOI: 10.1038/s41598-023-27641-0] [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: 05/26/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Thoracic insufficiency syndromes are a genetically and phenotypically heterogeneous group of disorders characterized by congenital abnormalities or progressive deformation of the chest wall and/or vertebrae that result in restrictive lung disease and compromised respiratory capacity. We performed whole exome sequencing on a cohort of 42 children with thoracic insufficiency to elucidate the underlying molecular etiologies of syndromic and non-syndromic thoracic insufficiency and predict extra-skeletal manifestations and disease progression. Molecular diagnosis was established in 24/42 probands (57%), with 18/24 (75%) probands having definitive diagnoses as defined by laboratory and clinical criteria and 6/24 (25%) probands having strong candidate genes. Gene identified in cohort patients most commonly encoded components of the primary cilium, connective tissue, and extracellular matrix. A novel association between KIF7 and USP9X variants and thoracic insufficiency was identified. We report and expand the genetic and phenotypic spectrum of a cohort of children with thoracic insufficiency, reinforce the prevalence of extra-skeletal manifestations in thoracic insufficiency syndromes, and expand the phenotype of KIF7 and USP9X-related disease to include thoracic insufficiency.
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Affiliation(s)
- Alanna Strong
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Meckenzie Behr
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carina Lott
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abigail J Clark
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frank Mentch
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Renata Pellegrino Da Silva
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Danielle R Rux
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert Campbell
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Cara Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Xiang Wang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jason B Anari
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin Sinder
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patrick J Cahill
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Patrick Sleiman
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
- Endowed Chair in Genomic Research, Division of Pulmonary Medicine, The Joseph Stokes, Jr. Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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9
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Elu N, Osinalde N, Ramirez J, Presa N, Rodriguez JA, Prieto G, Mayor U. Identification of substrates for human deubiquitinating enzymes (DUBs): An up-to-date review and a case study for neurodevelopmental disorders. Semin Cell Dev Biol 2022; 132:120-131. [PMID: 35042675 DOI: 10.1016/j.semcdb.2022.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 12/15/2022]
Abstract
Similar to the reversal of kinase-mediated protein phosphorylation by phosphatases, deubiquitinating enzymes (DUBs) oppose the action of E3 ubiquitin ligases and reverse the ubiquitination of proteins. A total of 99 human DUBs, classified in 7 families, allow in this way for a precise control of cellular function and homeostasis. Ubiquitination regulates a myriad of cellular processes, and is altered in many pathological conditions. Thus, ubiquitination-regulating enzymes are increasingly regarded as potential candidates for therapeutic intervention. In this context, given the predicted easier pharmacological control of DUBs relative to E3 ligases, a significant effort is now being directed to better understand the processes and substrates regulated by each DUB. Classical studies have identified specific DUB substrate candidates by traditional molecular biology techniques in a case-by-case manner. Lately, single experiments can identify thousands of ubiquitinated proteins at a specific cellular context and narrow down which of those are regulated by a given DUB, thanks to the development of new strategies to isolate and enrich ubiquitinated material and to improvements in mass spectrometry detection capabilities. Here we present an overview of both types of studies, discussing the criteria that, in our view, need to be fulfilled for a protein to be considered as a high-confidence substrate of a given DUB. Applying these criteria, we have manually reviewed the relevant literature currently available in a systematic manner, and identified 650 high-confidence substrates of human DUBs. We make this information easily accessible to the research community through an updated version of the DUBase website (https://ehubio.ehu.eus/dubase/). Finally, in order to illustrate how this information can contribute to a better understanding of the physiopathological role of DUBs, we place a special emphasis on a subset of these enzymes that have been associated with neurodevelopmental disorders.
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Affiliation(s)
- Nagore Elu
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Natalia Presa
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), Bilbao 48013, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain; Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain.
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10
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Senatore E, Feliciello A. Proteolysis at work: when time matters for a sensory organelle. Bioessays 2022; 44:e2200137. [PMID: 35876401 DOI: 10.1002/bies.202200137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Emanuela Senatore
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Antonio Feliciello
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
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11
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Garousi S, Jahanbakhsh Godehkahriz S, Esfahani K, Lohrasebi T, Mousavi A, Hatef Salmanian A, Rezvani M, Moein M. Meta-Analysis of EGF-Stimulated Normal and Cancer Cell Lines to Discover EGF-Associated Oncogenic Signaling Pathways and Prognostic Biomarkers. IRANIAN JOURNAL OF BIOTECHNOLOGY 2022; 20:e3245. [PMID: 36381277 PMCID: PMC9618017 DOI: 10.30498/ijb.2022.323464.3245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Although epidermal growth factor (EGF) controls many crucial processes in the human body, it can increase the risk of developing cancer when overexpresses. OBJECTIVES This study focused on detecting cancer-associated genes that are dysregulated by EGF overexpression. MATERIALS AND METHODS To identify differentially expressed genes (DEGs), two independent meta-analyses with normal and cancer RNA-Seq samples treated by EGF were conducted. The new DEGs detected only via two meta-analyses were used in all downstream analyses. To reach count data, the tools of FastQC, Trimmomatic, HISAT2, SAMtools, and HTSeq-count were employed. DEGs in each individual RNA-Seq study and the meta-analysis of RNA-Seq studies were identified using DESeq2 and metaSeq R package, respectively. MCODE detected densely interconnected top clusters in the protein-protein interaction (PPI) network of DEGs obtained from normal and cancer datasets. The DEGs were then introduced to Enrichr and ClueGO/CluePedia, and terms, pathways, and hub genes enriched in Gene Ontology (GO) and KEGG and Reactome were detected. RESULTS The meta-analysis of normal and cancer datasets revealed 990 and 541 new DEGs, all upregulated. A number of DEGs were enriched in protein K48-linked deubiquitination, ncRNA processing, ribosomal large subunit binding, and protein processing in endoplasmic reticulum. Hub genes overexpression (DHX33, INTS8, NMD3, OTUD4, P4HB, RPS3A, SEC13, SKP1, USP34, USP9X, and YOD1) in tumor samples were validated by TCGA and GTEx databases. Overall survival and disease-free survival analysis also confirmed worse survival in patients with hub genes overexpression. CONCLUSIONS The detected hub genes could be used as cancer biomarkers when EGF overexpresses.
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Affiliation(s)
- Shahrokh Garousi
- Department of plant genetics and production engineering, Faculty of agriculture and natural resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Sodabeh Jahanbakhsh Godehkahriz
- Department of plant genetics and production engineering, Faculty of agriculture and natural resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Kasra Esfahani
- Plant Bioproducts Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Tahmineh Lohrasebi
- Plant Bioproducts Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Amir Mousavi
- Plant Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Ali Hatef Salmanian
- Plant Bioproducts Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mahsa Rezvani
- Institute of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Maryam Moein
- Institute of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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12
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Habeck G, Schweiggert J. Proteolytic control in ciliogenesis: Temporal restriction or early initiation? Bioessays 2022; 44:e2200087. [PMID: 35739619 DOI: 10.1002/bies.202200087] [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: 05/01/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 12/19/2022]
Abstract
Cellular processes are highly dependent on a dynamic proteome that undergoes structural and functional rearrangements to allow swift conversion between different cellular states. By inducing proteasomal degradation of inhibitory or stimulating factors, ubiquitylation is particularly well suited to trigger such transitions. One prominent example is the remodelling of the centrosome upon cell cycle exit, which is required for the formation of primary cilia - antenna-like structures on the surface of most cells that act as integrative hubs for various extracellular signals. Over the last decade, many reports on ubiquitin-related events involved in the regulation of ciliogenesis have emerged. Very often, these processes are considered to be initiated ad hoc, that is, directly before its effect on cilia biogenesis becomes evident. While such a temporal restriction may hold true for the majority of events, there is evidence that some of them are initiated earlier during the cell cycle. Here, we provide an overview of ubiquitin-dependent processes in ciliogenesis and discuss available data that indicate such an early onset of proteolytic regulation within preceding cell cycle stages.
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Affiliation(s)
- Gregor Habeck
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany
| | - Jörg Schweiggert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany
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13
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Senatore E, Iannucci R, Chiuso F, Delle Donne R, Rinaldi L, Feliciello A. Pathophysiology of Primary Cilia: Signaling and Proteostasis Regulation. Front Cell Dev Biol 2022; 10:833086. [PMID: 35646931 PMCID: PMC9130585 DOI: 10.3389/fcell.2022.833086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/21/2022] [Indexed: 01/29/2023] Open
Abstract
Primary cilia are microtubule-based, non-motile sensory organelles present in most types of growth-arrested eukaryotic cells. They are transduction hubs that receive and transmit external signals to the cells in order to control growth, differentiation and development. Mutations of genes involved in the formation, maintenance or disassembly of ciliary structures cause a wide array of developmental genetic disorders, also known as ciliopathies. The primary cilium is formed during G1 in the cell cycle and disassembles at the G2/M transition. Following the completion of the cell division, the cilium reassembles in G1. This cycle is finely regulated at multiple levels. The ubiquitin-proteasome system (UPS) and the autophagy machinery, two main protein degradative systems in cells, play a fundamental role in cilium dynamics. Evidence indicate that UPS, autophagy and signaling pathways may act in synergy to control the ciliary homeostasis. However, the mechanisms involved and the links between these regulatory systems and cilium biogenesis, dynamics and signaling are not well defined yet. Here, we discuss the reciprocal regulation of signaling pathways and proteolytic machineries in the control of the assembly and disassembly of the primary cilium, and the impact of the derangement of these regulatory networks in human ciliopathies.
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14
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Focșa IO, Budișteanu M, Burloiu C, Khan S, Sadeghpour A, Bohîlțea LC, Davis EE, Bălgrădean M. A case of Bardet-Biedl syndrome caused by a recurrent variant in BBS12: A case report. Biomed Rep 2021; 15:103. [PMID: 34760276 PMCID: PMC8567465 DOI: 10.3892/br.2021.1479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a clinically and genetically heterogenous disorder that manifests as a result of primary cilia impairment. Cilia are present on most cell types, thus BBS is a multisystemic condition involving the majority of organ systems. The core features of the syndrome include retinal degeneration, obesity, polydactyly, cognitive impairment, renal anomalies and urogenital malformations. To date, pathogenic variants in 26 genes have been shown to be involved in the molecular basis of this rare ciliopathy. Of these causal loci, BBS12 accounts for ~8% of all cases. In this case report, an individual with BBS caused by a rare recurrent variant in BBS12 (NM_152618.3: c.1063C>T; p.Arg355*) is described and compared with others with the same DNA variant, placing this finding in the context of the current literature.
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Affiliation(s)
- Ina Ofelia Focșa
- Department of Medical Genetics, University of Medicine and Pharmacy 'Carol Davila', 021901 Bucharest, Romania
| | - Magdalena Budișteanu
- Department of Pediatric Neurology, 'Prof. Dr. Alexandru Obregia' Clinical Hospital of Psychiatry, 041914 Bucharest, Romania.,Medical Genetic Laboratory, 'Victor Babeș' National Institute of Pathology, 050096 Bucharest, Romania.,Department of Medical Genetics, Titu Maiorescu University, 040441 Bucharest, Romania
| | - Carmen Burloiu
- Department of Pediatric Neurology, 'Prof. Dr. Alexandru Obregia' Clinical Hospital of Psychiatry, 041914 Bucharest, Romania
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan Institute of Engineering and Applied Sciences, Islamabad 38000, Pakistan.,Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA.,Duke Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27708, USA
| | - Laurențiu C Bohîlțea
- Department of Medical Genetics, University of Medicine and Pharmacy 'Carol Davila', 021901 Bucharest, Romania
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.,Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mihaela Bălgrădean
- Department of Pediatrics and Pediatric Nephrology, Emergency Clinical Hospital for Children 'Maria Skłodowska Curie', 077120 Bucharest, Romania.,Department of Pediatrics, University of Medicine and Pharmacy 'Carol Davila', 077120 Bucharest, Romania
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15
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Basar MA, Beck DB, Werner A. Deubiquitylases in developmental ubiquitin signaling and congenital diseases. Cell Death Differ 2021; 28:538-556. [PMID: 33335288 PMCID: PMC7862630 DOI: 10.1038/s41418-020-00697-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate's stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
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Affiliation(s)
- Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Beck
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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16
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Nishimura Y, Inagaki M. [Targeting the ubiquitin system for treatment of cilia-related diseases]. Nihon Yakurigaku Zasshi 2021; 156:4-8. [PMID: 33390480 DOI: 10.1254/fpj.20072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The ubiquitin system regulates a wide variety of cellular functions. Not surprisingly, dysregulation of the ubiquitin system is associated with various disorders. Therefore, drugs that can modulate the functions of the ubiquitin system have been actively developed to treat these disorders. Chemical knockdown of pathogenic proteins using the ubiquitin-proteasome system is also a promising approach. The ubiquitin system regulates the assemble and disassemble of primary cilia through balanced control over the ubiquitination and deubiquitination of ciliary proteins. Primary cilia are antenna-like structures present in many vertebrate cells that sense and transduce extracellular cues to control cellular processes such as proliferation and differentiation. Impairment of primary cilia is associated with many diseases, including cancer and ciliopathy, a group of multisystem developmental disorders. In this review, we focus on the role of the ubiquitin system on cilia-related disorders and discuss the possibility of the ubiquitin system as therapeutic targets for these diseases through regulation of primary cilia formation.
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Affiliation(s)
- Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine.,Glocal Center for Advanced Medical Research, Mie University
| | - Masaki Inagaki
- Glocal Center for Advanced Medical Research, Mie University.,Department of Physiology, Mie University Graduate School of Medicine
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17
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Shiromizu T, Yuge M, Kasahara K, Yamakawa D, Matsui T, Bessho Y, Inagaki M, Nishimura Y. Targeting E3 Ubiquitin Ligases and Deubiquitinases in Ciliopathy and Cancer. Int J Mol Sci 2020; 21:E5962. [PMID: 32825105 PMCID: PMC7504095 DOI: 10.3390/ijms21175962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/17/2022] Open
Abstract
Cilia are antenna-like structures present in many vertebrate cells. These organelles detect extracellular cues, transduce signals into the cell, and play an essential role in ensuring correct cell proliferation, migration, and differentiation in a spatiotemporal manner. Not surprisingly, dysregulation of cilia can cause various diseases, including cancer and ciliopathies, which are complex disorders caused by mutations in genes regulating ciliary function. The structure and function of cilia are dynamically regulated through various mechanisms, among which E3 ubiquitin ligases and deubiquitinases play crucial roles. These enzymes regulate the degradation and stabilization of ciliary proteins through the ubiquitin-proteasome system. In this review, we briefly highlight the role of cilia in ciliopathy and cancer; describe the roles of E3 ubiquitin ligases and deubiquitinases in ciliogenesis, ciliopathy, and cancer; and highlight some of the E3 ubiquitin ligases and deubiquitinases that are potential therapeutic targets for these disorders.
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Affiliation(s)
- Takashi Shiromizu
- Department of Integrative Pharmacology, Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan; (T.S.); (M.Y.)
| | - Mizuki Yuge
- Department of Integrative Pharmacology, Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan; (T.S.); (M.Y.)
| | - Kousuke Kasahara
- Department of Physiology, Graduate School of Medicine, Mie University, Tsu, Mie 514-5807, Japan; (K.K.); (D.Y.); (M.I.)
| | - Daishi Yamakawa
- Department of Physiology, Graduate School of Medicine, Mie University, Tsu, Mie 514-5807, Japan; (K.K.); (D.Y.); (M.I.)
| | - Takaaki Matsui
- Gene Regulation Research, Division of Biological Sciences, Nara Institute of Science and Technology, Takayama, Nara 630-0192, Japan; (T.M.); (Y.B.)
| | - Yasumasa Bessho
- Gene Regulation Research, Division of Biological Sciences, Nara Institute of Science and Technology, Takayama, Nara 630-0192, Japan; (T.M.); (Y.B.)
| | - Masaki Inagaki
- Department of Physiology, Graduate School of Medicine, Mie University, Tsu, Mie 514-5807, Japan; (K.K.); (D.Y.); (M.I.)
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Graduate School of Medicine, Mie University, Tsu, Mie 514-8507, Japan; (T.S.); (M.Y.)
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18
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Yu T, Matsuda M. Epb41l5 interacts with Iqcb1 and regulates ciliary function in zebrafish embryos. J Cell Sci 2020; 133:jcs240648. [PMID: 32501287 PMCID: PMC7338265 DOI: 10.1242/jcs.240648] [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: 10/21/2019] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Erythrocyte protein band 4.1 like 5 (EPB41L5) is an adaptor protein beneath the plasma membrane that functions to control epithelial morphogenesis. Here we report a previously uncharacterized role of EPB41L5 in controlling ciliary function. We found that EPB41L5 forms a complex with IQCB1 (previously known as NPHP5), a ciliopathy protein. Overexpression of EPB41L5 reduced IQCB1 localization at the ciliary base in cultured mammalian epithelial cells. Conversely, epb41l5 knockdown increased IQCB1 localization at the ciliary base. epb41l5-deficient zebrafish embryos or embryos expressing C-terminally modified forms of Epb41l5 developed cilia with reduced motility and exhibited left-right patterning defects, an outcome of abnormal ciliary function. We observed genetic synergy between epb41l5 and iqcb1. Moreover, EPB41L5 decreased IQCB1 interaction with CEP290, another ciliopathy protein and a component of the ciliary base and centrosome. Together, these observations suggest that EPB41L5 regulates the composition of the ciliary base and centrosome through IQCB1 and CEP290.
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Affiliation(s)
- Tiffany Yu
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07302, USA
| | - Miho Matsuda
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07302, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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19
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Toulis V, Marfany G. By the Tips of Your Cilia: Ciliogenesis in the Retina and the Ubiquitin-Proteasome System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:303-310. [PMID: 32274763 DOI: 10.1007/978-3-030-38266-7_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Primary cilia are microtubule-based sensory organelles that are involved in the organization of numerous key signals during development and in differentiated tissue homeostasis. In fact, the formation and resorption of cilia highly depends on the cell cycle phase in replicative cells, and the ubiquitin proteasome pathway (UPS) proteins, such as E3 ligases and deubiquitinating enzymes, promote microtubule assembly and disassembly by regulating the degradation/availability of ciliary regulatory proteins. Also, many differentiated tissues display cilia, and mutations in genes encoding ciliary proteins are associated with several human pathologies, named ciliopathies, which are multi-organ rare diseases. The retina is one of the organs most affected by ciliary gene mutations because photoreceptors are ciliated cells. Photoreception and phototransduction occur in the outer segment, a highly specialized neurosensory cilium. In this review, we focus on the function of UPS proteins in ciliogenesis and cilia length control in replicative cells and compare it with the scanty data on the identified UPS genes that cause syndromic and non-syndromic inherited retinal disorders. Clearly, further work using animal models and gene-edited mutants of ciliary genes in cells and organoids will widen the landscape of UPS involvement in ciliogenesis and cilia homeostasis.
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Affiliation(s)
- Vasileios Toulis
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.,CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain. .,CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain. .,Institut de Biomedicina (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain.
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20
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Hossain D, Barbelanne M, Tsang WY. Requirement of NPHP5 in the hierarchical assembly of basal feet associated with basal bodies of primary cilia. Cell Mol Life Sci 2020; 77:195-212. [PMID: 31177295 PMCID: PMC11104825 DOI: 10.1007/s00018-019-03181-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/13/2019] [Accepted: 05/31/2019] [Indexed: 11/29/2022]
Abstract
During ciliogenesis, the mother centriole transforms into a basal body competent to nucleate a cilium. The mother centriole and basal body possess sub-distal appendages (SDAs) and basal feet (BF), respectively. SDAs and BF are thought to be equivalent structures. In contrast to SDA assembly, little is known about the players involved in BF assembly and its assembly order. Furthermore, the contribution of BF to ciliogenesis is not understood. Here, we found that SDAs are distinguishable from BF and that the protein NPHP5 is a novel SDA and BF component. Remarkably, NPHP5 is specifically required for BF assembly in cells able to form basal bodies but is dispensable for SDA assembly. Determination of the hierarchical assembly reveals that NPHP5 cooperates with a subset of SDA/BF proteins to organize BF. The assembly pathway of BF is similar but not identical to that of SDA. Loss of NPHP5 or a BF protein simultaneously inhibits BF assembly and primary ciliogenesis, and these phenotypes could be rescued by manipulating the expression of certain components in the BF assembly pathway. These findings define a novel role for NPHP5 in specifically regulating BF assembly, a process which is tightly coupled to primary ciliogenesis.
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Affiliation(s)
- Delowar Hossain
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Marine Barbelanne
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Département de Pathologie et Biologie Cellulaire, Faculté de Médecine, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - William Y Tsang
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Département de Pathologie et Biologie Cellulaire, Faculté de Médecine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.
- Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada.
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21
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Wang P, Xia J, Zhang L, Zhao S, Li S, Wang H, Cheng S, Li H, Yin W, Pei D, Shu X. SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis. Cells 2019; 8:cells8111335. [PMID: 31671755 PMCID: PMC6912348 DOI: 10.3390/cells8111335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/15/2019] [Accepted: 10/27/2019] [Indexed: 12/12/2022] Open
Abstract
Centriolar satellites are non-membrane cytoplasmic granules that deliver proteins to centrosome during centrosome biogenesis and ciliogenesis. Centriolar satellites are highly dynamic during cell cycle or ciliogenesis and how they are regulated remains largely unknown. We report here that sorting nexin 17 (SNX17) regulates the homeostasis of a subset of centriolar satellite proteins including PCM1, CEP131, and OFD1 during serum-starvation-induced ciliogenesis. Mechanistically, SNX17 recruits the deubiquitinating enzyme USP9X to antagonize the mindbomb 1 (MIB1)-induced ubiquitination and degradation of PCM1. SNX17 deficiency leads to enhanced degradation of USP9X as well as PCM1 and disrupts ciliogenesis upon serum starvation. On the other hand, SNX17 is dispensable for the homeostasis of PCM1 and USP9X in serum-containing media. These findings reveal a SNX17/USP9X mediated pathway essential for the homeostasis of centriolar satellites under serum starvation, and provide insight into the mechanism of USP9X in ciliogenesis, which may lead to a better understating of USP9X-deficiency-related human diseases such as X-linked mental retardation and neurodegenerative diseases.
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Affiliation(s)
- Pengtao Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
- Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Jianhong Xia
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Leilei Zhang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Shaoyang Zhao
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Shengbiao Li
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Haiyun Wang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Shan Cheng
- Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Heying Li
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Wenguang Yin
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China.
| | - Xiaodong Shu
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
- Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China.
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 511436, China.
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22
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Shang Z, Zhao J, Zhang Q, Cao C, Tian S, Zhang K, Liu L, Shi L, Yu N, Yang S. USP9X-mediated deubiquitination of B-cell CLL/lymphoma 9 potentiates Wnt signaling and promotes breast carcinogenesis. J Biol Chem 2019; 294:9844-9857. [PMID: 31073027 DOI: 10.1074/jbc.ra119.007655] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
Hyperactivation of the canonical Wnt-signaling pathway is a prominent feature of a number of human malignancies. Transcriptional activation of this signaling cascade depends on the formation of the β-catenin-B-cell CLL/lymphoma 9 (BCL9)-pygopus (PYGO) family plant homeodomain finger 1 complex, yet how the assembly of this complex is regulated remains to be investigated. Here, using MCF-7, HeLa, HEK293T, MDA-MB-231, and Sf9 cells, along with immunoblotting and immunofluorescence, nano-HPLC-MS/MS, deubiquitination, immunoprecipitation, and chromatin immunoprecipitation (ChIP) assays, we report that BCL9 physically associates with a protein deubiquitinase, ubiquitin-specific peptidase 9, X-linked (USP9X), and that USP9X removes Lys-63-linked polyubiquitin on Lys-212 of BCL9. Importantly, the USP9X-mediated BCL9 deubiquitination facilitated the formation of the β-catenin-BCL9-PYGO complex, thereby potentiating the transcriptional activation of Wnt/β-catenin target genes. We also show that USP9X-mediated BCL9 deubiquitination promotes the proliferation and invasion of breast cancer cells. Together, these results uncover USP9X as a deubiquitinase of BCL9, implicating USP9X in Wnt/β-catenin signaling and breast carcinogenesis.
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Affiliation(s)
- Zesen Shang
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Jiao Zhao
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Qi Zhang
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Cheng Cao
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Shanshan Tian
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Kai Zhang
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Ling Liu
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Lei Shi
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Na Yu
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and
| | - Shangda Yang
- From the 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China and .,the State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, 300020 Tianjin, China
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23
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Wang Q, Peng Z, Long H, Deng X, Huang K. Polyubiquitylation of α-tubulin at K304 is required for flagellar disassembly in Chlamydomonas. J Cell Sci 2019; 132:jcs.229047. [PMID: 30765466 DOI: 10.1242/jcs.229047] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/06/2019] [Indexed: 12/20/2022] Open
Abstract
Cilia/flagella are structurally conserved and dynamic organelles; their assembly and disassembly are coordinated with the cell cycle and cell differentiation. Several post-translational modifications, including acetylation, methylation, phosphorylation and ubiquitylation, participate in ciliary disassembly. However, the detailed mechanism and the role of ubiquitylation in ciliary disassembly are unclear. This study identified 20 proteins that were ubiquitylated in shortening flagella of Chlamydomonas α-Tubulin was the most abundant ubiquitylated protein and it was labeled with K63 polyubiquitin chains primarily at K304. Expression of an α-tubulin mutant (K304R), which could not be ubiquitylated, decreased the rate of flagellar disassembly and resulted in an enrichment of the mutant form in the axoneme, suggesting that ubiquitylation of α-tubulin is required for the normal kinetics of axonemal disassembly. Immunoprecipitation and glutathione-S-transferase pulldown assays demonstrated that the retrograde intraflagellar transport (IFT) protein, IFT139, interacted with a variety of ubiquitylated proteins, including α-tubulin, suggesting that IFT-A was responsible for transporting ubiquitylated proteins out of the flagella. Our data suggest an important role for ubiquitylation and retrograde IFT in ciliary disassembly.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Qiyu Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhao Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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24
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Han KJ, Wu Z, Pearson CG, Peng J, Song K, Liu CW. Deubiquitylase USP9X maintains centriolar satellite integrity by stabilizing pericentriolar material 1 protein. J Cell Sci 2019; 132:jcs.221663. [PMID: 30584065 DOI: 10.1242/jcs.221663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Centriolar satellites are small cytoplasmic granules that play important roles in regulating the formation of centrosomes and primary cilia. Ubiquitylation of satellite proteins, including the core satellite scaffold protein pericentriolar material 1 (PCM1), regulates centriolar satellite integrity. Currently, deubiquitylases that control centriolar satellite integrity have not been identified. In this study, we find that the deubiquitylase USP9X binds PCM1, and antagonizes PCM1 ubiquitylation to protect it from proteasomal degradation. Knockdown of USP9X in human cell lines reduces PCM1 protein levels, disrupts centriolar satellite particles and causes localization of satellite proteins, such as CEP290, to centrosomes. Interestingly, knockdown of mindbomb 1 (MIB1), a ubiquitin ligase that promotes PCM1 ubiquitylation and degradation, in USP9X-depleted cells largely restores PCM1 protein levels and corrects defects caused by the loss of USP9X. Overall, our study reveals that USP9X is a constituent of centriolar satellites and functions to maintain centriolar satellite integrity by stabilizing PCM1.
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Affiliation(s)
- Ke-Jun Han
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chad G Pearson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kunhua Song
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chang-Wei Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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25
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Pang Y, Liu Z, Liu S. Identification of Key Potential Targets and Pathway for Arsenic Trioxide by Systemic Bioinformatics Analysis in Pancreatic Cancer. Pathol Oncol Res 2018; 25:681-690. [PMID: 30506130 DOI: 10.1007/s12253-018-0543-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 11/16/2018] [Indexed: 11/26/2022]
Abstract
Arsenic trioxide is an approved chemotheraputic agent for the treatment of acute promyelocytic leukemia (APL). Recently, numerous studies suggested that arsenic trioxide acts as anti-cancer roles in various human malignancies. However, the molecular mechanisms are not fully elucidated. In this study, we explored the critical targets of arsenic trioxide and their interaction network systematically by searching the publicly available published database like DrugBank (DB) and STRING. Seven direct protein targets (DPTs) and 111 DPT-associated genes were identified. The enrichment analysis of arsenic trioxide associated genes/proteins revealed 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these pathways, phosphatidylinositol-4,5-bisphosphate-3-kinase -Akt (PI3K-Akt) single pathway and pancreatic cancer pathway are highly correlated with arsenic trioxide and have 5 overlapped targets. Then we investigated the gene alternation of selected critical genes in pancreatic cancer studies using cBio portal. These results indicated that arsenic trioxide could act anti-tumor function through PI3K-Akt single pathway and identified critical genes might be therapeutic targets for pancreatic cancer.
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Affiliation(s)
- Yanan Pang
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Zhiyong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Shanrong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China.
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26
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Hossain D, Tsang WY. The role of ubiquitination in the regulation of primary cilia assembly and disassembly. Semin Cell Dev Biol 2018; 93:145-152. [PMID: 30213760 DOI: 10.1016/j.semcdb.2018.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 01/02/2023]
Abstract
The primary cilium is a cellular antenna found on the surface of many eukaryotic cells, whose main role is to sense and transduce signals that regulate growth, development, and differentiation. Although once believed to be a vestigial organelle without important function, it has become clear that defects in primary cilium are responsible for a wide variety of genetic diseases affecting many organs and tissues, including the brain, eyes, heart, kidneys, liver, and pancreas. The primary cilium is mainly present in quiescent and differentiated cells, and controls must exist to ensure that this organelle is assembled or disassembled at the right time. Although many protein components required for building the cilium have been identified, mechanistic details of how these proteins are spatially and temporally regulated and how these regulations are connected to external cues are beginning to emerge. This review article highlights the role of ubiquitination and in particular, E3 ubiquitin ligases and deubiquitinases, in the control of primary cilia assembly and disassembly.
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Affiliation(s)
- Delowar Hossain
- Institut de recherches cliniques de Montréal, Montreal, Quebec, H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - William Y Tsang
- Institut de recherches cliniques de Montréal, Montreal, Quebec, H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada; Department of Pathology and Cell Biology, Université de Montréal, Montreal, Quebec, H3C 3J7, Canada.
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27
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Hossain D, Ferreira Barbosa JA, Cohen ÉA, Tsang WY. HIV-1 Vpr hijacks EDD-DYRK2-DDB1 DCAF1 to disrupt centrosome homeostasis. J Biol Chem 2018; 293:9448-9460. [PMID: 29724823 PMCID: PMC6005440 DOI: 10.1074/jbc.ra117.001444] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
Viruses exploit the host cell machinery for their own profit. To evade innate immune sensing and promote viral replication, HIV type 1 (HIV-1) subverts DNA repair regulatory proteins and induces G2/M arrest. The preintegration complex of HIV-1 is known to traffic along microtubules and accumulate near the microtubule-organizing center. The centrosome is the major microtubule-organizing center in most eukaryotic cells, but precisely how HIV-1 impinges on centrosome biology remains poorly understood. We report here that the HIV-1 accessory protein viral protein R (Vpr) localized to the centrosome through binding to DCAF1, forming a complex with the ubiquitin ligase EDD-DYRK2-DDB1DCAF1 and Cep78, a resident centrosomal protein previously shown to inhibit EDD-DYRK2-DDB1DCAF1 Vpr did not affect ubiquitination of Cep78. Rather, it enhanced ubiquitination of an EDD-DYRK2-DDB1DCAF1 substrate, CP110, leading to its degradation, an effect that could be overcome by Cep78 expression. The down-regulation of CP110 and elongation of centrioles provoked by Vpr were independent of G2/M arrest. Infection of T lymphocytes with HIV-1, but not with HIV-1 lacking Vpr, promoted CP110 degradation and centriole elongation. Elongated centrioles recruited more γ-tubulin to the centrosome, resulting in increased microtubule nucleation. Our results suggest that Vpr is targeted to the centrosome where it hijacks a ubiquitin ligase, disrupting organelle homeostasis, which may contribute to HIV-1 pathogenesis.
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Affiliation(s)
- Delowar Hossain
- From the Institut de recherches cliniques de Montréal, Montreal, Quebec H2W 1R7, Canada
- the Division of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | | | - Éric A Cohen
- From the Institut de recherches cliniques de Montréal, Montreal, Quebec H2W 1R7, Canada
- the Division of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- the Department of Microbiology, Infectiology, and Immunology, Université de Montréal, Montreal, Quebec H3C 3J7, Canada, and
| | - William Y Tsang
- From the Institut de recherches cliniques de Montréal, Montreal, Quebec H2W 1R7, Canada,
- the Division of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- the Department of Pathology and Cell Biology, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
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28
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Darling S, Fielding AB, Sabat-Pośpiech D, Prior IA, Coulson JM. Regulation of the cell cycle and centrosome biology by deubiquitylases. Biochem Soc Trans 2017; 45:1125-1136. [PMID: 28900014 PMCID: PMC5652225 DOI: 10.1042/bst20170087] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
Abstract
Post-translational modification of proteins by ubiquitylation is increasingly recognised as a highly complex code that contributes to the regulation of diverse cellular processes. In humans, a family of almost 100 deubiquitylase enzymes (DUBs) are assigned to six subfamilies and many of these DUBs can remove ubiquitin from proteins to reverse signals. Roles for individual DUBs have been delineated within specific cellular processes, including many that are dysregulated in diseases, particularly cancer. As potentially druggable enzymes, disease-associated DUBs are of increasing interest as pharmaceutical targets. The biology, structure and regulation of DUBs have been extensively reviewed elsewhere, so here we focus specifically on roles of DUBs in regulating cell cycle processes in mammalian cells. Over a quarter of all DUBs, representing four different families, have been shown to play roles either in the unidirectional progression of the cell cycle through specific checkpoints, or in the DNA damage response and repair pathways. We catalogue these roles and discuss specific examples. Centrosomes are the major microtubule nucleating centres within a cell and play a key role in forming the bipolar mitotic spindle required to accurately divide genetic material between daughter cells during cell division. To enable this mitotic role, centrosomes undergo a complex replication cycle that is intimately linked to the cell division cycle. Here, we also catalogue and discuss DUBs that have been linked to centrosome replication or function, including centrosome clustering, a mitotic survival strategy unique to cancer cells with supernumerary centrosomes.
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Affiliation(s)
- Sarah Darling
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Andrew B Fielding
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Dorota Sabat-Pośpiech
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Ian A Prior
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Judy M Coulson
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K.
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