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Fujii T, Liang L, Nakayama K, Katoh Y. Defects in diffusion barrier function of ciliary transition zone caused by ciliopathy variations of TMEM218. Hum Mol Genet 2024; 33:1442-1453. [PMID: 38751342 DOI: 10.1093/hmg/ddae083] [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: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 08/09/2024] Open
Abstract
Primary cilia are antenna-like structures protruding from the surface of various eukaryotic cells, and have distinct protein compositions in their membranes. This distinct protein composition is maintained by the presence of the transition zone (TZ) at the ciliary base, which acts as a diffusion barrier between the ciliary and plasma membranes. Defects in cilia and the TZ are known to cause a group of disorders collectively called the ciliopathies, which demonstrate a broad spectrum of clinical features, such as perinatally lethal Meckel syndrome (MKS), relatively mild Joubert syndrome (JBTS), and nonsyndromic nephronophthisis (NPHP). Proteins constituting the TZ can be grouped into the MKS and NPHP modules. The MKS module is composed of several transmembrane proteins and three soluble proteins. TMEM218 was recently reported to be mutated in individuals diagnosed as MKS and JBTS. However, little is known about how TMEM218 mutations found in MKS and JBTS affect the functions of cilia. In this study, we found that ciliary membrane proteins were not localized to cilia in TMEM218-knockout cells, indicating impaired barrier function of the TZ. Furthermore, the exogenous expression of JBTS-associated TMEM218 variants but not MKS-associated variants in TMEM218-knockout cells restored the localization of ciliary membrane proteins. In particular, when expressed in TMEM218-knockout cells, the TMEM218(R115H) variant found in JBTS was able to restore the barrier function of cells, whereas the MKS variant TMEM218(R115C) could not. Thus, the severity of symptoms of MKS and JBTS individuals appears to correlate with the degree of their ciliary defects at the cellular level.
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Affiliation(s)
- Taiju Fujii
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Luxiaoxue Liang
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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2
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Yamaguchi I, Katoh H. Merlin/NF2 regulates SLC7A11/xCT expression and cell viability under glucose deprivation at high cell density in glioblastoma cells. J Biochem 2024; 175:313-322. [PMID: 38102738 DOI: 10.1093/jb/mvad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
The cystine/glutamate transporter SLC7A11/xCT is highly expressed in many cancer cells and plays an important role in antioxidant activity by supplying cysteine for glutathione synthesis. Under glucose-depleted conditions, however, SLC7A11-mediated cystine uptake causes oxidative stress and cell death called disulfidptosis, a new form of cell death. We previously reported that high cell density (HD) promotes lysosomal degradation of SLC7A11 in glioblastoma cells, allowing them to survive under glucose-depleted conditions. In this study, we found that the neurofibromatosis type 2 gene, Merlin/NF2 is a key regulator of SLC7A11 in glioblastoma cells at HD. Deletion of Merlin increased SLC7A11 protein level and cystine uptake at HD, leading to promotion of cell death under glucose deprivation. Furthermore, HD significantly decreased SLC7A11 mRNA level, which was restored by Merlin deletion. This study suggests that Merlin suppresses glucose deprivation-induced cell death by downregulating SLC7A11 expression in glioblastoma cells at HD.
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Affiliation(s)
- Itsuki Yamaguchi
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Biological Chemistry, Graduate School of Science, Osaka Metropolitan University, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Hironori Katoh
- Department of Biological Chemistry, Graduate School of Science, Osaka Metropolitan University, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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3
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Ninomiya K, Ohta K, Kawasaki U, Chiba S, Inoue T, Kuranaga E, Ohashi K, Mizuno K. Calcium influx promotes PLEKHG4B localization to cell-cell junctions and regulates the integrity of junctional actin filaments. Mol Biol Cell 2024; 35:ar24. [PMID: 38088892 PMCID: PMC10881155 DOI: 10.1091/mbc.e23-05-0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/01/2023] [Accepted: 12/07/2023] [Indexed: 01/14/2024] Open
Abstract
PLEKHG4B is a Cdc42-targeting guanine-nucleotide exchange factor implicated in forming epithelial cell-cell junctions. Here we explored the mechanism regulating PLEKHG4B localization. PLEKHG4B localized to the basal membrane in normal Ca2+ medium but accumulated at cell-cell junctions upon ionomycin treatment. Ionomycin-induced junctional localization of PLEKHG4B was suppressed upon disrupting its annexin-A2 (ANXA2)-binding ability. Thus, Ca2+ influx and ANXA2 binding are crucial for PLEKHG4B localization to cell-cell junctions. Treatments with low Ca2+ or BAPTA-AM (an intracellular Ca2+ chelator) suppressed PLEKHG4B localization to the basal membrane. Mutations of the phosphoinositide-binding motif in the pleckstrin homology (PH) domain of PLEKHG4B or masking of membrane phosphatidylinositol-4,5-biphosphate [PI(4,5)P2] suppressed PLEKHG4B localization to the basal membrane, indicating that basal membrane localization of PLEKHG4B requires suitable intracellular Ca2+ levels and PI(4,5)P2 binding of the PH domain. Activation of mechanosensitive ion channels (MSCs) promoted PLEKHG4B localization to cell-cell junctions, and their inhibition suppressed it. Moreover, similar to the PLEKHG4B knockdown phenotypes, inhibition of MSCs or treatment with BAPTA-AM disturbed the integrity of actin filaments at cell-cell junctions. Taken together, our results suggest that Ca2+ influx plays crucial roles in PLEKHG4B localization to cell-cell junctions and the integrity of junctional actin organization, with MSCs contributing to this process.
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Affiliation(s)
- Komaki Ninomiya
- Laboratory of Molecular and Cellular Biology, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
- Laboratory for Histogenetic Dynamics, Graduate School of Life Sciences, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
| | - Kai Ohta
- Laboratory of Molecular and Cellular Biology, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
| | - Ukyo Kawasaki
- Laboratory of Molecular and Cellular Biology, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
| | - Shuhei Chiba
- Laboratory of Molecular and Cellular Biology, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
| | - Takanari Inoue
- Department of Cell Biology and Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Erina Kuranaga
- Laboratory for Histogenetic Dynamics, Graduate School of Life Sciences, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
- Laboratory for Histogenetic Dynamics, Graduate School and Faculty of Pharmaceutical Sciences, Kyoto University, Kyoto 606‑8304, Japan
| | - Kazumasa Ohashi
- Laboratory of Molecular and Cellular Biology, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
| | - Kensaku Mizuno
- Laboratory of Molecular and Cellular Biology, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aobayama, Sendai, Miyagi 980-8578, Japan
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4
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Accogli A, Shakya S, Yang T, Insinna C, Kim SY, Bell D, Butov KR, Severino M, Niceta M, Scala M, Lee HS, Yoo T, Stauffer J, Zhao H, Fiorillo C, Pedemonte M, Diana MC, Baldassari S, Zakharova V, Shcherbina A, Rodina Y, Fagerberg C, Roos LS, Wierzba J, Dobosz A, Gerard A, Potocki L, Rosenfeld JA, Lalani SR, Scott TM, Scott D, Azamian MS, Louie R, Moore HW, Champaigne NL, Hollingsworth G, Torella A, Nigro V, Ploski R, Salpietro V, Zara F, Pizzi S, Chillemi G, Ognibene M, Cooney E, Do J, Linnemann A, Larsen MJ, Specht S, Walters KJ, Choi HJ, Choi M, Tartaglia M, Youkharibache P, Chae JH, Capra V, Park SG, Westlake CJ. Variants in the WDR44 WD40-repeat domain cause a spectrum of ciliopathy by impairing ciliogenesis initiation. Nat Commun 2024; 15:365. [PMID: 38191484 PMCID: PMC10774338 DOI: 10.1038/s41467-023-44611-2] [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: 11/09/2022] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
WDR44 prevents ciliogenesis initiation by regulating RAB11-dependent vesicle trafficking. Here, we describe male patients with missense and nonsense variants within the WD40 repeats (WDR) of WDR44, an X-linked gene product, who display ciliopathy-related developmental phenotypes that we can model in zebrafish. The patient phenotypic spectrum includes developmental delay/intellectual disability, hypotonia, distinct craniofacial features and variable presence of brain, renal, cardiac and musculoskeletal abnormalities. We demonstrate that WDR44 variants associated with more severe disease impair ciliogenesis initiation and ciliary signaling. Because WDR44 negatively regulates ciliogenesis, it was surprising that pathogenic missense variants showed reduced abundance, which we link to misfolding of WDR autonomous repeats and degradation by the proteasome. We discover that disease severity correlates with increased RAB11 binding, which we propose drives ciliogenesis initiation dysregulation. Finally, we discover interdomain interactions between the WDR and NH2-terminal region that contains the RAB11 binding domain (RBD) and show patient variants disrupt this association. This study provides new insights into WDR44 WDR structure and characterizes a new syndrome that could result from impaired ciliogenesis.
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Affiliation(s)
- Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre (MUHC), Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Saurabh Shakya
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Taewoo Yang
- Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 08826, Seoul, Republic of Korea
| | - Christine Insinna
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, 03080, Seoul, Republic of Korea
| | - David Bell
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kirill R Butov
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | | | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Hyun Sik Lee
- School of Biological Sciences, Seoul National University, 08826, Seoul, Republic of Korea
| | - Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Jimmy Stauffer
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Huijie Zhao
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Chiara Fiorillo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Child Neuropsychiatry, IRCCS Istituto G.Gaslini, DINOGMI University of Genova, Largo Gaslini 5, Genoa, Italy
| | - Marina Pedemonte
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria C Diana
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Simona Baldassari
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Viktoria Zakharova
- National Medical Research Center for Endocrinology, Clinical data analysis department, Moscow, Russian Federation, Russia
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Yulia Rodina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Laura Sønderberg Roos
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, København, Denmark
| | - Jolanta Wierzba
- Department of Pediatrics and Internal Medicine Nursing, Department of Rare Disorders, Medical University of Gdansk, Gdansk, Poland
| | - Artur Dobosz
- Department of Medical Genetics, Faculty of Medicine, Jagiellonian University Medical College, 30-663, Krakow, Poland
| | - Amanda Gerard
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lorraine Potocki
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Seema R Lalani
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tiana M Scott
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Daryl Scott
- Baylor Genetics Laboratories, Houston, TX, USA
| | | | | | | | | | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Pawińskiego 3C, 02-106, Warsaw, Poland
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University. College London, London, WC1N 3BG, UK
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy
| | - Marzia Ognibene
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Erin Cooney
- Division of Medical Genetics and Metabolism, Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Jenny Do
- Division of Medical Genetics and Metabolism, Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Anders Linnemann
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Suzanne Specht
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Kylie J Walters
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Hee-Jung Choi
- School of Biological Sciences, Seoul National University, 08826, Seoul, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Phillippe Youkharibache
- Cancer Science Data Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, 03080, Seoul, Republic of Korea
| | - Valeria Capra
- Child Neuropsychiatry, IRCCS Istituto G.Gaslini, DINOGMI University of Genova, Largo Gaslini 5, Genoa, Italy
| | - Sung-Gyoo Park
- Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 08826, Seoul, Republic of Korea.
| | - Christopher J Westlake
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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Takasugi M, Ohtani N, Takemura K, Emmrich S, Zakusilo FT, Yoshida Y, Kutsukake N, Mariani JN, Windrem MS, Chandler-Militello D, Goldman SA, Satoh J, Ito S, Seluanov A, Gorbunova V. CD44 correlates with longevity and enhances basal ATF6 activity and ER stress resistance. Cell Rep 2023; 42:113130. [PMID: 37708026 PMCID: PMC10591879 DOI: 10.1016/j.celrep.2023.113130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/14/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
The naked mole rat (NMR) is the longest-lived rodent, resistant to multiple age-related diseases including neurodegeneration. However, the mechanisms underlying the NMR's resistance to neurodegenerative diseases remain elusive. Here, we isolated oligodendrocyte progenitor cells (OPCs) from NMRs and compared their transcriptome with that of other mammals. Extracellular matrix (ECM) genes best distinguish OPCs of long- and short-lived species. Notably, expression levels of CD44, an ECM-binding protein that has been suggested to contribute to NMR longevity by mediating the effect of hyaluronan (HA), are not only high in OPCs of long-lived species but also positively correlate with longevity in multiple cell types/tissues. We found that CD44 localizes to the endoplasmic reticulum (ER) and enhances basal ATF6 activity. CD44 modifies proteome and membrane properties of the ER and enhances ER stress resistance in a manner dependent on unfolded protein response regulators without the requirement of HA. HA-independent role of CD44 in proteostasis regulation may contribute to mammalian longevity.
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Affiliation(s)
- Masaki Takasugi
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan.
| | - Naoko Ohtani
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan.
| | - Kazuaki Takemura
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Frances T Zakusilo
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yuya Yoshida
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Nobuyuki Kutsukake
- Research Center for Integrative Evolutionary Science, SOKENDAI, The Graduate University for Advanced Studies, Kanagawa, Japan
| | - John N Mariani
- Center for Translational Neuromedicine and the Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martha S Windrem
- Center for Translational Neuromedicine and the Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Devin Chandler-Militello
- Center for Translational Neuromedicine and the Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Steven A Goldman
- Center for Translational Neuromedicine and the Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Junko Satoh
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester Medical Center, Rochester, NY 14642 USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA; Department of Medicine, University of Rochester Medical Center, Rochester, NY 14642 USA.
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6
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Tasaki K, Zhou Z, Ishida Y, Katoh Y, Nakayama K. Compound heterozygous IFT81 variations in a skeletal ciliopathy patient cause Bardet-Biedl syndrome-like ciliary defects. Hum Mol Genet 2023; 32:2887-2900. [PMID: 37427975 DOI: 10.1093/hmg/ddad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023] Open
Abstract
Owing to their crucial roles in development and homeostasis, defects in cilia cause ciliopathies with diverse clinical manifestations. The intraflagellar transport (IFT) machinery, containing the IFT-A and IFT-B complexes, mediates not only the intraciliary bidirectional trafficking but also import and export of ciliary proteins together with the kinesin-2 and dynein-2 motor complexes. The BBSome, containing eight subunits encoded by causative genes of Bardet-Biedl syndrome (BBS), connects the IFT machinery to ciliary membrane proteins to mediate their export from cilia. Although mutations in subunits of the IFT-A and dynein-2 complexes cause skeletal ciliopathies, mutations in some IFT-B subunits are also known to cause skeletal ciliopathies. We here show that compound heterozygous variations of an IFT-B subunit, IFT81, found in a patient with skeletal ciliopathy cause defects in its interactions with other IFT-B subunits, and in ciliogenesis and ciliary protein trafficking when one of the two variants was expressed in IFT81-knockout (KO) cells. Notably, we found that IFT81-KO cells expressing IFT81(Δ490-519), which lacks the binding site for the IFT25-IFT27 dimer, causes ciliary defects reminiscent of those found in BBS cells and those in IFT74-KO cells expressing a BBS variant of IFT74, which forms a heterodimer with IFT81. In addition, IFT81-KO cells expressing IFT81(Δ490-519) in combination with the other variant, IFT81 (L645*), which mimics the cellular conditions of the above skeletal ciliopathy patient, demonstrated essentially the same phenotype as those expressing only IFT81(Δ490-519). Thus, our data indicate that BBS-like defects can be caused by skeletal ciliopathy variants of IFT81.
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Affiliation(s)
- Koshi Tasaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Zhuang Zhou
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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7
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Hiyamizu S, Qiu H, Tsurumi Y, Hamada Y, Katoh Y, Nakayama K. Dynein-2-driven intraciliary retrograde trafficking indirectly requires multiple interactions of IFT54 in the IFT-B complex with the dynein-2 complex. Biol Open 2023; 12:bio059976. [PMID: 37309605 PMCID: PMC10320715 DOI: 10.1242/bio.059976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023] Open
Abstract
Within cilia, the dynein-2 complex needs to be transported as an anterograde cargo to achieve its role as a motor to drive retrograde trafficking of the intraflagellar transport (IFT) machinery containing IFT-A and IFT-B complexes. We previously showed that interactions of WDR60 and the DYNC2H1-DYNC2LI1 dimer of dynein-2 with multiple IFT-B subunits, including IFT54, are required for the trafficking of dynein-2 as an IFT cargo. However, specific deletion of the IFT54-binding site from WDR60 demonstrated only a minor effect on dynein-2 trafficking and function. We here show that the C-terminal coiled-coil region of IFT54, which participates in its interaction with the DYNC2H1-DYNC2LI1 dimer of dynein-2 and with IFT20 of the IFT-B complex, is essential for IFT-B function, and suggest that the IFT54 middle linker region between the N-terminal WDR60-binding region and the C-terminal coiled-coil is required for ciliary retrograde trafficking, probably by mediating the effective binding of IFT-B to the dynein-2 complex, and thereby ensuring dynein-2 loading onto the anterograde IFT trains. The results presented here agree with the notion predicted from the previous structural models that the dynein-2 loading onto the anterograde IFT train relies on intricate, multivalent interactions between the dynein-2 and IFT-B complexes.
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Affiliation(s)
- Shunya Hiyamizu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuta Tsurumi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Hamada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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8
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Ma X, Zhang Y, Zhang Y, Zhang X, Huang Y, He K, Chen C, Hao J, Zhao D, LeBrasseur NK, Kirkland JL, Chini EN, Wei Q, Ling K, Hu J. A stress-induced cilium-to-PML-NB route drives senescence initiation. Nat Commun 2023; 14:1840. [PMID: 37019904 PMCID: PMC10076330 DOI: 10.1038/s41467-023-37362-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Cellular senescence contributes to tissue homeostasis and age-related pathologies. However, how senescence is initiated in stressed cells remains vague. Here, we discover that exposure to irradiation, oxidative or inflammatory stressors induces transient biogenesis of primary cilia, which are then used by stressed cells to communicate with the promyelocytic leukemia nuclear bodies (PML-NBs) to initiate senescence responses in human cells. Mechanistically, a ciliary ARL13B-ARL3 GTPase cascade negatively regulates the association of transition fiber protein FBF1 and SUMO-conjugating enzyme UBC9. Irreparable stresses downregulate the ciliary ARLs and release UBC9 to SUMOylate FBF1 at the ciliary base. SUMOylated FBF1 then translocates to PML-NBs to promote PML-NB biogenesis and PML-NB-dependent senescence initiation. Remarkably, Fbf1 ablation effectively subdues global senescence burden and prevents associated health decline in irradiation-treated mice. Collectively, our findings assign the primary cilium a key role in senescence induction in mammalian cells and, also, a promising target in future senotherapy strategies.
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Affiliation(s)
- Xiaoyu Ma
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Yingyi Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Yuanyuan Zhang
- Department of Clinical Genetics, ShengJing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xu Zhang
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Yan Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Kai He
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jielu Hao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Debiao Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Nathan K LeBrasseur
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Eduardo N Chini
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Anesthesiology, Mayo Clinic, Jacksonville, FL, USA
| | - Qing Wei
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China.
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Mayo Clinic Robert M. and Billie Kelley Pirnie Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA.
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.
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9
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A Toolkit for Effective and Successive Genome Engineering of Escherichia coli. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation9010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The bacterium Escherichia coli has been well-justified as an effective workhorse for industrial applications. In this study, we developed a toolkit for flexible genome engineering of this microorganism, including site-specific insertion of heterologous genes and inactivation of endogenous genes, such that bacterial hosts can be effectively engineered for biomanufacturing. We first constructed a base strain by genomic implementation of the cas9 and λRed recombineering genes. Then, we constructed plasmids for expressing gRNA, DNA cargo, and the Vibrio cholerae Tn6677 transposon and type I-F CRISPR-Cas machinery. Genomic insertion of a DNA cargo up to 5.5 kb was conducted using a transposon-associated CRISPR-Cas system, whereas gene inactivation was mediated by a classic CRISPR-Cas9 system coupled with λRed recombineering. With this toolkit, we can exploit the synergistic functions of CRISPR-Cas, λRed recombineering, and Tn6677 transposon for successive genomic manipulations. As a demonstration, we used the developed toolkit to derive a plasmid-free strain for heterologous production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) by genomic knock-in and knockout of several key genes with high editing efficiencies.
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10
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Satoda Y, Noguchi T, Fujii T, Taniguchi A, Katoh Y, Nakayama K. BROMI/TBC1D32 together with CCRK/CDK20 and FAM149B1/JBTS36 contributes to intraflagellar transport turnaround involving ICK/CILK1. Mol Biol Cell 2022; 33:ar79. [PMID: 35609210 PMCID: PMC9582636 DOI: 10.1091/mbc.e22-03-0089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Primary cilia are antenna-like organelles that contain specific proteins, and are crucial for tissue morphogenesis. Anterograde and retrograde trafficking of ciliary proteins are mediated by the intraflagellar transport (IFT) machinery. BROMI/TBC1D32 interacts with CCRK/CDK20, which phosphorylates and activates the intestinal cell kinase (ICK)/CILK1 kinase, to regulate the change in direction of the IFT machinery at the ciliary tip. Mutations in BROMI, CCRK, and ICK in humans cause ciliopathies, and mice defective in these genes are also known to demonstrate ciliopathy phenotypes. We show here that BROMI interacts not only with CCRK but also with CFAP20, an evolutionarily conserved ciliary protein, and with FAM149B1/ Joubert syndrome (JBTS)36, a protein in which mutations cause JBTS. In addition, we show that FAM149B1 interacts directly with CCRK as well as with BROMI. Ciliary defects observed in CCRK-knockout (KO), BROMI-KO, and FAM149B1-KO cells, including abnormally long cilia and accumulation of the IFT machinery and ICK at the ciliary tip, resembled one another, and BROMI mutants that are defective in binding to CCRK and CFAP20 were unable to rescue the ciliary defects of BROMI-KO cells. These data indicate that CCRK, BROMI, FAM149B1, and probably CFAP20 altogether regulate the IFT turnaround process under the control of ICK.
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Affiliation(s)
- Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Taiju Fujii
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Aoi Taniguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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11
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Ishida Y, Tasaki K, Katoh Y, Nakayama K. Molecular basis underlying the ciliary defects caused by IFT52 variations found in skeletal ciliopathies. Mol Biol Cell 2022; 33:ar83. [PMID: 35704471 PMCID: PMC9582644 DOI: 10.1091/mbc.e22-05-0188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Bidirectional protein trafficking within cilia is mediated by the intraflagellar transport (IFT) machinery, which contains the IFT-A and IFT-B complexes powered by the kinesin-2 and dynein-2 motors. Mutations in genes encoding subunits of the IFT-A and dynein-2 complexes cause skeletal ciliopathies. Some subunits of the IFT-B complex, including IFT52, IFT80, and IFT172, are also mutated in skeletal ciliopathies. We here show that IFT52 variants found in individuals with short-rib polydactyly syndrome (SRPS) are compromised in terms of formation of the IFT-B holocomplex from two subcomplexes and its interaction with heterotrimeric kinesin-II. IFT52-knockout (KO) cells expressing IFT52 variants that mimic the cellular conditions of individuals with SRPS demonstrated mild ciliogenesis defects and a decrease in ciliary IFT-B level. Furthermore, in IFT52-KO cells expressing an SRPS variant of IFT52, ciliary tip localization of ICK/CILK1 and KIF17, both of which are likely to be transported to the tip via binding to the IFT-B complex, was significantly impaired. Altogether these results indicate that impaired anterograde trafficking caused by a decrease in the ciliary level of IFT-B or in its binding to kinesin-II underlies the ciliary defects found in skeletal ciliopathies caused by IFT52 variations.
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Affiliation(s)
- Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koshi Tasaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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12
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Kawamura A, Yoshida S, Aoki K, Shimoyama Y, Yamada K, Yoshida K. DYRK2 maintains genome stability via neddylation of cullins in response to DNA damage. J Cell Sci 2022; 135:jcs259514. [PMID: 35582972 DOI: 10.1242/jcs.259514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
Neural precursor cell-expressed developmentally down-regulated 8 (NEDD8), an ubiquitin-like protein, is an essential regulator of the DNA damage response. Numerous studies have shown that neddylation (conjugation of NEDD8 to target proteins) dysfunction causes several human diseases, such as cancer. Hence clarifying the regulatory mechanism of neddylation could provide insight into the mechanism of genome stability underlying the DNA damage response (DDR) and carcinogenesis. Here, we demonstrate that dual-specificity tyrosine-regulated kinase 2 (DYRK2) is a novel regulator of neddylation and maintains genome stability. Deletion of DYRK2 leads to persistent DNA double-strand breaks (DSBs) and subsequent genome instability. Mechanistically, DYRK2 promotes neddylation through forming a complex with NAE1, which is a component of NEDD8-activating enzyme E1, and maintaining its protein level by suppressing polyubiquitylation. The present study is the first to demonstrate that DYRK2 controls neddylation and is necessary for maintaining genome stability. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Akira Kawamura
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Saishu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Katsuhiko Aoki
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Yuya Shimoyama
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
- Department of Surgery, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Kohji Yamada
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Kiyotsugu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
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13
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Tamura Y, Nakamizo Y, Watanabe Y, Kimura I, Katoh H. Filamin A forms a complex with EphA2 and regulates EphA2 serine 897 phosphorylation and glioblastoma cell proliferation. Biochem Biophys Res Commun 2022; 597:64-70. [PMID: 35124461 DOI: 10.1016/j.bbrc.2022.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
EphA2 is phosphorylated on serine 897 (S897) in response to growth factors such as epidermal growth factor (EGF) and on tyrosine 588 (Y588) in response to its ligand ephrinA1, causing different cellular responses. In this study, we show that the actin-binding protein Filamin A forms a complex with EphA2 and promotes its S897 phosphorylation and glioblastoma cell proliferation. Suppression of Filamin A expression by siRNAs inhibited glioblastoma cell proliferation induced by EGF stimulation or overexpression of EphA2. Knockdown of Filamin A inhibited EGF-induced S897 phosphorylation of EphA2, whereas it had little effect on ephrinA1-induced Y588 phosphorylation of EphA2. Furthermore, Filamin A expression affected the subcellular localization of EphA2. This study suggests that Filamin A selectively promotes EphA2 S897 phosphorylation and plays an important role in glioblastoma cell proliferation.
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Affiliation(s)
- Yuho Tamura
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan; Department of Pharmacology, Division of Pathological Sciences, Kyoto Pharmaceutical University, Misasagi Nakauchi-cho 5, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Yuta Nakamizo
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuzo Watanabe
- Proteomics Facility, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ikuo Kimura
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hironori Katoh
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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14
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Hayashima K, Katoh H. Expression of gamma-glutamyltransferase 1 in glioblastoma cells confers resistance to cystine deprivation-induced ferroptosis. J Biol Chem 2022; 298:101703. [PMID: 35148992 PMCID: PMC8897698 DOI: 10.1016/j.jbc.2022.101703] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/15/2023] Open
Abstract
Ferroptosis is an iron-dependent mode of cell death caused by excessive oxidative damage to lipids. Lipid peroxidation is normally suppressed by glutathione peroxidase 4, which requires reduced glutathione. Cystine is a major resource for glutathione synthesis, especially in cancer cells. Therefore, cystine deprivation or inhibition of cystine uptake promotes ferroptosis in cancer cells. However, the roles of other molecules involved in cysteine deprivation–induced ferroptosis are unexplored. We report here that the expression of gamma-glutamyltransferase 1 (GGT1), an enzyme that cleaves extracellular glutathione, determines the sensitivity of glioblastoma cells to cystine deprivation–induced ferroptosis at high cell density (HD). In glioblastoma cells expressing GGT1, pharmacological inhibition or deletion of GGT1 suppressed the cell density–induced increase in intracellular glutathione levels and cell viability under cystine deprivation, which were restored by the addition of cysteinylglycine, the GGT product of glutathione cleavage. On the other hand, cystine deprivation induced glutathione depletion and ferroptosis in GGT1-deficient glioblastoma cells even at an HD. Exogenous expression of GGT1 in GGT1-deficient glioblastoma cells inhibited cystine deprivation–induced glutathione depletion and ferroptosis at an HD. This suggests that GGT1 plays an important role in glioblastoma cell survival under cystine-limited and HD conditions. We conclude that combining GGT inhibitors with ferroptosis inducers may provide an effective therapeutic approach for treating glioblastoma.
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Affiliation(s)
- Kazuki Hayashima
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hironori Katoh
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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15
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Hindul NL, Jhita A, Oprea DG, Hussain TA, Gonchar O, Campillo MAM, O'Regan L, Kanemaki MT, Fry AM, Hirota K, Tanaka K. Construction of a human hTERT RPE-1 cell line with inducible Cre for editing of endogenous genes. Biol Open 2022; 11:274087. [PMID: 35067715 PMCID: PMC8864296 DOI: 10.1242/bio.059056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/11/2022] [Indexed: 11/20/2022] Open
Abstract
The human retinal pigment epithelial RPE-1 cell line immortalized with hTERT retains a stable karyotype with a modal chromosome number of 46 and has been widely used to study physiological events in human cell culture systems. To facilitate inducible knock-out or knock-in experiments in this cell line, we have modified the AAVS1 locus to harbour a DNA fragment encoding ERT2-Cre-ERT2 fusion protein under regulation of a Tet-On expression system. In the generated cell line, active Cre recombinase was induced by simple addition of doxycycline and tamoxifen to the culture medium. As proof of concept, we successfully introduced an oncogenic point mutation to the endogenous KRAS gene locus of this cell line. The cell line will serve as a powerful tool to conduct functional analyses of human genes. Summary: A near wild-type human hTERT RPE-1 cell line with inducible Cre recombinase integrated at the AAVS1 was generated for inducible genetic knock-in and knock-out. It facilitates human gene functional studies.
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Affiliation(s)
- Naushin L. Hindul
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Amarjot Jhita
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Daiana G. Oprea
- Department of Molecular and Cell Biology, University of Leicester, UK
| | | | - Oksana Gonchar
- Department of Molecular and Cell Biology, University of Leicester, UK
| | | | - Laura O'Regan
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Masato T. Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Andrew M. Fry
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Kayoko Tanaka
- Department of Molecular and Cell Biology, University of Leicester, UK
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16
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Qiu H, Tsurumi Y, Katoh Y, Nakayama K. Combinations of deletion and missense variations of the dynein-2 DYNC2LI1 subunit found in skeletal ciliopathies cause ciliary defects. Sci Rep 2022; 12:31. [PMID: 34997029 PMCID: PMC8742128 DOI: 10.1038/s41598-021-03950-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cilia play crucial roles in sensing and transducing extracellular signals. Bidirectional protein trafficking within cilia is mediated by the intraflagellar transport (IFT) machinery containing IFT-A and IFT-B complexes, with the aid of kinesin-2 and dynein-2 motors. The dynein-2 complex drives retrograde trafficking of the IFT machinery after its transportation to the ciliary tip as an IFT cargo. Mutations in genes encoding the dynein-2-specific subunits (DYNC2H1, WDR60, WDR34, DYNC2LI1, and TCTEX1D2) are known to cause skeletal ciliopathies. We here demonstrate that several pathogenic variants of DYNC2LI1 are compromised regarding their ability to interact with DYNC2H1 and WDR60. When expressed in DYNC2LI1-knockout cells, deletion variants of DYNC2LI1 were unable to rescue the ciliary defects of these cells, whereas missense variants, as well as wild-type DYNC2LI1, restored the normal phenotype. DYNC2LI1-knockout cells coexpressing one pathogenic deletion variant together with wild-type DYNC2LI1 demonstrated a normal phenotype. In striking contrast, DYNC2LI1-knockout cells coexpressing the deletion variant in combination with a missense variant, which mimics the situation of cells of compound heterozygous ciliopathy individuals, demonstrated ciliary defects. Thus, DYNC2LI1 deletion variants found in individuals with skeletal ciliopathies cause ciliary defects when combined with a missense variant, which expressed on its own does not cause substantial defects.
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Affiliation(s)
- Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuta Tsurumi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.,General Research Institute, Hoyu Co., Ltd., Nagakute, Aichi, 480-1136, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.
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17
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Zhou Z, Qiu H, Castro-Araya RF, Takei R, Nakayama K, Katoh Y. Impaired cooperation between IFT74/BBS22-IFT81 and IFT25-IFT27/BBS19 causes Bardet-Biedl syndrome. Hum Mol Genet 2021; 31:1681-1693. [PMID: 34888642 DOI: 10.1093/hmg/ddab354] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 02/03/2023] Open
Abstract
The IFT-B complex mediates ciliary anterograde protein trafficking and membrane protein export together with the BBSome. Bardet-Biedl syndrome (BBS) is caused by mutations in not only all BBSome subunits, but also in some IFT-B subunits, including IFT74/BBS22 and IFT27/BBS19, which form heterodimers with IFT81 and IFT25, respectively. We found that the IFT25-IFT27 dimer bind the C-terminal region of the IFT74-IFT81 dimer, and that the IFT25-IFT27-binding region encompasses the region deleted in the BBS variants of IFT74. In addition, we found that the missense BBS variants of IFT27 are impaired in IFT74-IFT81 binding, and are unable to rescue the BBS-like phenotypes of IFT27-knockout cells. Furthermore, the BBS variants of IFT74 rescued the ciliogenesis defect of IFT74-knockout cells, but the rescued cells demonstrated BBS-like abnormal phenotypes. Taken together, we conclude that the impaired interaction between IFT74-IFT81 and IFT25-IFT27 causes the BBS-associated ciliary defects.
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Affiliation(s)
- Zhuang Zhou
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Roiner-Francisco Castro-Araya
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Ryota Takei
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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18
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Noguchi T, Nakamura K, Satoda Y, Katoh Y, Nakayama K. CCRK/CDK20 regulates ciliary retrograde protein trafficking via interacting with BROMI/TBC1D32. PLoS One 2021; 16:e0258497. [PMID: 34624068 PMCID: PMC8500422 DOI: 10.1371/journal.pone.0258497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/28/2021] [Indexed: 01/02/2023] Open
Abstract
CCRK/CDK20 was reported to interact with BROMI/TBC1D32 and regulate ciliary Hedgehog signaling. In various organisms, mutations in the orthologs of CCRK and those of the kinase ICK/CILK1, which is phosphorylated by CCRK, are known to result in cilia elongation. Furthermore, we recently showed that ICK regulates retrograde ciliary protein trafficking and/or the turnaround event at the ciliary tips, and that its mutations result in the elimination of intraflagellar transport (IFT) proteins that have overaccumulated at the bulged ciliary tips as extracellular vesicles, in addition to cilia elongation. However, how these proteins cooperate to regulate ciliary protein trafficking has remained unclear. We here show that the phenotypes of CCRK-knockout (KO) cells closely resemble those of ICK-KO cells; namely, the overaccumulation of IFT proteins at the bulged ciliary tips, which appear to be eliminated as extracellular vesicles, and the enrichment of GPR161 and Smoothened on the ciliary membrane. The abnormal phenotypes of CCRK-KO cells were rescued by the exogenous expression of wild-type CCRK but not its kinase-dead mutant or a mutant defective in BROMI binding. These results together indicate that CCRK regulates the turnaround process at the ciliary tips in concert with BROMI and probably via activating ICK.
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Affiliation(s)
- Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kentaro Nakamura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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19
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Tang Q, Liu M, Liu Y, Hwang RD, Zhang T, Wang J. NDST3 deacetylates α-tubulin and suppresses V-ATPase assembly and lysosomal acidification. EMBO J 2021; 40:e107204. [PMID: 34435379 PMCID: PMC8488563 DOI: 10.15252/embj.2020107204] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 12/18/2022] Open
Abstract
Lysosomes are key organelles maintaining cellular homeostasis in health and disease. Here, we report the identification of N‐deacetylase and N‐sulfotransferase 3 (NDST3) as a potent regulator of lysosomal functions through an unbiased genetic screen. NDST3 constitutes a new member of the histone deacetylase (HDAC) family and catalyzes the deacetylation of α‐tubulin. Loss of NDST3 promotes assembly of the V‐ATPase holoenzyme on the lysosomal membrane and thereby increases the acidification of the organelle. NDST3 is downregulated in tissues and cells from patients carrying the C9orf72 hexanucleotide repeat expansion linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Deficiency in C9orf72 decreases the level of NDST3, and downregulation of NDST3 exacerbates the proteotoxicity of poly‐dipeptides generated from the C9orf72 hexanucleotide repeats. These results demonstrate a previously unknown regulatory mechanism through which microtubule acetylation regulates lysosomal activities and suggest that NDST3 could be targeted to modulate microtubule and lysosomal functions in relevant diseases.
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Affiliation(s)
- Qing Tang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Mingming Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ran-Der Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tao Zhang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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20
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Fujisawa S, Qiu H, Nozaki S, Chiba S, Katoh Y, Nakayama K. ARL3 and ARL13B GTPases participate in distinct steps of INPP5E targeting to the ciliary membrane. Biol Open 2021; 10:bio058843. [PMID: 34447983 PMCID: PMC8496693 DOI: 10.1242/bio.058843] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
INPP5E, a phosphoinositide 5-phosphatase, localizes on the ciliary membrane via its C-terminal prenyl moiety, and maintains the distinct ciliary phosphoinositide composition. The ARL3 GTPase contributes to the ciliary membrane localization of INPP5E by stimulating the release of PDE6D bound to prenylated INPP5E. Another GTPase, ARL13B, which is localized on the ciliary membrane, contributes to the ciliary membrane retention of INPP5E by directly binding to its ciliary targeting sequence. However, as ARL13B was shown to act as a guanine nucleotide exchange factor (GEF) for ARL3, it is also possible that ARL13B indirectly mediates the ciliary INPP5E localization via activating ARL3. We here show that INPP5E is delocalized from cilia in both ARL3-knockout (KO) and ARL13B-KO cells. However, some of the abnormal phenotypes were different between these KO cells, while others were found to be common, indicating the parallel roles of ARL3 and ARL13B, at least concerning some cellular functions. For several variants of ARL13B, their ability to interact with INPP5E, rather than their ability as an ARL3-GEF, was associated with whether they could rescue the ciliary localization of INPP5E in ARL13B-KO cells. These observations together indicate that ARL13B determines the ciliary localization of INPP5E, mainly by its direct binding to INPP5E.
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Affiliation(s)
- Sayaka Fujisawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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21
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De-Castro ARG, Quintas-Gonçalves J, Silva-Ribeiro T, Rodrigues DRM, De-Castro MJG, Abreu CM, Dantas TJ. The IFT20 homolog in Caenorhabditis elegans is required for ciliogenesis and cilia-mediated behavior. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 33997658 PMCID: PMC8114103 DOI: 10.17912/micropub.biology.000396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cilia are microtubule-based organelles that carry out a wide range of critical functions throughout the development of higher animals. Regardless of their type, all cilia rely on a motor-driven, bidirectional transport system known as intraflagellar transport (IFT). Of the many components of the IFT machinery, IFT20 is one of the smallest subunits. Nevertheless, IFT20 has been shown to play critical roles in the assembly of several types of mammalian cilia. Here we show that the IFT20 homolog in Caenorhabditis elegans, IFT-20, is also important for correct cilium assembly in sensory neurons. Strikingly, however, we find that IFT-20-deficient animals are able to assemble short, vestigial cilia. In spite of this, we show that practically all IFT-20-deficient animals fail to respond to environmental cues that are normally detected by cilia to modulate their behavior. Altogether, our results indicate that IFT-20 is critical for both the correct assembly and function of cilia in C. elegans.
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Affiliation(s)
- Ana R G De-Castro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Joana Quintas-Gonçalves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Tiago Silva-Ribeiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Diogo R M Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Maria J G De-Castro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Carla M Abreu
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Tiago J Dantas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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22
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Park HS, Papanastasi E, Blanchard G, Chiticariu E, Bachmann D, Plomann M, Morice-Picard F, Vabres P, Smahi A, Huber M, Pich C, Hohl D. ARP-T1-associated Bazex-Dupré-Christol syndrome is an inherited basal cell cancer with ciliary defects characteristic of ciliopathies. Commun Biol 2021; 4:544. [PMID: 33972689 PMCID: PMC8110579 DOI: 10.1038/s42003-021-02054-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/30/2021] [Indexed: 01/20/2023] Open
Abstract
Actin-Related Protein-Testis1 (ARP-T1)/ACTRT1 gene mutations cause the Bazex-Dupré-Christol Syndrome (BDCS) characterized by follicular atrophoderma, hypotrichosis, and basal cell cancer. Here, we report an ARP-T1 interactome (PXD016557) that includes proteins involved in ciliogenesis, endosomal recycling, and septin ring formation. In agreement, ARP-T1 localizes to the midbody during cytokinesis and the basal body of primary cilia in interphase. Tissue samples from ARP-T1-associated BDCS patients have reduced ciliary length. The severity of the shortened cilia significantly correlates with the ARP-T1 levels, which was further validated by ACTRT1 knockdown in culture cells. Thus, we propose that ARP-T1 participates in the regulation of cilia length and that ARP-T1-associated BDCS is a case of skin cancer with ciliopathy characteristics. Park et al. characterise the interactome, localisation and function of Actin-Related Protein-Testis1 protein (ARP-T1), encoded by the ACTRT1 gene, associated with inherited basal cell cancer. They find that ARP-T1 is localised to the primary cilia basal body in epidermal cells, interacts with the cilia machinery, and is needed for proper ciliogenesis.
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Affiliation(s)
- Hyun-Sook Park
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland
| | - Eirini Papanastasi
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland
| | - Gabriela Blanchard
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland
| | - Elena Chiticariu
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland
| | - Daniel Bachmann
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland
| | - Markus Plomann
- Center for Biochemistry, University of Cologne, Cologne, Germany
| | | | - Pierre Vabres
- Department of Dermatology, CHU, Hôpital du Bocage, Dijon, France
| | - Asma Smahi
- Paris Descartes University, Sorbonne Paris Cité, Paris, France.,IMAGINE Institute INSERM UMR 1163, Paris, France
| | - Marcel Huber
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland
| | - Christine Pich
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland
| | - Daniel Hohl
- Department of Dermatology, CHUV-FBM UNIL, Hôpital de Beaumont, Lausanne, Switzerland.
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23
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Lu H, Liu J, Feng T, Guo Z, Yin Y, Gao F, Cao G, Du X, Wu S. A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor. Genome Res 2021; 31:900-909. [PMID: 33795333 PMCID: PMC8092013 DOI: 10.1101/gr.271312.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Targeted mutagenesis in model organisms is key for gene functional annotation and biomedical research. Despite technological advances in gene editing by the CRISPR-Cas9 systems, rapid and efficient introduction of site-directed mutations remains a challenge in large animal models. Here, we developed a robust and flexible insertional mutagenesis strategy, homology-independent targeted trapping (HIT-trapping), which is generic and can efficiently target-trap an endogenous gene of interest independent of homology arm and embryonic stem cells. Further optimization and equipping the HIT-trap donor with a site-specific DNA inversion mechanism enabled one-step generation of reversible and conditional alleles in a single experiment. As a proof of concept, we successfully created mutant alleles for 21 disease-related genes in primary porcine fibroblasts with an average knock-in frequency of 53.2%, a great improvement over previous approaches. The versatile HIT-trapping strategy presented here is expected to simplify the targeted generation of mutant alleles and facilitate large-scale mutagenesis in large mammals such as pigs.
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Affiliation(s)
- Hengxing Lu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jun Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tao Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610200, China
| | - Zihang Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yunjun Yin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fei Gao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Gengsheng Cao
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Science, Henan University, Kaifeng 475004, China
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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24
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Ishida Y, Kobayashi T, Chiba S, Katoh Y, Nakayama K. Molecular basis of ciliary defects caused by compound heterozygous IFT144/WDR19 mutations found in cranioectodermal dysplasia. Hum Mol Genet 2021; 30:213-225. [PMID: 33517396 DOI: 10.1093/hmg/ddab034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/28/2020] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Primary cilia contain specific proteins to achieve their functions as cellular antennae. Ciliary protein trafficking is mediated by the intraflagellar transport (IFT) machinery containing the IFT-A and IFT-B complexes. Mutations in genes encoding the IFT-A subunits (IFT43, IFT121/WDR35, IFT122, IFT139/TTC21B, IFT140 and IFT144/WDR19) often result in skeletal ciliopathies, including cranioectodermal dysplasia (CED). We here characterized the molecular and cellular defects of CED caused by compound heterozygous mutations in IFT144 [the missense variant IFT144(L710S) and the nonsense variant IFT144(R1103*)]. These two variants were distinct with regard to their interactions with other IFT-A subunits and with the IFT-B complex. When exogenously expressed in IFT144-knockout (KO) cells, IFT144(L710S) as well as IFT144(WT) rescued both moderately compromised ciliogenesis and the abnormal localization of ciliary proteins. As the homozygous IFT144(L710S) mutation was found to cause autosomal recessive retinitis pigmentosa, IFT144(L710S) is likely to be hypomorphic at the cellular level. In striking contrast, the exogenous expression of IFT144(R1103*) in IFT144-KO cells exacerbated the ciliogenesis defects. The expression of IFT144(R1103*) together with IFT144(WT) restored the abnormal phenotypes of IFT144-KO cells. However, the coexpression of IFT144(R1103*) with the hypomorphic IFT144(L710S) variant in IFT144-KO cells, which mimics the genotype of compound heterozygous CED patients, resulted in severe ciliogenesis defects. Taken together, these observations demonstrate that compound heterozygous mutations in IFT144 cause severe ciliary defects via a complicated mechanism, where one allele can cause severe ciliary defects when combined with a hypomorphic allele.
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Affiliation(s)
- Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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25
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Qiu H, Fujisawa S, Nozaki S, Katoh Y, Nakayama K. Interaction of INPP5E with ARL13B is essential for its ciliary membrane retention but dispensable for its ciliary entry. Biol Open 2021; 10:bio057653. [PMID: 33372066 PMCID: PMC7860134 DOI: 10.1242/bio.057653] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Compositions of proteins and lipids within cilia and on the ciliary membrane are maintained to be distinct from those of the cytoplasm and plasma membrane, respectively, by the presence of the ciliary gate. INPP5E is a phosphoinositide 5-phosphatase that is localized on the ciliary membrane by anchorage via its C-terminal prenyl moiety. In addition, the ciliary membrane localization of INPP5E is determined by the small GTPase ARL13B. However, it remained unclear as to how ARL13B participates in the localization of INPP5E. We here show that wild-type INPP5E, INPP5E(WT), in ARL13B-knockout cells and an INPP5E mutant defective in ARL13B binding, INPP5E(ΔCTS), in control cells were unable to show steady-state localization on the ciliary membrane. However, not only INPP5E(WT) but also INPP5E(ΔCTS) was able to rescue the abnormal localization of ciliary proteins in INPP5E-knockout cells. Analysis using the chemically induced dimerization system demonstrated that INPP5E(WT) in ARL13B-knockout cells and INPP5E(ΔCTS) in control cells were able to enter cilia, but neither was retained on the ciliary membrane due to the lack of the INPP5E-ARL13B interaction. Thus, our data demonstrate that binding of INPP5E to ARL13B is essential for its steady-state localization on the ciliary membrane but is dispensable for its entry into cilia.
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Affiliation(s)
- Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sayaka Fujisawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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26
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Role of ferritinophagy in cystine deprivation-induced cell death in glioblastoma cells. Biochem Biophys Res Commun 2021; 539:56-63. [PMID: 33421769 DOI: 10.1016/j.bbrc.2020.12.075] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 12/11/2022]
Abstract
Ferroptosis is a form of cell death caused by iron-dependent lipid peroxidation. Cancer cells increase cystine uptake for the synthesis of glutathione (GSH), which is used by glutathione peroxidase 4 to reduce lipid peroxides. Here, we report that cystine deprivation in glioblastoma cells, but not inhibition of GSH synthesis by l-buthionine sulfoximine (BSO), induces ferroptosis. We found that cystine deprivation decreased the protein levels of ferritin heavy chain FTH1, whereas it was increased by BSO treatment. The lysosome inhibitor bafilomycin A1 or deletion of nuclear receptor coactivator 4 (NCOA4) inhibited cystine deprivation-induced decrease in FTH1 protein levels and cell death. In addition, cystine deprivation induced microtubule-associated protein light chain 3 (LC3)-II protein accumulation, suggesting that cystine deprivation induces ferritinophagy. BSO causes cell death when glioblastoma cells are treated with iron inducers, ferrous ammonium sulfate or hemin. On the other hand, cystine deprivation-induced degradation of FTH1 and cell death required glutamine. This study suggests that ferritinophagy, in addition to GSH depletion, plays an important role in cystine deprivation-induced ferroptosis in glioblastoma cells.
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27
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Abstract
Functional characterizations and molecular dissections of long noncoding RNAs (lncRNAs) are critical to understand their involvement in the cellular regulatory network. LncRNAs exert their effects through functional RNA domains that interact with other molecules, including proteins, DNA, and RNA. Here, we describe experimental procedures for generating genomic deletions in a human haploid cell line using the CRISPR/Cas9 system. This method can be applied to examine functions of lncRNAs and their domains by establishing knockout and partial deletion mutant cell lines. In addition, we describe a CRISPR-mediated knockin method for artificial tethering of partner RNA-binding proteins to lncRNAs and its use to validate lncRNA-mediated functions.
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28
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Kobayashi T, Ishida Y, Hirano T, Katoh Y, Nakayama K. Cooperation of the IFT-A complex with the IFT-B complex is required for ciliary retrograde protein trafficking and GPCR import. Mol Biol Cell 2021; 32:45-56. [PMID: 33175651 PMCID: PMC8098818 DOI: 10.1091/mbc.e20-08-0556] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Cilia sense and transduce extracellular signals via specific receptors. The intraflagellar transport (IFT) machinery mediates not only bidirectional protein trafficking within cilia but also the import/export of ciliary proteins across the ciliary gate. The IFT machinery is known to comprise two multisubunit complexes, namely, IFT-A and IFT-B; however, little is known about how the two complexes cooperate to mediate ciliary protein trafficking. We here show that IFT144-IFT122 from IFT-A and IFT88-IFT52 from IFT-B make major contributions to the interface between the two complexes. Exogenous expression of the IFT88(Δα) mutant, which has decreased binding to IFT-A, partially restores the ciliogenesis defect of IFT88-knockout (KO) cells. However, IFT88(Δα)-expressing IFT88-KO cells demonstrate a defect in IFT-A entry into cilia, aberrant accumulation of IFT-B proteins at the bulged ciliary tips, and impaired import of ciliary G protein-coupled receptors (GPCRs). Furthermore, overaccumulated IFT proteins at the bulged tips appeared to be released as extracellular vesicles. These phenotypes of IFT88(Δα)-expressing IFT88-KO cells resembled those of IFT144-KO cells. These observations together indicate that the IFT-A complex cooperates with the IFT-B complex to mediate the ciliary entry of GPCRs as well as retrograde trafficking of the IFT machinery from the ciliary tip.
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Affiliation(s)
- Takuya Kobayashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yamato Ishida
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Tomoaki Hirano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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29
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Nakamura K, Noguchi T, Takahara M, Omori Y, Furukawa T, Katoh Y, Nakayama K. Anterograde trafficking of ciliary MAP kinase-like ICK/CILK1 by the intraflagellar transport machinery is required for intraciliary retrograde protein trafficking. J Biol Chem 2020; 295:13363-13376. [PMID: 32732286 PMCID: PMC7504932 DOI: 10.1074/jbc.ra120.014142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
ICK (also known as CILK1) is a mitogen-activated protein kinase-like kinase localized at the ciliary tip. Its deficiency is known to result in the elongation of cilia and causes ciliopathies in humans. However, little is known about how ICK is transported to the ciliary tip. We here show that the C-terminal noncatalytic region of ICK interacts with the intraflagellar transport (IFT)-B complex of the IFT machinery and participates in its transport to the ciliary tip. Furthermore, total internal reflection fluorescence microscopy demonstrated that ICK undergoes bidirectional movement within cilia, similarly to IFT particles. Analysis of ICK knockout cells demonstrated that ICK deficiency severely impairs the retrograde trafficking of IFT particles and ciliary G protein-coupled receptors. In addition, we found that in ICK knockout cells, ciliary proteins are accumulated at the bulged ciliary tip, which appeared to be torn off and released into the environment as an extracellular vesicle. The exogenous expression of various ICK constructs in ICK knockout cells indicated that the IFT-dependent transport of ICK, as well as its kinase activity and phosphorylation at the canonical TDY motif, is essential for ICK function. Thus, we unequivocally show that ICK transported to the ciliary tip is required for retrograde ciliary protein trafficking and consequently for normal ciliary function.
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Affiliation(s)
- Kentaro Nakamura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mariko Takahara
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshihiro Omori
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
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30
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Okazaki M, Kobayashi T, Chiba S, Takei R, Liang L, Nakayama K, Katoh Y. Formation of the B9-domain protein complex MKS1-B9D2-B9D1 is essential as a diffusion barrier for ciliary membrane proteins. Mol Biol Cell 2020; 31:2259-2268. [PMID: 32726168 PMCID: PMC7550698 DOI: 10.1091/mbc.e20-03-0208] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 01/20/2023] Open
Abstract
Cilia are plasma membrane protrusions that act as cellular antennae and propellers in eukaryotes. To achieve their sensory and motile functions, cilia maintain protein and lipid compositions that are distinct from those of the cell body. The transition zone (TZ) is a specialized region located at the ciliary base, which functions as a barrier separating the interior and exterior of cilia. The TZ comprises a number of transmembrane and soluble proteins. Meckel syndrome (MKS)1, B9 domain (B9D)1/MKS9, and B9D2/MKS10 are soluble TZ proteins that are encoded by causative genes of MKS and have a B9D in common. We here demonstrate the interaction mode of these B9D proteins to be MKS1-B9D2-B9D1 and demonstrate their interdependent localization to the TZ. Phenotypic analyses of MKS1-knockout (KO) and B9D2-KO cells show that the B9D proteins are involved in, although not essential for, normal cilia biogenesis. Rescue experiments of these KO cells show that formation of the B9D protein complex is crucial for creating a diffusion barrier for ciliary membrane proteins.
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Affiliation(s)
- Misato Okazaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Ryota Takei
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Luxiaoxue Liang
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Katoh Y, Chiba S, Nakayama K. Practical method for superresolution imaging of primary cilia and centrioles by expansion microscopy using an amplibody for fluorescence signal amplification. Mol Biol Cell 2020; 31:2195-2206. [PMID: 32726175 PMCID: PMC7550703 DOI: 10.1091/mbc.e20-04-0250] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Primary cilia are microtubule-based protrusions from the cell surface that are approximately 0.3 µm in diameter and 3 µm in length. Because size approximates the optical diffraction limit, ciliary structures at the subdiffraction level can be observed only by using a superresolution microscope or electron microscope. Expansion microscopy (ExM) is an alternative superresolution imaging technique that uses a swellable hydrogel that enables the physical expansion of specimens. However, the efficacy of ExM has not been fully verified, and further improvements in the method are anticipated. In this study, we applied ExM to the observation of primary cilia and centrioles and compared the acquired images with those obtained using conventional superresolution microscopy. Furthermore, we developed a new tool, called the amplibody, for fluorescence signal amplification, to compensate for the substantial decrease in fluorescence signal per unit volume inherent to physical expansion and for the partial proteolytic digestion of cellular proteins before expansion. We also demonstrate that the combinatorial use of the ExM protocol optimized for amplibodies and Airyscan superresolution microscopy enables the practical observation of cilia and centrioles with high brightness and resolution.
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Affiliation(s)
- Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Graduate School of Medicine, Osaka City University, Asahi-machi, 1-4-3 Abeno, Osaka 545-8585, Japan
| | - Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Oguchi ME, Okuyama K, Homma Y, Fukuda M. A comprehensive analysis of Rab GTPases reveals a role for Rab34 in serum starvation-induced primary ciliogenesis. J Biol Chem 2020; 295:12674-12685. [PMID: 32669361 DOI: 10.1074/jbc.ra119.012233] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 07/14/2020] [Indexed: 12/17/2022] Open
Abstract
Primary cilia are sensors of chemical and mechanical signals in the extracellular environment. The formation of primary cilia (i.e. ciliogenesis) requires dynamic membrane trafficking events, and several Rab small GTPases, key regulators of membrane trafficking, have recently been reported to participate in ciliogenesis. However, the precise mechanisms of Rab-mediated membrane trafficking during ciliogenesis remain largely unknown. In the present study, we used a collection of siRNAs against 62 human Rabs to perform a comprehensive knockdown screening for Rabs that regulate serum starvation-induced ciliogenesis in human telomerase reverse transcriptase retinal pigment epithelium 1 (hTERT-RPE1) cells and succeeded in identifying Rab34 as an essential Rab. Knockout (KO) of Rab34, but not of Rabs previously reported to regulate ciliogenesis (e.g. Rab8 and Rab10) in hTERT-RPE1 cells, drastically impaired serum starvation-induced ciliogenesis. Rab34 was also required for serum starvation-induced ciliogenesis in NIH/3T3 cells and MCF10A cells but not for ciliogenesis in Madin-Darby canine kidney (MDCK)-II cysts. We then attempted to identify a specific region(s) of Rab34 that is essential for ciliogenesis by performing deletion and mutation analyses of Rab34. Unexpectedly, instead of a specific sequence in the switch II region, which is generally important for recognizing effector proteins (e.g. Rab interacting lysosomal protein [RILP]), a unique long N-terminal region of Rab34 before the conserved GTPase domain was found to be essential. These findings suggest that Rab34 is an atypical Rab that regulates serum starvation-induced ciliogenesis through its unique N-terminal region.
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Affiliation(s)
- Mai E Oguchi
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, Japan
| | - Koki Okuyama
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, Japan
| | - Yuta Homma
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, Japan
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Buck TM, Wijnholds J. Recombinant Adeno-Associated Viral Vectors (rAAV)-Vector Elements in Ocular Gene Therapy Clinical Trials and Transgene Expression and Bioactivity Assays. Int J Mol Sci 2020; 21:E4197. [PMID: 32545533 PMCID: PMC7352801 DOI: 10.3390/ijms21124197] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Inherited retinal dystrophies and optic neuropathies cause chronic disabling loss of visual function. The development of recombinant adeno-associated viral vectors (rAAV) gene therapies in all disease fields have been promising, but the translation to the clinic has been slow. The safety and efficacy profiles of rAAV are linked to the dose of applied vectors. DNA changes in the rAAV gene cassette affect potency, the expression pattern (cell-specificity), and the production yield. Here, we present a library of rAAV vectors and elements that provide a workflow to design novel vectors. We first performed a meta-analysis on recombinant rAAV elements in clinical trials (2007-2020) for ocular gene therapies. We analyzed 33 unique rAAV gene cassettes used in 57 ocular clinical trials. The rAAV gene therapy vectors used six unique capsid variants, 16 different promoters, and six unique polyadenylation sequences. Further, we compiled a list of promoters, enhancers, and other sequences used in current rAAV gene cassettes in preclinical studies. Then, we give an update on pro-viral plasmid backbones used to produce the gene therapy vectors, inverted terminal repeats, production yield, and rAAV safety considerations. Finally, we assess rAAV transgene and bioactivity assays applied to cells or organoids in vitro, explants ex vivo, and clinical studies.
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Affiliation(s)
- Thilo M. Buck
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands;
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands;
- Netherlands Institute of Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands
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Nakayama K, Katoh Y. Architecture of the IFT ciliary trafficking machinery and interplay between its components. Crit Rev Biochem Mol Biol 2020; 55:179-196. [PMID: 32456460 DOI: 10.1080/10409238.2020.1768206] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cilia and flagella serve as cellular antennae and propellers in various eukaryotic cells, and contain specific receptors and ion channels as well as components of axonemal microtubules and molecular motors to achieve their sensory and motile functions. Not only the bidirectional trafficking of specific proteins within cilia but also their selective entry and exit across the ciliary gate is mediated by the intraflagellar transport (IFT) machinery with the aid of motor proteins. The IFT-B complex, which is powered by the kinesin-2 motor, mediates anterograde protein trafficking from the base to the tip of cilia, whereas the IFT-A complex together with the dynein-2 complex mediates retrograde protein trafficking. The BBSome complex connects ciliary membrane proteins to the IFT machinery. Defects in any component of this trafficking machinery lead to abnormal ciliogenesis and ciliary functions, and results in a broad spectrum of disorders, collectively called the ciliopathies. In this review article, we provide an overview of the architectures of the components of the IFT machinery and their functional interplay in ciliary protein trafficking.
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Affiliation(s)
- Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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Bosch JA, Colbeth R, Zirin J, Perrimon N. Gene Knock-Ins in Drosophila Using Homology-Independent Insertion of Universal Donor Plasmids. Genetics 2020; 214:75-89. [PMID: 31685521 PMCID: PMC6944404 DOI: 10.1534/genetics.119.302819] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/25/2019] [Indexed: 11/18/2022] Open
Abstract
Targeted genomic knock-ins are a valuable tool to probe gene function. However, knock-in methods involving homology-directed repair (HDR) can be laborious. Here, we adapt the mammalian CRISPaint [clustered regularly interspaced short palindromic repeat (CRISPR)-assisted insertion tagging] homology-independent knock-in method for Drosophila melanogaster, which uses CRISPR/Cas9 and nonhomologous end joining to insert "universal" donor plasmids into the genome. Using this method in cultured S2R+ cells, we efficiently tagged four endogenous proteins with the bright fluorescent protein mNeonGreen, thereby demonstrating that an existing collection of CRISPaint universal donor plasmids is compatible with insect cells. In addition, we inserted the transgenesis marker 3xP3-red fluorescent protein into seven genes in the fly germ line, producing heritable loss-of-function alleles that were isolated by simple fluorescence screening. Unlike in cultured cells, insertions/deletions always occurred at the genomic insertion site, which prevents predictably matching the insert coding frame to the target gene. Despite this effect, we were able to isolate T2A-Gal4 insertions in four genes that serve as in vivo expression reporters. Therefore, homology-independent insertion in Drosophila is a fast and simple alternative to HDR that will enable researchers to dissect gene function.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Ryan Colbeth
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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Stroik S, Kurtz K, Hendrickson EA. CtIP is essential for telomere replication. Nucleic Acids Res 2019; 47:8927-8940. [PMID: 31378812 PMCID: PMC6755089 DOI: 10.1093/nar/gkz652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
The maintenance of telomere length is critical to longevity and survival. Specifically, the failure to properly replicate, resect, and/or form appropriate telomeric structures drives telomere shortening and, in turn, genomic instability. The endonuclease CtIP is a DNA repair protein that is well-known to promote genome stability through the resection of endogenous DNA double-stranded breaks. Here, we describe a novel role for CtIP. We show that in the absence of CtIP, human telomeres shorten rapidly to non-viable lengths. This telomere dysfunction results in an accumulation of fusions, breaks, and frank telomere loss. Additionally, CtIP suppresses the generation of circular, extrachromosomal telomeric DNA. These latter structures appear to arise from arrested DNA replication forks that accumulate in the absence of CtIP. Hence, CtIP is required for faithful replication through telomeres via its roles at stalled replication tracts. Our findings demonstrate a new role for CtIP as a protector of human telomere integrity.
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Affiliation(s)
- Susanna Stroik
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kevin Kurtz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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Shohayeb B, Ho U, Yeap YY, Parton RG, Millard SS, Xu Z, Piper M, Ng DCH. The association of microcephaly protein WDR62 with CPAP/IFT88 is required for cilia formation and neocortical development. Hum Mol Genet 2019; 29:248-263. [DOI: 10.1093/hmg/ddz281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023] Open
Abstract
Abstract
WDR62 mutations that result in protein loss, truncation or single amino-acid substitutions are causative for human microcephaly, indicating critical roles in cell expansion required for brain development. WDR62 missense mutations that retain protein expression represent partial loss-of-function mutants that may therefore provide specific insights into radial glial cell processes critical for brain growth. Here we utilized CRISPR/Cas9 approaches to generate three strains of WDR62 mutant mice; WDR62 V66M/V66M and WDR62R439H/R439H mice recapitulate conserved missense mutations found in humans with microcephaly, with the third strain being a null allele (WDR62stop/stop). Each of these mutations resulted in embryonic lethality to varying degrees and gross morphological defects consistent with ciliopathies (dwarfism, anophthalmia and microcephaly). We find that WDR62 mutant proteins (V66M and R439H) localize to the basal body but fail to recruit CPAP. As a consequence, we observe deficient recruitment of IFT88, a protein that is required for cilia formation. This underpins the maintenance of radial glia as WDR62 mutations caused premature differentiation of radial glia resulting in reduced generation of neurons and cortical thinning. These findings highlight the important role of the primary cilium in neocortical expansion and implicate ciliary dysfunction as underlying the pathology of MCPH2 patients.
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Affiliation(s)
- Belal Shohayeb
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Uda Ho
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Yvonne Y Yeap
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia 4072, Australia
| | - S Sean Millard
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Michael Piper
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
| | - Dominic C H Ng
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, St Lucia 4072, Australia
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Katoh Y. [Architectures and functions of motor proteins underlying the intraflagellar transport machinery]. Nihon Yakurigaku Zasshi 2019; 154:186-191. [PMID: 31597897 DOI: 10.1254/fpj.154.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Primary cilia, which protrude from the surfaces of most human cells, function as cellular antennae that receive extracellular signals. To serve as antennae, primary cilia contain unique proteins, such as G-protein-coupled receptors and ion channels. Defects in the assembly and functions of primary cilia cause hereditary disorders with a wide range of symptoms, including cystic kidney and retinal degeneration. The assembly and maintenance of cilia depend on protein trafficking mediated by the intraflagellar transport (IFT) machinery, which contains three protein complexes (IFT-A, IFT-B, and BBSome) and two motor proteins (kinesin-2 and dynein-2 complex) and is composed of more than 40 subunits in total. We recently revealed the interaction between the kinesin-2 and IFT-B complexes and overall architecture of the dynein-2 complex by taking advantage of the visible immunoprecipitation (VIP) assay. In addition, we clarified the roles of dynein-2 subunits using gene knockout cell lines established using the CRISPR/Cas9 system. This review focuses on recent advances in the architectures and functions of two motor proteins underlying the IFT machinery.
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Affiliation(s)
- Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University
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Li L, Meng H, Zou Q, Zhang J, Cai L, Yang B, Weng J, Lai L, Yang H, Gao Y. Establishment of gene-edited pigs expressing human blood-coagulation factor VII and albumin for bioartificial liver use. J Gastroenterol Hepatol 2019; 34:1851-1859. [PMID: 30884543 DOI: 10.1111/jgh.14666] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND AND AIM Bioartificial livers (BALs) are considered as a solution to bridge patients with acute liver failure to liver transplantation or to assist in spontaneous recovery for patients with end-stage liver disease. Pig is the best donor of hepatocytes for BALs in clinical trials, because metabolic and detoxification function of its liver are close to human. However, using pig hepatocytes for BALs remains controversial for safety concern owing to nonhuman proteins secretion. Herein, we attempt to establish modified pigs expressing humanized liver proteins, blood-coagulation factor VII (F7), and albumin (ALB). These pigs should also be porcine endogenous retrovirus subtype C (PERV-C) free so that their ability of transmitting PERV to human could be diminished seriously. METHODS We devised both homology-dependent and independent knock-in approaches to insert a fusion of hF7 and hALB gene downstream the site of pig endogenous F7 promoter in pig fetal fibroblasts negative for PERV-C. The modified pigs were then generated through somatic cell nuclear transfer. RESULTS We obtained 14 and 10 cloned pigs by homology-dependent and independent approaches, respectively. Among them, 19 cloned pigs were with expected gene modification and 13 are alive to date. These modified pigs can successfully express hF7 and hALB in the liver and serum, and the expressed hF7 exhibits normal coagulation activity. CONCLUSIONS The gene-edited pigs expressing hF7 and hALB in the liver were generated successfully. We anticipate that our pigs could provide an alternative cell source for BALs as a promising treatment for patients with acute liver failure.
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Affiliation(s)
- Li Li
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hongyi Meng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qingjian Zou
- School of Chemical and Environmental Engineering, Wuyi University, Jiangmen, China
| | - Jianmin Zhang
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Cai
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Bin Yang
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jun Weng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Liangxue Lai
- South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Huaqiang Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yi Gao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Nozaki S, Castro Araya RF, Katoh Y, Nakayama K. Requirement of IFT-B-BBSome complex interaction in export of GPR161 from cilia. Biol Open 2019; 8:bio043786. [PMID: 31471295 PMCID: PMC6777367 DOI: 10.1242/bio.043786] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/24/2019] [Indexed: 12/22/2022] Open
Abstract
The intraflagellar transport (IFT) machinery, which includes the IFT-A and IFT-B complexes, mediates bidirectional trafficking of ciliary proteins. In addition to these complexes, the BBSome, which is composed of eight subunits that are encoded by the causative genes of Bardet-Biedl syndrome (BBS), has been proposed to connect the IFT machinery to ciliary membrane proteins, such as G protein-coupled receptors, to mediate their export from cilia. However, little is known about the connection between the IFT machinery and the BBSome. Using the visible immunoprecipitation assay, we here identified the interaction between IFT38 from the IFT-B complex and BBS1, BBS2 and BBS9 from the BBSome. Furthermore, by analyzing phenotypes of IFT38-knockout cells exogenously expressing wild-type IFT38 or its mutant lacking the ability to interact with BBS1+BBS2+BBS9, we showed that knockout cells expressing the IFT38 mutant have restored ciliogenesis; however, similar to BBS1-knockout cells, they demonstrated significant accumulation of GPR161 within cilia upon stimulation of Hedgehog signaling. These results indicate that the IFT-B-BBSome interaction is required for the export of GPR161 across the ciliary gate.
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Affiliation(s)
- Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Roiner Francisco Castro Araya
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Qin J, Yang T, Zeng N, Wan C, Gao L, Li X, Chen L, Shen Y, Wen F. Differential coexpression networks in bronchiolitis and emphysema phenotypes reveal heterogeneous mechanisms of chronic obstructive pulmonary disease. J Cell Mol Med 2019; 23:6989-6999. [PMID: 31419013 PMCID: PMC6787516 DOI: 10.1111/jcmm.14585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 06/23/2019] [Accepted: 07/14/2019] [Indexed: 02/05/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease with multiple molecular mechanisms. To investigate and contrast the molecular processes differing between bronchiolitis and emphysema phenotypes of COPD, we downloaded the GSE69818 microarray data set from the Gene Expression Omnibus (GEO), which based on lung tissues from 38 patients with emphysema and 32 patients with bronchiolitis. Then, weighted gene coexpression network analysis (WGCNA) and differential coexpression (DiffCoEx) analysis were performed, followed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analysis (KEGG) analysis. Modules and hub genes for bronchiolitis and emphysema were identified, and we found that genes in modules linked to neutrophil degranulation, Rho protein signal transduction and B cell receptor signalling were coexpressed in emphysema. DiffCoEx analysis showed that four hub genes (IFT88, CCDC103, MMP10 and Bik) were consistently expressed in emphysema patients; these hub genes were enriched, respectively, for functions of cilium assembly and movement, proteolysis and apoptotic mitochondrial changes. In our re‐analysis of GSE69818, gene expression networks in relation to emphysema deepen insights into the molecular mechanism of COPD and also identify some promising therapeutic targets.
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Affiliation(s)
- Jiangyue Qin
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Ting Yang
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Ni Zeng
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Chun Wan
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Lijuan Gao
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoou Li
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Lei Chen
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Yongchun Shen
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
| | - Fuqiang Wen
- Division of Pulmonary Diseases, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy of China, West China Hospital of Sichuan University, Chengdu, China
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Rozov SM, Permyakova NV, Deineko EV. The Problem of the Low Rates of CRISPR/Cas9-Mediated Knock-ins in Plants: Approaches and Solutions. Int J Mol Sci 2019; 20:E3371. [PMID: 31323994 PMCID: PMC6651222 DOI: 10.3390/ijms20133371] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
The main number of genome editing events in plant objects obtained during the last decade with the help of specific nucleases zinc finger (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas are the microindels causing frameshift and subsequent gene knock-out. The knock-ins of genes or their parts, i.e., the insertion of them into a target genome region, are between one and two orders of magnitude less frequent. First and foremost, this is associated with the specific features of the repair systems of higher eukaryotes and the availability of the donor template in accessible proximity during double-strand break (DSB) repair. This review briefs the main repair pathways in plants according to the aspect of their involvement in genome editing. The main methods for increasing the frequency of knock-ins are summarized both along the homologous recombination pathway and non-homologous end joining, which can be used for plant objects.
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Affiliation(s)
- Serge M Rozov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Natalya V Permyakova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Deineko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Plant Physiology and Biotechnology, Tomsk State University, Tomsk 634050, Russia
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43
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Teramoto K, Katoh H. The cystine/glutamate antiporter xCT is a key regulator of EphA2 S897 phosphorylation under glucose-limited conditions. Cell Signal 2019; 62:109329. [PMID: 31152846 DOI: 10.1016/j.cellsig.2019.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 01/06/2023]
Abstract
EphA2, which belongs to the Eph family of receptor tyrosine kinases, is overexpressed in a variety of human cancers. Serine 897 (S897) phosphorylation of EphA2 is known to promote cancer cell migration and proliferation in a ligand-independent manner. In this study, we show that glucose deprivation induces S897 phosphorylation of EphA2 in glioblastoma cells. The phosphorylation requires the activity of the cystine/glutamate antiporter xCT and reactive oxygen species (ROS)-dependent ERK and RSK activation. Furthermore, depletion of EphA2 in glioblastoma cells leads to decreased cell viability under glucose starvation. Our results suggest a role of EphA2 in glioblastoma cell viability under glucose-limited conditions.
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Affiliation(s)
- Koji Teramoto
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hironori Katoh
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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44
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Takahara M, Kunii M, Nakamura K, Harada A, Hirano T, Katoh Y, Nakayama K. C11ORF74 interacts with the IFT-A complex and participates in ciliary BBSome localization. J Biochem 2019; 165:257-267. [PMID: 30476139 DOI: 10.1093/jb/mvy100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/20/2018] [Indexed: 12/18/2022] Open
Abstract
Cilia are organelles that serve as cellular antennae. Intraflagellar transport particles containing the IFT-A and IFT-B complexes mediate bidirectional trafficking of ciliary proteins. Particularly, in concert with the BBSome complex, IFT particles play an essential role in trafficking of ciliary G-protein-coupled receptors (GPCRs). Therefore, proteins interacting with the IFT components are potential regulators of ciliary protein trafficking. We here revealed that an uncharacterized protein, C11ORF74, interacts with the IFT-A complex via the IFT122 subunit and is accumulated at the distal tip in the absence of an IFT-A subunit IFT139, suggesting that at least a fraction of C11ORF74 molecules can be transported towards the ciliary tip by associating with the IFT-A complex, although its majority might be out of cilia at steady state. In C11ORF74-knockout (KO) cells, the BBSome components cannot enter cilia. However, trafficking of Smoothened or GPR161, both of which are ciliary GPCRs involved in Hedgehog signalling and undergo BBSome-dependent trafficking, was not affected in the absence of C11ORF74. In addition, C11orf74/B230118H07Rik- KO mice demonstrated no obvious anatomical abnormalities associated with ciliary dysfunctions. Given that C11ORF74 is conserved across vertebrates, but not found in other ciliated organisms, such as nematodes and Chlamydomonas, it might play limited roles involving cilia.
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Affiliation(s)
- Mariko Takahara
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-ku, Kyoto, Japan
| | - Masataka Kunii
- Department of Cell Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
| | - Kentaro Nakamura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-ku, Kyoto, Japan
| | - Akihiro Harada
- Department of Cell Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, Japan
| | - Tomoaki Hirano
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-ku, Kyoto, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-ku, Kyoto, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-ku, Kyoto, Japan
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45
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Tsurumi Y, Hamada Y, Katoh Y, Nakayama K. Interactions of the dynein-2 intermediate chain WDR34 with the light chains are required for ciliary retrograde protein trafficking. Mol Biol Cell 2019; 30:658-670. [PMID: 30649997 PMCID: PMC6589695 DOI: 10.1091/mbc.e18-10-0678] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/02/2019] [Accepted: 01/08/2019] [Indexed: 01/20/2023] Open
Abstract
The dynein-2 complex drives retrograde ciliary protein trafficking by associating with the intraflagellar transport (IFT) machinery, containing IFT-A and IFT-B complexes. We recently showed that the dynein-2 complex, which comprises 11 subunits, can be divided into three subcomplexes: DYNC2H1-DYNC2LI1, WDR34-DYNLL1/DYNLL2-DYNLRB1/DYNLRB2, and WDR60-TCTEX1D2-DYNLT1/DYNLT3. In this study, we demonstrated that the WDR34 intermediate chain interacts with the two light chains, DYNLL1/DYNLL2 and DYNLRB1/DYNLRB2, via its distinct sites. Phenotypic analyses of WDR34-knockout cells exogenously expressing various WDR34 constructs showed that the interactions of the WDR34 intermediate chain with the light chains are crucial for ciliary retrograde protein trafficking. Furthermore, we found that expression of the WDR34 N-terminal construct encompassing the light chain-binding sites but lacking the WD40 repeat domain inhibits ciliary biogenesis and retrograde trafficking in a dominant-negative manner, probably by sequestering WDR60 or the light chains. Taken together with phenotypic differences of several WDR34-knockout cell lines, these results indicate that incorporation of DYNLL1/DYNLL2 and DYNLRB1/DYNLRB2 into the dynein-2 complex via interactions with the WDR34 intermediate chain is crucial for dynein-2 function in retrograde ciliary protein trafficking.
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Affiliation(s)
- Yuta Tsurumi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Hamada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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46
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Toyama M, Hamaoka Y, Katoh H. EphA3 is up-regulated by epidermal growth factor and promotes formation of glioblastoma cell aggregates. Biochem Biophys Res Commun 2019; 508:715-721. [PMID: 30528229 DOI: 10.1016/j.bbrc.2018.12.002] [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: 11/22/2018] [Accepted: 12/01/2018] [Indexed: 11/27/2022]
Abstract
EphA3, a member of the Eph family of receptor tyrosine kinases, has been reported to be overexpressed in some human cancers including glioblastoma. Here, we found that expression of EphA3 is up-regulated in response to epidermal growth factor (EGF) stimulation and promotes formation of cell aggregates in suspension culture of glioblastoma cells. Suppression of EphA3 expression by short hairpin RNA-mediated knockdown or CRISPR/Cas9-mediated gene deletion inhibited EGF-induced promotion of cell aggregate formation, whereas overexpression of EphA3 promoted formation of cell aggregates in suspension culture. EGF-induced EphA3 expression and promotion of cell aggregate formation required Akt activity. Furthermore, N-cadherin, whose expression was regulated by EGF and EphA3, contributed to the formation of cell aggregates in suspension culture. These results suggest that the regulation of EphA3 expression plays a critical role in glioblastoma cell growth in non-adherent conditions.
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Affiliation(s)
- Moe Toyama
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuho Hamaoka
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hironori Katoh
- Laboratory of Molecular Neurobiology, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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47
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Hsiao CJ, Chang CH, Ibrahim RB, Lin IH, Wang CH, Wang WJ, Tsai JW. Gli2 modulates cell cycle re-entry through autophagy-mediated regulation of the length of primary cilia. J Cell Sci 2018; 131:jcs.221218. [PMID: 30463852 DOI: 10.1242/jcs.221218] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/12/2018] [Indexed: 12/18/2022] Open
Abstract
The primary cilium is a tiny cell protrusion known to transduce key extracellular signals, including those of the sonic hedgehog pathway, which activates Gli transcription factors for various cellular functions. To understand the significance of the Gli2 transcription factor in fibroblasts, we establish a Gli2-knockout NIH3T3 cell line by CRISPR/Cas9 technology. Surprisingly, NIH3T3 fibroblasts lacking Gli2 expression through gene knockout or RNA interference possess longer primary cilia after stimulation of ciliogenesis by serum starvation. This lengthening of primary cilia is associated with enhanced autophagy-mediated Ofd1 degradation, and can be reversed by pharmacological and genetic inhibition of autophagy. Meanwhile, flow cytometry reveals that Gli2-/- NIH3T3 fibroblasts exhibit a delay in cell cycle re-entry after serum re-stimulation. Ablation of their primary cilia through Kif3a knockdown rescues the delay in cell cycle re-entry. These results suggest that Gli2 plays an unexpected role in cell cycle re-entry through an autophagy-mediated regulation on ciliary length in fibroblasts.
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Affiliation(s)
- Ching-Ju Hsiao
- Institute of Brain Science, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Chia-Hsiang Chang
- Institute of Brain Science, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan.,Taiwan International Graduate Program (TIGP) in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 112, Taiwan
| | - Ridwan Babatunde Ibrahim
- Institute of Brain Science, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan.,Taiwan International Graduate Program (TIGP) in Interdisciplinary Neuroscience, National Yang-Ming University and Academia Sinica, Taipei 112, Taiwan
| | - I-Hsuan Lin
- Taiwan International Graduate Program (TIGP) in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 112, Taiwan.,Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chun-Hung Wang
- Institute of Brain Science, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Won-Jing Wang
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Jin-Wu Tsai
- Institute of Brain Science, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan .,Brain Research Center (BRC), and Biophotonics and Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
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48
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Duek P, Gateau A, Bairoch A, Lane L. Exploring the Uncharacterized Human Proteome Using neXtProt. J Proteome Res 2018; 17:4211-4226. [DOI: 10.1021/acs.jproteome.8b00537] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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49
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Funabashi T, Katoh Y, Okazaki M, Sugawa M, Nakayama K. Interaction of heterotrimeric kinesin-II with IFT-B-connecting tetramer is crucial for ciliogenesis. J Cell Biol 2018; 217:2867-2876. [PMID: 29903877 PMCID: PMC6080941 DOI: 10.1083/jcb.201801039] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/27/2018] [Accepted: 05/18/2018] [Indexed: 12/31/2022] Open
Abstract
Intraflagellar transport (IFT) is crucial for the assembly and maintenance of cilia and is mediated by IFT particles containing IFT-A and IFT-B complexes. IFT-B powered by heterotrimeric kinesin-II and IFT-A powered by the dynein-2 complex are responsible for anterograde and retrograde protein trafficking, respectively. However, little is known about the molecular basis of the trafficking of these IFT particles regulated by kinesin and dynein motors. Using the visible immunoprecipitation assay, we identified in this study a three-to-four protein interaction involving the kinesin-II trimer KIF3A-KIF3B-KAP3 and the IFT-B-connecting tetramer IFT38-IFT52-IFT57-IFT88; among the kinesin-II subunits, KIF3B contributed mainly to IFT-B binding. Furthermore, we showed that the ciliogenesis defect of KIF3B-knockout cells can be rescued by the exogenous expression of wild-type KIF3B but not by that of its mutant compromised with respect to IFT-B binding. Thus, interaction of heterotrimeric kinesin-II with the IFT-B-connecting tetramer is crucial for ciliogenesis via the powering of IFT particles to move in the anterograde direction.
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Affiliation(s)
- Teruki Funabashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Misato Okazaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Maho Sugawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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50
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Chekuri A, Guru AA, Biswas P, Branham K, Borooah S, Soto-Hermida A, Hicks M, Khan NW, Matsui H, Alapati A, Raghavendra PB, Roosing S, Sarangapani S, Mathavan S, Telenti A, Heckenlively JR, Riazuddin SA, Frazer KA, Sieving PA, Ayyagari R. IFT88 mutations identified in individuals with non-syndromic recessive retinal degeneration result in abnormal ciliogenesis. Hum Genet 2018; 137:447-458. [PMID: 29978320 DOI: 10.1007/s00439-018-1897-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/21/2018] [Indexed: 12/26/2022]
Abstract
Whole genome sequencing (WGS) was performed to identify the variants responsible for inherited retinal degeneration (IRD) in a Caucasian family. Segregation analysis of selected rare variants with pathogenic potential identified a set of compound heterozygous changes p.Arg266*:c.796C>T and p.Ala568Thr:c.1702G>A in the intraflagellar transport protein-88 (IFT88) gene segregating with IRD. Expression of IFT88 with the p.Arg266* and p.Ala568Thr mutations in mIMDC3 cells by transient transfection and in HeLa cells by introducing the mutations using CRISPR-cas9 system suggested that both mutations result in the formation of abnormal ciliary structures. The introduction of the IFT88 p.Arg266* variant in the homozygous state in HeLa cells by CRISPR-Cas9 genome-editing revealed that the mutant transcript undergoes nonsense-mediated decay leading to a significant depletion of IFT88 transcript. Additionally, abnormal ciliogenesis was observed in these cells. These observations suggest that the rare and unique combination of IFT88 alleles observed in this study provide insight into the physiological role of IFT88 in humans and the likely mechanism underlying retinal pathology in the pedigree with IRD.
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Affiliation(s)
- Anil Chekuri
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Aditya A Guru
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Pooja Biswas
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA.,School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Kari Branham
- Ophthalmology and Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, MI, USA
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | | | - Naheed W Khan
- Ophthalmology and Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, MI, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA
| | - Pongali B Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India.,School of Regenerative Medicine, Manipal University-MAHE, Bangalore, India
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Nijmegen Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | | | | | - John R Heckenlively
- Ophthalmology and Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, MI, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Genome Information Sciences, Department of Pediatrics, Rady Children's Hospital, San Diego, CA, USA
| | - Paul A Sieving
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, 9415 Campus Point Drive, JRC 206, La Jolla, CA, 92093, USA.
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