2
|
Takeda Y, Chinen T, Honda S, Takatori S, Okuda S, Yamamoto S, Fukuyama M, Takeuchi K, Tomita T, Hata S, Kitagawa D. Molecular basis promoting centriole triplet microtubule assembly. Nat Commun 2024; 15:2216. [PMID: 38519454 PMCID: PMC10960023 DOI: 10.1038/s41467-024-46454-x] [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: 09/24/2023] [Accepted: 02/28/2024] [Indexed: 03/25/2024] Open
Abstract
The triplet microtubule, a core structure of centrioles crucial for the organization of centrosomes, cilia, and flagella, consists of unclosed incomplete microtubules. The mechanisms of its assembly represent a fundamental open question in biology. Here, we discover that the ciliopathy protein HYLS1 and the β-tubulin isotype TUBB promote centriole triplet microtubule assembly. HYLS1 or a C-terminal tail truncated version of TUBB generates tubulin-based superstructures composed of centriole-like incomplete microtubule chains when overexpressed in human cells. AlphaFold-based structural models and mutagenesis analyses further suggest that the ciliopathy-related residue D211 of HYLS1 physically traps the wobbling C-terminal tail of TUBB, thereby suppressing its inhibitory role in the initiation of the incomplete microtubule assembly. Overall, our findings provide molecular insights into the biogenesis of atypical microtubule architectures conserved for over a billion years.
Collapse
Affiliation(s)
- Yutaka Takeda
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Takumi Chinen
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Shunnosuke Honda
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Shotaro Okuda
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Shohei Yamamoto
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Masamitsu Fukuyama
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Koh Takeuchi
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Shoji Hata
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Daiju Kitagawa
- Laboratory of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| |
Collapse
|
3
|
Curinha A, Huang Z, Anglen T, Strong MA, Gliech CR, Jewett CE, Friskes A, Holland AJ. Centriole structural integrity defects are a crucial feature of Hydrolethalus Syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583733. [PMID: 38496445 PMCID: PMC10942441 DOI: 10.1101/2024.03.06.583733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Hydrolethalus Syndrome (HLS) is a lethal, autosomal recessive ciliopathy caused by the mutation of the conserved centriole protein HYLS1. However, how HYLS1 facilitates the centriole-based templating of cilia is poorly understood. Here, we show that mice harboring the HYLS1 disease mutation die shortly after birth and exhibit developmental defects that recapitulate several manifestations of the human disease. These phenotypes arise from tissue-specific defects in cilia assembly and function caused by a loss of centriole integrity. We show that HYLS1 is recruited to the centriole by CEP120 and functions to recruit centriole inner scaffold proteins that stabilize the centriolar microtubule wall. The HLS mutation disrupts the interaction of HYLS1 with CEP120 leading to HYLS1 displacement and degeneration of the centriole distal end. We propose that tissue-specific defects in centriole integrity caused by the HYLS1 mutation prevent ciliogenesis and drive HLS phenotypes.
Collapse
Affiliation(s)
- Ana Curinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhaoyu Huang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Taylor Anglen
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Margaret A Strong
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin R Gliech
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cayla E Jewett
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anoek Friskes
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
4
|
Zhu X, Ma S, Wong WH. Genetic effects of sequence-conserved enhancer-like elements on human complex traits. Genome Biol 2024; 25:1. [PMID: 38167462 PMCID: PMC10759394 DOI: 10.1186/s13059-023-03142-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The vast majority of findings from human genome-wide association studies (GWAS) map to non-coding sequences, complicating their mechanistic interpretations and clinical translations. Non-coding sequences that are evolutionarily conserved and biochemically active could offer clues to the mechanisms underpinning GWAS discoveries. However, genetic effects of such sequences have not been systematically examined across a wide range of human tissues and traits, hampering progress to fully understand regulatory causes of human complex traits. RESULTS Here we develop a simple yet effective strategy to identify functional elements exhibiting high levels of human-mouse sequence conservation and enhancer-like biochemical activity, which scales well to 313 epigenomic datasets across 106 human tissues and cell types. Combined with 468 GWAS of European (EUR) and East Asian (EAS) ancestries, these elements show tissue-specific enrichments of heritability and causal variants for many traits, which are significantly stronger than enrichments based on enhancers without sequence conservation. These elements also help prioritize candidate genes that are functionally relevant to body mass index (BMI) and schizophrenia but were not reported in previous GWAS with large sample sizes. CONCLUSIONS Our findings provide a comprehensive assessment of how sequence-conserved enhancer-like elements affect complex traits in diverse tissues and demonstrate a generalizable strategy of integrating evolutionary and biochemical data to elucidate human disease genetics.
Collapse
Affiliation(s)
- Xiang Zhu
- Department of Statistics, The Pennsylvania State University, 326 Thomas Building, University Park, 16802, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, 201 Huck Life Sciences Building, University Park, 16802, PA, USA.
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA.
| | - Shining Ma
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road MC5464, Stanford, 94305, CA, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, 94305, CA, USA.
- Department of Biomedical Data Science, Stanford University School of Medicine, 1265 Welch Road MC5464, Stanford, 94305, CA, USA.
| |
Collapse
|
5
|
Claus LR, Chen C, Stallworth J, Turner JL, Slaats GG, Hawks AL, Mabillard H, Senum SR, Srikanth S, Flanagan-Steet H, Louie RJ, Silver J, Lerner-Ellis J, Morel C, Mighton C, Sleutels F, van Slegtenhorst M, van Ham T, Brooks AS, Dorresteijn EM, Barakat TS, Dahan K, Demoulin N, Goffin EJ, Olinger E, Larsen M, Hertz JM, Lilien MR, Obeidová L, Seeman T, Stone HK, Kerecuk L, Gurgu M, Yousef Yengej FA, Ammerlaan CME, Rookmaaker MB, Hanna C, Rogers RC, Duran K, Peters E, Sayer JA, van Haaften G, Harris PC, Ling K, Mason JM, van Eerde AM, Steet R. Certain heterozygous variants in the kinase domain of the serine/threonine kinase NEK8 can cause an autosomal dominant form of polycystic kidney disease. Kidney Int 2023; 104:995-1007. [PMID: 37598857 PMCID: PMC10592035 DOI: 10.1016/j.kint.2023.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/22/2023] [Accepted: 07/28/2023] [Indexed: 08/22/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) resulting from pathogenic variants in PKD1 and PKD2 is the most common form of PKD, but other genetic causes tied to primary cilia function have been identified. Biallelic pathogenic variants in the serine/threonine kinase NEK8 cause a syndromic ciliopathy with extra-kidney manifestations. Here we identify NEK8 as a disease gene for ADPKD in 12 families. Clinical evaluation was combined with functional studies using fibroblasts and tubuloids from affected individuals. Nek8 knockout mouse kidney epithelial (IMCD3) cells transfected with wild type or variant NEK8 were further used to study ciliogenesis, ciliary trafficking, kinase function, and DNA damage responses. Twenty-one affected monoallelic individuals uniformly exhibited cystic kidney disease (mostly neonatal) without consistent extra-kidney manifestations. Recurrent de novo mutations of the NEK8 missense variant p.Arg45Trp, including mosaicism, were seen in ten families. Missense variants elsewhere within the kinase domain (p.Ile150Met and p.Lys157Gln) were also identified. Functional studies demonstrated normal localization of the NEK8 protein to the proximal cilium and no consistent cilia formation defects in patient-derived cells. NEK8-wild type protein and all variant forms of the protein expressed in Nek8 knockout IMCD3 cells were localized to cilia and supported ciliogenesis. However, Nek8 knockout IMCD3 cells expressing NEK8-p.Arg45Trp and NEK8-p.Lys157Gln showed significantly decreased polycystin-2 but normal ANKS6 localization in cilia. Moreover, p.Arg45Trp NEK8 exhibited reduced kinase activity in vitro. In patient derived tubuloids and IMCD3 cells expressing NEK8-p.Arg45Trp, DNA damage signaling was increased compared to healthy passage-matched controls. Thus, we propose a dominant-negative effect for specific heterozygous missense variants in the NEK8 kinase domain as a new cause of PKD.
Collapse
Affiliation(s)
- Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Joshua L Turner
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Gisela G Slaats
- Department of Nephrology and Hypertension, Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandra L Hawks
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Holly Mabillard
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Sujata Srikanth
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Raymond J Louie
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Josh Silver
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Chantal Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Frank Sleutels
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tjakko van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eiske M Dorresteijn
- Department of Pediatric Nephrology, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Karin Dahan
- Institute Pathology and Genetic, Center of Human Genetics, Charleroi, Belgium
| | - Nathalie Demoulin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Jean Goffin
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Recherche Expérimentale et Clinique, UCLouvain, Brussels, Belgium
| | - Eric Olinger
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Martin Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marc R Lilien
- Department of Pediatric Nephrology, Wilhelmina Children's Hospital, Utrecht, the Netherlands
| | - Lena Obeidová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomas Seeman
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic; Department of Pediatrics, University Hospital Ostrava, Ostrava, Czech Republic; Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Hillarey K Stone
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Larissa Kerecuk
- Birmingham Women's and Children's National Health Services (NHS) Foundation Trust, National Institute for Health Care and Research (NIHR) Clinical Research Network (CRN) West Midlands, Birmingham, UK
| | - Mihai Gurgu
- Fundeni Clinical Institute, Bucharest, Romania
| | - Fjodor A Yousef Yengej
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Carola M E Ammerlaan
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands; Hubrecht Institute for Developmental Biology and Stem Cell Research-KNAW, Utrecht, the Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Christian Hanna
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA; Division of Pediatric Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - R Curtis Rogers
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Karen Duran
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Edith Peters
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - John A Sayer
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK; National Institute for Health and Care Research (NIHR) Biomedical Research Centre, Newcastle, UK
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
| | - Jennifer M Mason
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA.
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Richard Steet
- Research Division, Greenwood Genetic Center, Greenwood, South Carolina, USA.
| |
Collapse
|