51
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Wang P, Xia J, Zhang L, Zhao S, Li S, Wang H, Cheng S, Li H, Yin W, Pei D, Shu X. SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis. Cells 2019; 8:cells8111335. [PMID: 31671755 PMCID: PMC6912348 DOI: 10.3390/cells8111335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/15/2019] [Accepted: 10/27/2019] [Indexed: 12/12/2022] Open
Abstract
Centriolar satellites are non-membrane cytoplasmic granules that deliver proteins to centrosome during centrosome biogenesis and ciliogenesis. Centriolar satellites are highly dynamic during cell cycle or ciliogenesis and how they are regulated remains largely unknown. We report here that sorting nexin 17 (SNX17) regulates the homeostasis of a subset of centriolar satellite proteins including PCM1, CEP131, and OFD1 during serum-starvation-induced ciliogenesis. Mechanistically, SNX17 recruits the deubiquitinating enzyme USP9X to antagonize the mindbomb 1 (MIB1)-induced ubiquitination and degradation of PCM1. SNX17 deficiency leads to enhanced degradation of USP9X as well as PCM1 and disrupts ciliogenesis upon serum starvation. On the other hand, SNX17 is dispensable for the homeostasis of PCM1 and USP9X in serum-containing media. These findings reveal a SNX17/USP9X mediated pathway essential for the homeostasis of centriolar satellites under serum starvation, and provide insight into the mechanism of USP9X in ciliogenesis, which may lead to a better understating of USP9X-deficiency-related human diseases such as X-linked mental retardation and neurodegenerative diseases.
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Affiliation(s)
- Pengtao Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
- Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Jianhong Xia
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Leilei Zhang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Shaoyang Zhao
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Shengbiao Li
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Haiyun Wang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Shan Cheng
- Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Heying Li
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Wenguang Yin
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China.
| | - Xiaodong Shu
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou 510530, China.
- Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China.
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 511436, China.
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52
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Tsurusaki Y, Kuroda Y, Yamanouchi Y, Kondo E, Ouchi K, Kimura Y, Enomoto Y, Aida N, Masuno M, Kurosawa K. Novel USP9X variants in two patients with X-linked intellectual disability. Hum Genome Var 2019; 6:49. [PMID: 31666975 PMCID: PMC6804943 DOI: 10.1038/s41439-019-0081-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 01/04/2023] Open
Abstract
USP9X variants have been reported in patients with X-linked intellectual disability. Here, we report two female patients with intellectual disability and pigment abnormalities along Blaschko lines. Targeted resequencing identified two novel heterozygous variants, c.4068_4072del (p. (Leu1357Tyrfs*12)) and c.1201C>T (p. (Arg401*)), in USP9X. Our findings provide further evidence that USP9X variants cause intellectual disability.
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Affiliation(s)
- Yoshinori Tsurusaki
- 1Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan.,2Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Yukiko Kuroda
- 3Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yasuko Yamanouchi
- 4Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Eisuke Kondo
- 5Department of Pediatrics, Kawasaki Medical School, Kurashiki, Japan
| | - Kazunobu Ouchi
- 5Department of Pediatrics, Kawasaki Medical School, Kurashiki, Japan
| | - Yuichi Kimura
- 1Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- 1Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriko Aida
- 6Department of Radiology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mitsuo Masuno
- 4Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan.,5Department of Pediatrics, Kawasaki Medical School, Kurashiki, Japan
| | - Kenji Kurosawa
- 3Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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53
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Jackson MR, Loring KE, Homan CC, Thai MH, Määttänen L, Arvio M, Jarvela I, Shaw M, Gardner A, Gecz J, Shoubridge C. Heterozygous loss of function of IQSEC2/ Iqsec2 leads to increased activated Arf6 and severe neurocognitive seizure phenotype in females. Life Sci Alliance 2019; 2:2/4/e201900386. [PMID: 31439632 PMCID: PMC6706959 DOI: 10.26508/lsa.201900386] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/25/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
Clinical presentations of mutations in the IQSEC2 gene on the X-chromosome initially implicated to cause non-syndromic intellectual disability (ID) in males have expanded to include early onset seizures in males as well as in females. The molecular pathogenesis is not well understood, nor the mechanisms driving disease expression in heterozygous females. Using a CRISPR/Cas9-edited Iqsec2 KO mouse model, we confirm the loss of Iqsec2 mRNA expression and lack of Iqsec2 protein within the brain of both founder and progeny mice. Both male (52%) and female (46%) Iqsec2 KO mice present with frequent and recurrent seizures. Focusing on Iqsec2 KO heterozygous female mice, we demonstrate increased hyperactivity, altered anxiety and fear responses, decreased social interactions, delayed learning capacity and decreased memory retention/novel recognition, recapitulating psychiatric issues, autistic-like features, and cognitive deficits present in female patients with loss-of-function IQSEC2 variants. Despite Iqsec2 normally acting to activate Arf6 substrate, we demonstrate that mice modelling the loss of Iqsec2 function present with increased levels of activated Arf6. We contend that loss of Iqsec2 function leads to altered regulation of activated Arf6-mediated responses to synaptic signalling and immature synaptic networks. We highlight the importance of IQSEC2 function for females by reporting a novel nonsense variant c.566C > A, p.(S189*) in an elderly female patient with profound intellectual disability, generalised seizures, and behavioural disturbances. Our human and mouse data reaffirm IQSEC2 as another disease gene with an unexpected X-chromosome heterozygous female phenotype. Our Iqsec2 mouse model recapitulates the phenotypes observed in human patients despite the differences in the IQSEC2/Iqsec2 gene X-chromosome inactivation between the species.
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Affiliation(s)
- Matilda R Jackson
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Karagh E Loring
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Claire C Homan
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Monica Hn Thai
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Laura Määttänen
- Department of Child Neurology, Turku University Hospital, Turku, Finland
| | - Maria Arvio
- Department of Child Neurology, Turku University Hospital, Turku, Finland.,Joint Authority for Päijät-Häme Social and Health Care, Lahti, Finland.,PEDEGO, Oulu University Hospital, Oulu, Finland
| | - Irma Jarvela
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Marie Shaw
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Alison Gardner
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Jozef Gecz
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Cheryl Shoubridge
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia .,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
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54
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55
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Kodani A, Moyer T, Chen A, Holland A, Walsh CA, Reiter JF. SFI1 promotes centriole duplication by recruiting USP9X to stabilize the microcephaly protein STIL. J Cell Biol 2019; 218:2185-2197. [PMID: 31197030 PMCID: PMC6605807 DOI: 10.1083/jcb.201803041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 12/18/2018] [Accepted: 05/10/2019] [Indexed: 01/08/2023] Open
Abstract
In mammals, centrioles participate in brain development, and human mutations affecting centriole duplication cause microcephaly. Here, we identify a role for the mammalian homologue of yeast SFI1, involved in the duplication of the yeast spindle pole body, as a critical regulator of centriole duplication in mammalian cells. Mammalian SFI1 interacts with USP9X, a deubiquitylase associated with human syndromic mental retardation. SFI1 localizes USP9X to the centrosome during S phase to deubiquitylate STIL, a critical regulator of centriole duplication. USP9X-mediated deubiquitylation protects STIL from degradation. Consistent with a role for USP9X in stabilizing STIL, cells from patients with USP9X loss-of-function mutations have reduced STIL levels. Together, these results demonstrate that SFI1 is a centrosomal protein that localizes USP9X to the centrosome to stabilize STIL and promote centriole duplication. We propose that the USP9X protection of STIL to facilitate centriole duplication underlies roles of both proteins in human neurodevelopment.
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Affiliation(s)
- Andrew Kodani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA
| | - Tyler Moyer
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Allen Chen
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA
| | - Andrew Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
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56
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Lenberg JL, Pretorius DH, Rupe ES, Jones MC, Ramos GA, Andreasen TS. Whole-exome sequencing reveals novel USP9X variant in female fetus with isolated agenesis of the corpus callosum. Clin Case Rep 2019; 7:656-660. [PMID: 30997057 PMCID: PMC6452501 DOI: 10.1002/ccr3.2051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 09/05/2018] [Accepted: 01/22/2019] [Indexed: 01/06/2023] Open
Abstract
Whole-exome sequencing in a female fetus detected a USP9X variant. This X-linked gene was recently associated with intellectual disability and distinct pattern of malformation in females. Isolated agenesis of the corpus callosum has not been reported in association with USP9X. Identifying this variant impacted management of the subsequent pregnancy.
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Affiliation(s)
- Jerica L. Lenberg
- Department of Genetic CounselingAugustana UniversitySioux FallsSouth Dakota
| | | | - Eric S. Rupe
- Department of RadiologyUniversity of CaliforniaSan DiegoCalifornia
| | - Marilyn C. Jones
- Division of Genetics, Department of PediatricsUniversity of CaliforniaSan DiegoCalifornia
| | - Gladys A. Ramos
- Division of Maternal‐Fetal Medicine, Department of Reproductive MedicineUniversity of CaliforniaSan DiegoCalifornia
| | - Tara S. Andreasen
- Division of Genetics, Department of PediatricsUniversity of CaliforniaSan DiegoCalifornia
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57
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Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X. Proc Natl Acad Sci U S A 2019; 116:7288-7297. [PMID: 30914461 PMCID: PMC6462090 DOI: 10.1073/pnas.1815027116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ubiquitination is an important posttranslational modification that regulates almost every aspect of cellular functions. Ubiquitin can form chains of different topology; each has a distinctive role in dictating the function and fate of the modified proteins. Deubiquitinases (DUBs) reverse ubiquitination. How DUBs recognize ubiquitin chains is a topic of immense interest due to the therapeutic potentials of human DUBs. We obtained the atomic details of the USP9X catalytic core, a DUB involved in cancers and developmental disorders, and revealed its unusual mechanisms of action using a set of activity-based ubiquitin probes. These probes will propel future investigation of how DUBs recognize and process ubiquitin chains and identify potential new sites on DUBs for drug discovery. USP9X is a conserved deubiquitinase (DUB) that regulates multiple cellular processes. Dysregulation of USP9X has been linked to cancers and X-linked intellectual disability. Here, we report the crystal structure of the USP9X catalytic domain at 2.5-Å resolution. The structure reveals a canonical USP-fold comprised of fingers, palm, and thumb subdomains, as well as an unusual β-hairpin insertion. The catalytic triad of USP9X is aligned in an active configuration. USP9X is exclusively active against ubiquitin (Ub) but not Ub-like modifiers. Cleavage assays with di-, tri-, and tetraUb chains show that the USP9X catalytic domain has a clear preference for K11-, followed by K63-, K48-, and K6-linked polyUb chains. Using a set of activity-based diUb and triUb probes (ABPs), we demonstrate that the USP9X catalytic domain has an exo-cleavage preference for K48- and endo-cleavage preference for K11-linked polyUb chains. The structure model and biochemical data suggest that the USP9X catalytic domain harbors three Ub binding sites, and a zinc finger in the fingers subdomain and the β-hairpin insertion both play important roles in polyUb chain processing and linkage specificity. Furthermore, unexpected labeling of a secondary, noncatalytic cysteine located on a blocking loop adjacent to the catalytic site by K11-diUb ABP implicates a previously unreported mechanism of polyUb chain recognition. The structural features of USP9X revealed in our study are critical for understanding its DUB activity. The new Ub-based ABPs form a set of valuable tools to understand polyUb chain processing by the cysteine protease class of DUBs.
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58
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Blackburn PR, Davila JI, Jackson RA, Fadra N, Atiq MA, Pitel BA, Nair AA, VanDeWalker TJ, Hessler MG, Hovel SK, Wehrs RN, Fritchie KJ, Jenkins RB, Halling KC, Geiersbach KB. RNA sequencing identifies a novel
USP9X‐USP6
promoter swap gene fusion in a primary aneurysmal bone cyst. Genes Chromosomes Cancer 2019; 58:589-594. [DOI: 10.1002/gcc.22742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
| | - Jaime I. Davila
- Department of Health Science ResearchMayo Clinic Rochester Minnesota
| | - Rory A. Jackson
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Numrah Fadra
- Department of Health Science ResearchMayo Clinic Rochester Minnesota
| | - Mazen A. Atiq
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Beth A. Pitel
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Asha A. Nair
- Department of Health Science ResearchMayo Clinic Rochester Minnesota
| | - Todd J. VanDeWalker
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Mark G. Hessler
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Sara K. Hovel
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Rebecca N. Wehrs
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Karen J. Fritchie
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Robert B. Jenkins
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
| | - Kevin C. Halling
- Department of Laboratory Medicine and PathologyMayo Clinic Rochester Minnesota
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59
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Sinthuwiwat T, Ittiwut C, Porntaveetus T, Shotelersuk V. Female-restricted syndromic intellectual disability in a patient from Thailand. Am J Med Genet A 2019; 179:758-761. [DOI: 10.1002/ajmg.a.61106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/22/2019] [Accepted: 02/04/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Thivaratana Sinthuwiwat
- Interdisciplinary Program of Biomedical Sciences; Graduate School, Chulalongkorn University; Bangkok Thailand
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics; King Chulalongkorn Memorial Hospital, The Thai Red Cross Society; Bangkok Thailand
- Cytogenetics Unit, Research and International Relations Division; HRH Princess Chulabhorn College of Medical Science; Bangkok Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics; King Chulalongkorn Memorial Hospital, The Thai Red Cross Society; Bangkok Thailand
| | - Thantrira Porntaveetus
- Genomics and Precision Dentistry Research Unit, Department of Physiology; Faculty of Dentistry, Chulalongkorn University; Bangkok Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine; Chulalongkorn University; Bangkok Thailand
- Excellence Center for Medical Genetics; King Chulalongkorn Memorial Hospital, The Thai Red Cross Society; Bangkok Thailand
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60
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Han KJ, Wu Z, Pearson CG, Peng J, Song K, Liu CW. Deubiquitylase USP9X maintains centriolar satellite integrity by stabilizing pericentriolar material 1 protein. J Cell Sci 2019; 132:jcs.221663. [PMID: 30584065 DOI: 10.1242/jcs.221663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Centriolar satellites are small cytoplasmic granules that play important roles in regulating the formation of centrosomes and primary cilia. Ubiquitylation of satellite proteins, including the core satellite scaffold protein pericentriolar material 1 (PCM1), regulates centriolar satellite integrity. Currently, deubiquitylases that control centriolar satellite integrity have not been identified. In this study, we find that the deubiquitylase USP9X binds PCM1, and antagonizes PCM1 ubiquitylation to protect it from proteasomal degradation. Knockdown of USP9X in human cell lines reduces PCM1 protein levels, disrupts centriolar satellite particles and causes localization of satellite proteins, such as CEP290, to centrosomes. Interestingly, knockdown of mindbomb 1 (MIB1), a ubiquitin ligase that promotes PCM1 ubiquitylation and degradation, in USP9X-depleted cells largely restores PCM1 protein levels and corrects defects caused by the loss of USP9X. Overall, our study reveals that USP9X is a constituent of centriolar satellites and functions to maintain centriolar satellite integrity by stabilizing PCM1.
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Affiliation(s)
- Ke-Jun Han
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chad G Pearson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kunhua Song
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chang-Wei Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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61
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Wang X, Posey JE, Rosenfeld JA, Bacino CA, Scaglia F, Immken L, Harris JM, Hickey SE, Mosher TM, Slavotinek A, Zhang J, Beuten J, Leduc MS, He W, Vetrini F, Walkiewicz MA, Bi W, Xiao R, Liu P, Shao Y, Gezdirici A, Gulec EY, Jiang Y, Darilek SA, Hansen AW, Khayat MM, Pehlivan D, Piard J, Muzny DM, Hanchard N, Belmont JW, Van Maldergem L, Gibbs RA, Eldomery MK, Akdemir ZC, Adesina AM, Chen S, Lee YC, Lee B, Lupski JR, Eng CM, Xia F, Yang Y, Graham BH, Moretti P. Phenotypic expansion in DDX3X - a common cause of intellectual disability in females. Ann Clin Transl Neurol 2018; 5:1277-1285. [PMID: 30349862 PMCID: PMC6186933 DOI: 10.1002/acn3.622] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/21/2018] [Accepted: 06/24/2018] [Indexed: 12/14/2022] Open
Abstract
De novo variants in DDX3X account for 1–3% of unexplained intellectual disability (ID) cases and are amongst the most common causes of ID especially in females. Forty‐seven patients (44 females, 3 males) have been described. We identified 31 additional individuals carrying 29 unique DDX3X variants, including 30 postnatal individuals with complex clinical presentations of developmental delay or ID, and one fetus with abnormal ultrasound findings. Rare or novel phenotypes observed include respiratory problems, congenital heart disease, skeletal muscle mitochondrial DNA depletion, and late‐onset neurologic decline. Our findings expand the spectrum of DNA variants and phenotypes associated with DDX3X disorders.
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Affiliation(s)
- Xia Wang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Jennifer E Posey
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Jill A Rosenfeld
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Carlos A Bacino
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | - Fernando Scaglia
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | | | | | - Scott E Hickey
- Clinical Pediatrics The Ohio State University Columbus Ohio.,Division of Molecular & Human Genetics Nationwide Children's Hospital Columbus Ohio
| | - Theresa M Mosher
- Division of Molecular & Human Genetics Nationwide Children's Hospital Columbus Ohio
| | - Anne Slavotinek
- Department of Pediatrics Division of Genetics University of California San Francisco California
| | | | | | - Magalie S Leduc
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | | | | | - Magdalena A Walkiewicz
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Weimin Bi
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Rui Xiao
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Pengfei Liu
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Yunru Shao
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas
| | - Alper Gezdirici
- Department of Genetics Kanuni Sultan Suleyman Training and Research Hospital Instanbul Turkey
| | - Elif Y Gulec
- Department of Genetics Kanuni Sultan Suleyman Training and Research Hospital Instanbul Turkey
| | - Yunyun Jiang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Sandra A Darilek
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Adam W Hansen
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Michael M Khayat
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Davut Pehlivan
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Section of Neurology Department of Pediatrics Baylor College of Medicine Houston Texas
| | - Juliette Piard
- Centre de Génétique Humaine Université de Franche-Comté Besançon France
| | - Donna M Muzny
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Neil Hanchard
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - John W Belmont
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Richard A Gibbs
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | | | - Zeynep C Akdemir
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Adekunle M Adesina
- Texas Children's Hospital Houston Texas.,Pathology Baylor College of Medicine Houston Texas
| | - Shan Chen
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - Yi-Chien Lee
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | | | - Brendan Lee
- Molecular and Human Genetics Baylor College of Medicine Houston Texas
| | - James R Lupski
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas.,Human Genome Sequencing Center Baylor College of Medicine Houston Texas
| | - Christine M Eng
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Fan Xia
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Yaping Yang
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Baylor Genetics Houston Texas
| | - Brett H Graham
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Texas Children's Hospital Houston Texas.,Medical and Molecular Genetics Indiana University School of Medicine Indianapolis Indiana
| | - Paolo Moretti
- Molecular and Human Genetics Baylor College of Medicine Houston Texas.,Neurology Baylor College of Medicine and Michael E. DeBakey VA Medical Center Houston Texas.,Neurology University of Utah and George E. Wahlen VA Medical Center Salt Lake City Utah
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62
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Qiao XH, Wang Q, Wang J, Liu XY, Xu YJ, Huang RT, Xue S, Li YJ, Zhang M, Qu XK, Li RG, Qiu XB, Yang YQ. A novel NR2F2 loss-of-function mutation predisposes to congenital heart defect. Eur J Med Genet 2017; 61:197-203. [PMID: 29222010 DOI: 10.1016/j.ejmg.2017.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/06/2017] [Accepted: 12/04/2017] [Indexed: 02/06/2023]
Abstract
Congenital heart defect (CHD) is the most common type of birth defect in humans and a leading cause of infant morbidity and mortality. Previous studies have demonstrated that genetic defects play a pivotal role in the pathogenesis of CHD. However, the genetic basis of CHD remains poorly understood due to substantial genetic heterogeneity. In this study, the coding exons and splicing boundaries of the NR2F2 gene, which encodes a pleiotropic transcription factor required for normal cardiovascular development, were sequenced in 168 unrelated patients with CHD, and a novel mutation (c.247G > T, equivalent to p.G83X) was detected in a patient with double outlet right ventricle as well as ventricular septal defect. Genetic scanning of the mutation carrier's relatives available showed that the mutation was present in all affected family members but absent in unaffected family members. Analysis of the index patient's pedigree displayed that the mutation co-segregated with CHD, which was transmitted as an autosomal dominant trait with complete penetrance. The nonsense mutation was absent in 230 unrelated, ethnically-matched healthy individuals used as controls. Functional deciphers by using a dual-luciferase reporter assay system revealed that the mutant NR2F2 protein had no transcriptional activity as compared with its wild-type counterpart. Furthermore, the mutation abrogated the synergistic transcriptional activation between NR2F2 and GATA4, another core cardiac transcription factor associated with CHD. This study firstly associates NR2F2 loss-of-function mutation with an increased susceptibility to double outlet right ventricle in humans, which provides further significant insight into the molecular mechanisms underpinning CHD, suggesting potential implications for genetic counseling of CHD families and personalized treatment of CHD patients.
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Affiliation(s)
- Xiao-Hui Qiao
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qian Wang
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Juan Wang
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xing-Yuan Liu
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Ying-Jia Xu
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Ri-Tai Huang
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Song Xue
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan-Jie Li
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Min Zhang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Kai Qu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ruo-Gu Li
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China; Department of Cardiovascular Research Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
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63
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Carrel L, Brown CJ. When the Lyon(ized chromosome) roars: ongoing expression from an inactive X chromosome. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160355. [PMID: 28947654 PMCID: PMC5627157 DOI: 10.1098/rstb.2016.0355] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 12/21/2022] Open
Abstract
A tribute to Mary Lyon was held in October 2016. Many remarked about Lyon's foresight regarding many intricacies of the X-chromosome inactivation process. One such example is that a year after her original 1961 hypothesis she proposed that genes with Y homologues should escape from X inactivation to achieve dosage compensation between males and females. Fifty-five years later we have learned many details about these escapees that we attempt to summarize in this review, with a particular focus on recent findings. We now know that escapees are not rare, particularly on the human X, and that most lack functionally equivalent Y homologues, leading to their increasingly recognized role in sexually dimorphic traits. Newer sequencing technologies have expanded profiling of primary tissues that will better enable connections to sex-biased disorders as well as provide additional insights into the X-inactivation process. Chromosome organization, nuclear location and chromatin environments distinguish escapees from other X-inactivated genes. Nevertheless, several big questions remain, including what dictates their distinct epigenetic environment, the underlying basis of species differences in escapee regulation, how different classes of escapees are distinguished, and the roles that local sequences and chromosome ultrastructure play in escapee regulation.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Laura Carrel
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 500 University Drive, Mail code H171, Hershey, PA 17033, USA
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada BC V6T 1Z3
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64
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Qiao XH, Wang F, Zhang XL, Huang RT, Xue S, Wang J, Qiu XB, Liu XY, Yang YQ. MEF2C loss-of-function mutation contributes to congenital heart defects. Int J Med Sci 2017; 14:1143-1153. [PMID: 29104469 PMCID: PMC5666546 DOI: 10.7150/ijms.21353] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022] Open
Abstract
Congenital heart disease (CHD) is the most common type of developmental abnormality in humans, and is a leading cause for substantially increased morbidity and mortality in affected individuals. Increasing studies demonstrates a pivotal role of genetic defects in the pathogenesis of CHD, and presently mutations in more than 60 genes have been associated with CHD. Nevertheless, CHD is of pronounced genetic heterogeneity, and the genetic basis underpinning CHD in a large proportion of patients remains unclear. In the present study, the whole coding exons and splicing donors/acceptors of the MEF2C gene, which codes for a transcription factor essential for normal cardiovascular development, were sequenced in 200 unrelated patients affected with CHD, and a novel heterozygous missense mutation, p.L38P, was identified in an index patient with patent ductus arteriosus (PDA) and ventricular septal defect (VSD). Genetic scan of the mutation carrier's family members available showed that the mutation was present in all affected family members but absent in unaffected family members. Analysis of the proband's pedigree revealed that the mutation co-segregated with PDA, which was transmitted as an autosomal dominant trait with complete penetrance. The mutation changed the amino acid that was completely conserved evolutionarily, and did not exist in 300 unrelated, ethnically-matched healthy individuals used as controls. Functional deciphers by using a dual-luciferase reporter assay system unveiled that the mutant MEF2C protein had a significantly reduced transcriptional activity. Furthermore, the mutation significantly diminished the synergistic activation between MEF2C and GATA4, another cardiac core transcription factor that has been causally linked to CHD. In conclusion, this is the first report on the association of a MEF2C loss-of-function mutation with an increased vulnerability to CHD in humans, which provides novel insight into the molecular mechanisms underlying CHD, implying potential implications for early diagnosis and timely prophylaxis of CHD.
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Affiliation(s)
- Xiao-Hui Qiao
- Department of Pediatric Internal Medicine, Ningbo Women & Children's Hospital, 339 Liuding Street, Ningbo 315012, China
| | - Fei Wang
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
| | - Xian-Ling Zhang
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Middle Yanchang Road, Shanghai 200072, China
| | - Ri-Tai Huang
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 1630 Dongfang Road, Shanghai 200127, China
| | - Song Xue
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 1630 Dongfang Road, Shanghai 200127, China
| | - Juan Wang
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
| | - Xing-Yuan Liu
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai 200065, China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
- Department of Cardiovascular Research Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
- Department of Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, China
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65
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Das A, Qian J, Tsang WY. USP9X counteracts differential ubiquitination of NPHP5 by MARCH7 and BBS11 to regulate ciliogenesis. PLoS Genet 2017; 13:e1006791. [PMID: 28498859 PMCID: PMC5446187 DOI: 10.1371/journal.pgen.1006791] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/26/2017] [Accepted: 05/01/2017] [Indexed: 11/19/2022] Open
Abstract
Ciliogenesis is a fundamental biological process central to human health. Precisely how this process is coordinated with the cell cycle remains an open question. We report that nephrocystin-5 (NPHP5/IQCB1), a positive regulator of ciliogenesis, is a stable and low turnover protein subjected to cycles of ubiquitination and deubiquitination. NPHP5 directly binds to a deubiquitinating enzyme USP9X/FAM and two E3 ubiquitin ligases BBS11/TRIM32 and MARCH7/axotrophin. NPHP5 undergoes K63 ubiquitination in a cell cycle dependent manner and K48/K63 ubiquitination upon USP9X depletion or inhibition. In the G0/G1/S phase, a pool of cytoplasmic USP9X recruited to the centrosome by NPHP5 protects NPHP5 from ubiquitination, thus favouring cilia assembly. In the G2/M phase, USP9X dissociation from the centrosome allows BBS11 to K63 ubiquitinate NPHP5 which triggers protein delocalization and loss of cilia. BBS11 is a resident centrosomal protein, whereas cytoplasmic USP9X sequesters the majority of MARCH7 away from the centrosome during interphase. Depletion or inhibition of USP9X leads to an accumulation of centrosomal MARCH7 which K48 ubiquitinates NPHP5, triggering protein degradation and cilia loss. At the same time, BBS11 K63 ubiquitinates NPHP5. Our data suggest that dynamic ubiquitination and deubiquitination of NPHP5 plays a crucial role in the regulation of ciliogenesis. Centrosomes are non-membrane bound organelles that modulate a variety of cellular processes including cell division and formation of hair-like protrusions called primary cilia. Primary cilia function as cellular antennae to sense a wide variety of signals important for growth, development and differentiation. Defects in cilia formation or ciliogenesis can give rise to a bewildering array of human ciliary diseases collectively known as ciliopathies. Ciliogenesis is controlled in part by nephrocystin-5 (NPHP5/IQCB1), and NPHP5 dysfunction causes ciliopathies in humans, mice and dogs. We are interested in studying how the stability, localization and biological activity of NPHP5 are regulated at the molecular level. We present here that NPHP5 directly interacts with, and is a substrate of, one deubiquitinase (USP9X/FAM) and two ubiquitin ligases (BBS11/TRIM32 and MARCH7/axotrophin), enzymes involved in controlling protein stability, localization and activity. Our results suggest that timely ubiquitination and deubiquitination of NPHP5 is critical for the regulation of ciliogenesis.
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Affiliation(s)
- Arindam Das
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Faculté de Médecine, Département de pathologie et biologie cellulaire, Université de Montréal, Montréal, Québec, Canada
| | - Jin Qian
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - William Y. Tsang
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Faculté de Médecine, Département de pathologie et biologie cellulaire, Université de Montréal, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- * E-mail:
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66
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De Novo Variants Associated With Developmental Disability. Am J Med Genet A 2017; 173:1139-1140. [DOI: 10.1002/ajmg.a.38265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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67
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Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome. Proc Natl Acad Sci U S A 2017; 114:E4030-E4039. [PMID: 28461505 DOI: 10.1073/pnas.1702489114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Children with Down syndrome (DS) are prone to development of high-risk B-cell precursor ALL (DS-ALL), which differs genetically from most sporadic pediatric ALLs. Increased expression of cytokine receptor-like factor 2 (CRLF2), the receptor to thymic stromal lymphopoietin (TSLP), characterizes about half of DS-ALLs and also a subgroup of sporadic "Philadelphia-like" ALLs. To understand the pathogenesis of relapsed DS-ALL, we performed integrative genomic analysis of 25 matched diagnosis-remission and -relapse DS-ALLs. We found that the CRLF2 rearrangements are early events during DS-ALL evolution and generally stable between diagnoses and relapse. Secondary activating signaling events in the JAK-STAT/RAS pathway were ubiquitous but highly redundant between diagnosis and relapse, suggesting that signaling is essential but that no specific mutations are "relapse driving." We further found that activated JAK2 may be naturally suppressed in 25% of CRLF2pos DS-ALLs by loss-of-function aberrations in USP9X, a deubiquitinase previously shown to stabilize the activated phosphorylated JAK2. Interrogation of large ALL genomic databases extended our findings up to 25% of CRLF2pos, Philadelphia-like ALLs. Pharmacological or genetic inhibition of USP9X, as well as treatment with low-dose ruxolitinib, enhanced the survival of pre-B ALL cells overexpressing mutated JAK2. Thus, somehow counterintuitive, we found that suppression of JAK-STAT "hypersignaling" may be beneficial to leukemic B-cell precursors. This finding and the reduction of JAK mutated clones at relapse suggest that the therapeutic effect of JAK specific inhibitors may be limited. Rather, combined signaling inhibitors or direct targeting of the TSLP receptor may be a useful therapeutic strategy for DS-ALL.
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68
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Au PYB, Huang L, Broley S, Gallagher L, Creede E, Lahey D, Ordorica S, Mina K, Boycott KM, Baynam G, Dyment DA. Two females with mutations in USP9X highlight the variable expressivity of the intellectual disability syndrome. Eur J Med Genet 2017; 60:359-364. [PMID: 28377321 DOI: 10.1016/j.ejmg.2017.03.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 01/02/2023]
Abstract
The genetic causes of intellectual disability (ID) are heterogeneous and include both chromosomal and monogenic etiologies. The X-chromosome is known to contain many ID-related genes and males show a marked predominance for intellectual disability. Here we report two females with syndromic intellectual disability. The first individual was relatively mild in her presentation with mild-moderate intellectual disability, hydronephrosis and altered pigmentation along the lines of Blaschko without additional congenital anomalies. A second female presented shortly after birth with dysmorphic facial features, post-axial polydactyly and, on follow-up assessment, demonstrated moderate intellectual disability. Chromosomal studies for Individual 1 identified an X-chromosome deletion due to a de novo pericentric inversion; the inversion breakpoint was associated with deletion of the 5'UTR of the USP9X, a gene which has been implicated in a syndromic intellectual disability affecting females. The second individual had a de novo frameshift mutation detected by whole-exome sequencing that was predicted to be deleterious, NM_001039590.2 (USP9X): c.4104_4105del (p.(Arg1368Serfs*2)). Haploinsufficiency of USP9X in females has been associated with ID and congenital malformations that include heart defects, scoliosis, dental abnormalities, anal atresia, polydactyly, Dandy Walker malformation and hypoplastic corpus callosum. The extent of the congenital malformations observed in Individual 1 was less striking than Individual 2 and other individuals previously reported in the literature, and suggests that USP9X mutations in females can have a wider spectrum of presentation than previously appreciated.
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Affiliation(s)
- P Y B Au
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, AB, Canada
| | - L Huang
- Department of Pathology, University of British Columbia Women and Children's Hospital, Vancouver, Canada
| | - S Broley
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Subiaco, Australia
| | - L Gallagher
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - E Creede
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - D Lahey
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - S Ordorica
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - K Mina
- Diagnostic Genomics, PathWest, Department of Health, Government of Western Australia, WA, Australia
| | - K M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada; Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - G Baynam
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Subiaco, Australia; School of Paediatrics and Child Health, The University of Western Australia, Crawley, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia; Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, East Perth, Australia; Telethon Kids Institute, University of Western Australia, Subiaco, Australia; Western Australian Register of Developmental Anomalies, Subiaco, Australia; School of Spatial Sciences, Curtin University, Bentley, Australia
| | - D A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada; Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
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69
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Dikow N, Granzow M, Graul-Neumann LM, Karch S, Hinderhofer K, Paramasivam N, Behl LJ, Kaufmann L, Fischer C, Evers C, Schlesner M, Eils R, Borck G, Zweier C, Bartram CR, Carey JC, Moog U. DDX3X
mutations in two girls with a phenotype overlapping Toriello-Carey syndrome. Am J Med Genet A 2017; 173:1369-1373. [DOI: 10.1002/ajmg.a.38164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 12/20/2016] [Accepted: 01/05/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Nicola Dikow
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Martin Granzow
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | | | - Stephanie Karch
- Center for Child and Adolescent Medicine Pediatric Neurology; Heidelberg University Hospital; Heidelberg Germany
| | | | - Nagarajan Paramasivam
- Medical Faculty Heidelberg; Heidelberg University; Heidelberg Germany
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Laura-Jane Behl
- Genomics and Proteomics Core Facility; High Throughput Sequencing; German Cancer Research Center; Heidelberg Germany
| | - Lilian Kaufmann
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Christine Fischer
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Christina Evers
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg Germany
- Department for Bioinformatics and Functional Genomics; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant; Heidelberg University; Heidelberg Germany
| | - Guntram Borck
- Institute of Human Genetics; University of Ulm; Ulm Germany
| | - Christiane Zweier
- Institute of Human Genetics; Friedrich-Alexander-Universität Erlangen-Nürnberg; Erlangen Germany
| | - Claus R. Bartram
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
| | - John C. Carey
- Division of Medical Genetics; Department of Pediatrics; University of Utah School of Medicine; Salt Lake City Utah
| | - Ute Moog
- Institute of Human Genetics; Heidelberg University; Heidelberg Germany
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70
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Gonadal mosaicism of a novel IQSEC2 variant causing female limited intellectual disability and epilepsy. Eur J Hum Genet 2017; 25:763-767. [PMID: 28295038 DOI: 10.1038/ejhg.2017.29] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 02/01/2023] Open
Abstract
We report a family with four girls with moderate to severe intellectual disability and epilepsy. Two girls showed regression in adolescence and died of presumed sudden unexpected death in epilepsy at 16 and 22 years. Whole exome sequencing identified a truncating pathogenic variant in IQSEC2 at NM_001111125.2: c.2679_2680insA, p.(D894fs*10), a recently identified cause of epileptic encephalopathy in females (MIM 300522). The IQSEC2 variant was identified in both surviving affected sisters but in neither parent. We describe the phenotypic spectrum associated with IQSEC2 variants, highlighting how IQSEC2 is adding to a growing list of X-linked genes that have a female-specific phenotype typically associated with de novo mutations. This report illustrates the need for careful review of all whole exome data, incorporating all possible modes of inheritance including that suggested by the family history.
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71
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Mattiske T, Moey C, Vissers LE, Thorne N, Georgeson P, Bakshi M, Shoubridge C. An Emerging Female Phenotype with Loss-of-Function Mutations in the Aristaless-Related Homeodomain Transcription Factor ARX. Hum Mutat 2017; 38:548-555. [PMID: 28150386 DOI: 10.1002/humu.23190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/18/2016] [Accepted: 01/24/2017] [Indexed: 01/17/2023]
Abstract
The devastating clinical presentation of X-linked lissencephaly with abnormal genitalia (XLAG) is invariably caused by loss-of-function mutations in the Aristaless-related homeobox (ARX) gene. Mutations in this X-chromosome gene contribute to intellectual disability (ID) with co-morbidities including seizures and movement disorders such as dystonia in affected males. The detection of affected females with mutations in ARX is increasing. We present a family with multiple affected individuals, including two females. Two male siblings presenting with XLAG were deceased prior to full-term gestation or within the first few weeks of life. Of the two female siblings, one presented with behavioral disturbances, mild ID, a seizure disorder, and complete agenesis of the corpus callosum (ACC), similar to the mother's phenotype. A novel insertion mutation in Exon 2 of ARX was identified, c.982delCinsTTT predicted to cause a frameshift at p.(Q328Ffs* 37). Our finding is consistent with loss-of-function mutations in ARX causing XLAG in hemizygous males and extends the findings of ID and seizures in heterozygous females. We review the reported phenotypes of females with mutations in ARX and highlight the importance of screening ARX in male and female patients with ID, seizures, and in particular with complete ACC.
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Affiliation(s)
- Tessa Mattiske
- Department of Paediatrics, School of Medicine, University of Adelaide, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ching Moey
- Department of Paediatrics, School of Medicine, University of Adelaide, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Lisenka E Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Natalie Thorne
- Murdoch Children's Research Institute, Melbourne, Australia.,University of Melbourne, Melbourne, Australia.,Melbourne Genomics Health Alliance, Melbourne, Australia
| | - Peter Georgeson
- Melbourne Genomics Health Alliance, Melbourne, Australia.,Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Australia
| | - Madhura Bakshi
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, NSW, Australia
| | - Cheryl Shoubridge
- Department of Paediatrics, School of Medicine, University of Adelaide, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
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72
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Vulto-van Silfhout AT, Gilissen C, Goeman JJ, Jansen S, van Amen-Hellebrekers CJM, van Bon BWM, Koolen DA, Sistermans EA, Brunner HG, de Brouwer APM, de Vries BBA. Quantification of Phenotype Information Aids the Identification of Novel Disease Genes. Hum Mutat 2017; 38:594-599. [PMID: 28074630 DOI: 10.1002/humu.23176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/09/2017] [Indexed: 01/10/2023]
Abstract
Next-generation sequencing led to the identification of many potential novel disease genes. The presence of mutations in the same gene in multiple unrelated patients is, however, a priori insufficient to establish that these genes are truly involved in the respective disease. Here, we show how phenotype information can be incorporated within statistical approaches to provide additional evidence for the causality of mutations. We developed a broadly applicable statistical model that integrates gene-specific mutation rates, cohort size, mutation type, and phenotype frequency information to assess the chance of identifying de novo mutations affecting the same gene in multiple patients with shared phenotype features. We demonstrate our approach based on the frequency of phenotype features present in a unique cohort of 6,149 patients with intellectual disability. We show that our combined approach can decrease the number of patients required to identify novel disease genes, especially for patients with combinations of rare phenotypes. In conclusion, we show how integrating genotype-phenotype information can aid significantly in the interpretation of de novo mutations in potential novel disease genes.
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Affiliation(s)
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Jelle J Goeman
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Bregje W M van Bon
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression. Proc Natl Acad Sci U S A 2017; 114:1619-1624. [PMID: 28143937 DOI: 10.1073/pnas.1621356114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rett syndrome (RS) is a debilitating neurological disorder affecting mostly girls with heterozygous mutations in the gene encoding the methyl-CpG-binding protein MeCP2 on the X chromosome. Because restoration of MeCP2 expression in a mouse model reverses neurologic deficits in adult animals, reactivation of the wild-type copy of MeCP2 on the inactive X chromosome (Xi) presents a therapeutic opportunity in RS. To identify genes involved in MeCP2 silencing, we screened a library of 60,000 shRNAs using a cell line with a MeCP2 reporter on the Xi and found 30 genes clustered in seven functional groups. More than half encoded proteins with known enzymatic activity, and six were members of the bone morphogenetic protein (BMP)/TGF-β pathway. shRNAs directed against each of these six genes down-regulated X-inactive specific transcript (XIST), a key player in X-chromosome inactivation that encodes an RNA that coats the silent X chromosome, and modulation of regulators of this pathway both in cell culture and in mice demonstrated robust regulation of XIST. Moreover, we show that Rnf12, an X-encoded ubiquitin ligase important for initiation of X-chromosome inactivation and XIST transcription in ES cells, also plays a role in maintenance of the inactive state through regulation of BMP/TGF-β signaling. Our results identify pharmacologically suitable targets for reactivation of MeCP2 on the Xi and a genetic circuitry that maintains XIST expression and X-chromosome inactivation in differentiated cells.
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74
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Escape Artists of the X Chromosome. Trends Genet 2016; 32:348-359. [PMID: 27103486 DOI: 10.1016/j.tig.2016.03.007] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 01/24/2023]
Abstract
Inactivation of one X chromosome in mammalian females achieves dosage compensation between XX females and XY males; however, over 15% of human X-linked genes continue to be expressed from the inactive X chromosome. New genomic methodologies have improved our identification and characterization of these escape genes, revealing the importance of DNA sequence, chromatin structure, and chromosome ultrastructure in regulating expression from an otherwise inactive chromosome. Study of these exceptions to the rule of silencing highlights the interconnectedness of chromatin and chromosome structure in X-chromosome inactivation (XCI). Recent advances also demonstrate the importance of these genes in sexually dimorphic disease risk, particularly cancer.
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