Advertisement
Biological Psychiatry
Advanced SearchSave search
Archival Report| Volume 87, ISSUE 2, P100-112, January 15, 2020

Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor β Signaling

Published:June 29, 2019DOI:https://doi.org/10.1016/j.biopsych.2019.05.028
Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor β Signaling
Previous ArticleLooking at the Big Neurochemical Picture of Autism Spectrum Disorder
Next ArticleBrain Development in School-Age and Adolescent Girls: Effects of Turner Syndrome, Estrogen Therapy, and Genomic Imprinting

      Abstract

      Background

      The X-chromosome gene USP9X encodes a deubiquitylating enzyme that has been associated with neurodevelopmental disorders primarily in female subjects. USP9X escapes X inactivation, and in female subjects de novo heterozygous copy number loss or truncating mutations cause haploinsufficiency culminating in a recognizable syndrome with intellectual disability and signature brain and congenital abnormalities. In contrast, the involvement of USP9X in male neurodevelopmental disorders remains tentative.

      Methods

      We used clinically recommended guidelines to collect and interrogate the pathogenicity of 44 USP9X variants associated with neurodevelopmental disorders in males. Functional studies in patient-derived cell lines and mice were used to determine mechanisms of pathology.

      Results

      Twelve missense variants showed strong evidence of pathogenicity. We define a characteristic phenotype of the central nervous system (white matter disturbances, thin corpus callosum, and widened ventricles); global delay with significant alteration of speech, language, and behavior; hypotonia; joint hypermobility; visual system defects; and other common congenital and dysmorphic features. Comparison of in silico and phenotypical features align additional variants of unknown significance with likely pathogenicity. In support of partial loss-of-function mechanisms, using patient-derived cell lines, we show loss of only specific USP9X substrates that regulate neurodevelopmental signaling pathways and a united defect in transforming growth factor β signaling. In addition, we find correlates of the male phenotype in Usp9x brain-specific knockout mice, and further resolve loss of hippocampal-dependent learning and memory.

      Conclusions

      Our data demonstrate the involvement of USP9X variants in a distinctive neurodevelopmental and behavioral syndrome in male subjects and identify plausible mechanisms of pathogenesis centered on disrupted transforming growth factor β signaling and hippocampal function.

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribe:

      Subscribe to Biological Psychiatry
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Register: Create an account
      Institutional Access: Sign in to ScienceDirect

      References

        • Murtaza M.
        • Jolly L.A.
        • Gécz J.
        • Wood S.A.
        La FAM fatale: USP9X in development and disease.
        Cell Mol Life Sci. 2015; 72: 2075-2089
        View in Article
        • Pantaleon M.
        • Kanai-Azuma M.
        • Mattick J.S.
        • Kaibuchi K.
        • Kaye P.L.
        • Wood S.A.
        FAM deubiquitylating enzyme is essential for preimplantation mouse embryo development.
        Mech Dev. 2001; 109: 151-160
        View in Article
        • Reijnders M.R.
        • Zachariadis V.
        • Latour B.
        • Jolly L.
        • Mancini G.M.
        • Pfundt R.
        • et al.
        De novo loss-of-function mutations in USP9X cause a female-specific recognizable syndrome with developmental delay and congenital malformations.
        Am J Hum Genet. 2016; 98: 373-381
        View in Article
        • Homan C.C.
        • Kumar R.
        • Nguyen L.S.
        • Haan E.
        • Raymond F.L.
        • Abidi F.
        • et al.
        Mutations in USP9X are associated with X-linked intellectual disability and disrupt neuronal cell migration and growth.
        Am J Hum Genet. 2014; 94: 470-478
        View in Article
        • Paemka L.
        • Mahajan V.B.
        • Ehaideb S.N.
        • Skeie J.M.
        • Tan M.C.
        • Wu S.
        • et al.
        Seizures are regulated by ubiquitin-specific peptidase 9 X-linked (USP9X), a de-ubiquitinase.
        PLoS Genet. 2015; 11: e1005022
        View in Article
        • Agrawal P.
        • Chen Y.T.
        • Schilling B.
        • Gibson B.W.
        • Hughes R.E.
        Ubiquitin-specific peptidase 9, X-linked (USP9X) modulates activity of mammalian target of rapamycin (mTOR).
        J Biol Chem. 2012; 287: 21164-21175
        View in Article
        • Bridges C.R.
        • Tan M.C.
        • Premarathne S.
        • Nanayakkara D.
        • Bellette B.
        • Zencak D.
        • et al.
        USP9X deubiquitylating enzyme maintains RAPTOR protein levels, mTORC1 signalling and proliferation in neural progenitors.
        Sci Rep. 2017; 7: 391
        View in Article
        • Chen X.
        • Zhang B.
        • Fischer J.A.
        A specific protein substrate for a deubiquitinating enzyme: Liquid facets is the substrate of Fat facets.
        Genes Dev. 2002; 16: 289-294
        View in Article
        • Dupont S.
        • Mamidi A.
        • Cordenonsi M.
        • Montagner M.
        • Zacchigna L.
        • Adorno M.
        • et al.
        FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination.
        Cell. 2009; 136: 123-135
        View in Article
        • Mouchantaf R.
        • Azakir B.A.
        • McPherson P.S.
        • Millard S.M.
        • Wood S.A.
        • Angers A.
        The ubiquitin ligase itch is auto-ubiquitylated in vivo and in vitro but is protected from degradation by interacting with the deubiquitylating enzyme FAM/USP9X.
        J Biol Chem. 2006; 281: 38738-38747
        View in Article
        • Overstreet E.
        • Fitch E.
        • Fischer J.A.
        Fat facets and Liquid facets promote Delta endocytosis and Delta signaling in the signaling cells.
        Development. 2004; 131: 5355-5366
        View in Article
        • Premarathne S.
        • Murtaza M.
        • Matigian N.
        • Jolly L.A.
        • Wood S.A.
        Loss of Usp9x disrupts cell adhesion, and components of the Wnt and Notch signaling pathways in neural progenitors.
        Sci Rep. 2017; 7: 8109
        View in Article
        • Taya S.
        • Yamamoto T.
        • Kanai-Azuma M.
        • Wood S.A.
        • Kaibuchi K.
        The deubiquitinating enzyme Fam interacts with and stabilizes beta-catenin.
        Genes Cells. 1999; 4: 757-767
        View in Article
        • Tseng L.C.
        • Zhang C.
        • Cheng C.M.
        • Xu H.
        • Hsu C.H.
        • Jiang Y.J.
        New classes of mind bomb-interacting proteins identified from yeast two-hybrid screens.
        PLoS One. 2014; 9: e93394
        View in Article
        • Xie Y.
        • Avello M.
        • Schirle M.
        • McWhinnie E.
        • Feng Y.
        • Bric-Furlong E.
        • et al.
        Deubiquitinase FAM/USP9X interacts with the E3 ubiquitin ligase SMURF1 protein and protects it from ligase activity-dependent self-degradation.
        J Biol Chem. 2013; 288: 2976-2985
        View in Article
        • Jolly L.A.
        • Taylor V.
        • Wood S.A.
        USP9X enhances the polarity and self-renewal of embryonic stem cell-derived neural progenitors.
        Mol Biol Cell. 2009; 20: 2015-2029
        View in Article
        • Oishi S.
        • Premarathne S.
        • Harvey T.J.
        • Iyer S.
        • Dixon C.
        • Alexander S.
        • et al.
        Usp9x-deficiency disrupts the morphological development of the postnatal hippocampal dentate gyrus.
        Sci Rep. 2016; 6: 25783
        View in Article
        • Stegeman S.
        • Jolly L.A.
        • Premarathne S.
        • Gecz J.
        • Richards L.J.
        • Mackay-Sim A.
        • et al.
        Loss of Usp9x disrupts cortical architecture, hippocampal development and TGFbeta-mediated axonogenesis.
        PLoS One. 2013; 8: e68287
        View in Article
        • Liang C.C.
        • Park A.Y.
        • Guan J.L.
        In vitro scratch assay: A convenient and inexpensive method for analysis of cell migration in vitro.
        Nat Protoc. 2007; 2: 329-333
        View in Article
        • Jolly L.A.
        • Nguyen L.S.
        • Domingo D.
        • Sun Y.
        • Barry S.
        • Hancarova M.
        • et al.
        HCFC1 loss-of-function mutations disrupt neuronal and neural progenitor cells of the developing brain.
        Hum Mol Genet. 2015; 24: 3335-3347
        View in Article
        • Harris L.
        • Dixon C.
        • Cato K.
        • Heng Y.H.
        • Kurniawan N.D.
        • Ullmann J.F.
        • et al.
        Heterozygosity for nuclear factor one x affects hippocampal-dependent behaviour in mice.
        PLoS One. 2013; 8: e65478
        View in Article
        • Rogers D.C.
        • Fisher E.M.
        • Brown S.D.
        • Peters J.
        • Hunter A.J.
        • Martin J.E.
        Behavioral and functional analysis of mouse phenotype: SHIRPA, a proposed protocol for comprehensive phenotype assessment.
        Mamm Genome. 1997; 8: 711-713
        View in Article
        • Stuchlik A.
        • Petrasek T.
        • Prokopova I.
        • Holubova K.
        • Hatalova H.
        • Vales K.
        • et al.
        Place avoidance tasks as tools in the behavioral neuroscience of learning and memory.
        Physiol Res. 2013; 62: S1-S19
        View in Article
        • Firth H.V.
        • Richards S.M.
        • Bevan A.P.
        • Clayton S.
        • Corpas M.
        • Rajan D.
        • et al.
        DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
        Am J Hum Genet. 2009; 84: 524-533
        View in Article
        • Richards S.
        • Aziz N.
        • Bale S.
        • Bick D.
        • Das S.
        • Gastier-Foster J.
        • et al.
        Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
        Genet Med. 2015; 17: 405-424
        View in Article
        • Zhang Q.
        • Dong A.
        • Walker J.R.
        • Bountra C.
        • Arrowsmith C.H.
        • Edwards A.M.
        • et al.
        Crystal structure of a peptidase.
        (Available at:)
        http://www.rcsb.org/structure/5WCH
        Date: 2018
        (Accessed June 2, 2018)
        View in Article
        • Wang K.
        • Li M.
        • Hakonarson H.
        ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data.
        Nucleic Acids Res. 2010; 38: e164
        View in Article
        • Rentzsch P.
        • Witten D.
        • Cooper G.M.
        • Shendure J.
        • Kircher M.
        CADD: Predicting the deleteriousness of variants throughout the human genome.
        Nucleic Acids Res. 2019; 47: D886-D894
        View in Article
        • Pejaver V.
        • Urresti J.
        • Lugo-Martinez J.
        • Pagel K.A.
        • Lin G.N.
        • Nam H.
        • et al.
        MutPred2: Inferring the molecular and phenotypic impact of amino acid variants [published online ahead of print May 9].
        bioRxiv. 2017;
        View in Article
        • Ebisawa T.
        • Fukuchi M.
        • Murakami G.
        • Chiba T.
        • Tanaka K.
        • Imamura T.
        • et al.
        Smurf1 interacts with transforming growth factor-beta type I receptor through Smad7 and induces receptor degradation.
        J Biol Chem. 2001; 276: 12477-12480
        View in Article
        • Wiese K.E.
        • Nusse R.
        • van Amerongen R.
        Wnt signalling: Conquering complexity.
        Development. 2018; 145
        View in Article
        • Crino P.B.
        The mTOR signalling cascade: Paving new roads to cure neurological disease.
        Nat Rev Neurol. 2016; 12: 379-392
        View in Article
        • Vucic D.
        • Dixit V.M.
        • Wertz I.E.
        Ubiquitylation in apoptosis: A post-translational modification at the edge of life and death.
        Nat Rev Mol Cell Biol. 2011; 12: 439-452
        View in Article
        • Schiller M.
        • Javelaud D.
        • Mauviel A.
        TGF-beta-induced SMAD signaling and gene regulation: Consequences for extracellular matrix remodeling and wound healing.
        J Dermatol Sci. 2004; 35: 83-92
        View in Article
        • Berletch J.B.
        • Ma W.
        • Yang F.
        • Shendure J.
        • Noble W.S.
        • Disteche C.M.
        • et al.
        Escape from X inactivation varies in mouse tissues.
        PLoS Genet. 2015; 11: e1005079
        View in Article
        • Kashima R.
        • Hata A.
        The role of TGF-β superfamily signaling in neurological disorders.
        Acta Biochim Biophys Sin (Shanghai). 2018; 50: 106-120
        View in Article
        • Bialas A.R.
        • Stevens B.
        TGF-beta signaling regulates neuronal C1q expression and developmental synaptic refinement.
        Nat Neurosci. 2013; 16: 1773-1782
        View in Article
        • Gomes F.C.
        • Sousa Vde O.
        • Romao L.
        Emerging roles for TGF-beta1 in nervous system development.
        Int J Dev Neurosci. 2005; 23: 413-424
        View in Article
        • Caraci F.
        • Gulisano W.
        • Guida C.A.
        • Impellizzeri A.A.
        • Drago F.
        • Puzzo D.
        • et al.
        A key role for TGF-beta1 in hippocampal synaptic plasticity and memory.
        Sci Rep. 2015; 5: 11252
        View in Article
        • Fukushima T.
        • Liu R.Y.
        • Byrne J.H.
        Transforming growth factor-beta2 modulates synaptic efficacy and plasticity and induces phosphorylation of CREB in hippocampal neurons.
        Hippocampus. 2007; 17: 5-9
        View in Article
        • Snijders Blok L.
        • Madsen E.
        • Juusola J.
        • Gilissen C.
        • Baralle D.
        • Reijnders M.R.
        • et al.
        Mutations in DDX3X are a common cause of unexplained intellectual disability with gender-specific effects on Wnt signaling.
        Am J Hum Genet. 2015; 97: 343-352
        View in Article
        • Shoubridge C.
        • Harvey R.J.
        • Dudding-Byth T.
        IQSEC2 mutation update and review of the female-specific phenotype spectrum including intellectual disability and epilepsy.
        Hum Mutat. 2019; 40: 5-24
        View in Article
        • Fieremans N.
        • Van Esch H.
        • de Ravel T.
        • Van Driessche J.
        • Belet S.
        • Bauters M.
        • et al.
        Microdeletion of the escape genes KDM5C and IQSEC2 in a girl with severe intellectual disability and autistic features.
        Eur J Med Genet. 2015; 58: 324-327
        View in Article
        • Jansen S.
        • Kleefstra T.
        • Willemsen M.H.
        • de Vries P.
        • Pfundt R.
        • Hehir-Kwa J.Y.
        • et al.
        De novo loss-of-function mutations in X-linked SMC1A cause severe ID and therapy-resistant epilepsy in females: Expanding the phenotypic spectrum.
        Clin Genet. 2016; 90: 413-419
        View in Article
        • Epi K.C.
        • Epilepsy Phenome/Genome P.
        • Allen A.S.
        • Berkovic S.F.
        • Cossette P.
        • Delanty N.
        • et al.
        De novo mutations in epileptic encephalopathies.
        Nature. 2013; 501: 217-221
        View in Article
        • Sakakibara N.
        • Morisada N.
        • Nozu K.
        • Nagatani K.
        • Ohta T.
        • Shimizu J.
        • et al.
        Clinical spectrum of male patients with OFD1 mutations.
        J Hum Genet. 2019; 64: 3-9
        View in Article
        • Bostrom C.
        • Yau S.Y.
        • Majaess N.
        • Vetrici M.
        • Gil-Mohapel J.
        • Christie B.R.
        Hippocampal dysfunction and cognitive impairment in Fragile-X Syndrome.
        Neurosci Biobehav Rev. 2016; 68: 563-574
        View in Article
        • Penzes P.
        • Buonanno A.
        • Passafaro M.
        • Sala C.
        • Sweet R.A.
        Developmental vulnerability of synapses and circuits associated with neuropsychiatric disorders.
        J Neurochem. 2013; 126: 165-182
        View in Article
        • Nadel L.
        Down's syndrome: A genetic disorder in biobehavioral perspective.
        Genes Brain Behav. 2003; 2: 156-166
        View in Article
        • Deboer T.
        • Wu Z.
        • Lee A.
        • Simon T.J.
        Hippocampal volume reduction in children with chromosome 22q11.2 deletion syndrome is associated with cognitive impairment.
        Behav Brain Funct. 2007; 3: 54
        View in Article

      Article Info

      Publication History

      Published online: June 29, 2019
      Accepted: May 30, 2019
      Received in revised form: May 23, 2019
      Received: March 27, 2019

      Footnotes

      Authors from the Undiagnosed Diseases Network include Loren Pena, Vandana Shashi, Kelly Schoch and Jennifer A. Sullivan. We acknowledge the contributions of other collaborating members: Maria T. Acosta, David R. Adams, Aaron Aday, Mercedes E. Alejandro, Patrick Allard, Euan A. Ashley, Mahshid S. Azamian, Carlos A. Bacino, Guney Bademci, Eva Baker, Ashok Balasubramanyam, Dustin Baldridge, Deborah Barbouth, Gabriel F. Batzli, Alan H. Beggs, Hugo J. Bellen, Jonathan A. Bernstein, Gerard T. Berry, Anna Bican, David P. Bick, Camille L. Birch, Stephanie Bivona, Carsten Bonnenmann, Devon Bonner, Braden E. Boone, Bret L. Bostwick, Lauren C. Briere, Elly Brokamp, Donna M. Brown, Matthew Brush, Elizabeth A. Burke, Lindsay C. Burrage, Manish J. Butte, Olveen Carrasquillo, Ta Chen Peter Chang, Hsiao-Tuan Chao, Gary D. Clark, Terra R. Coakley, Laurel A. Cobban, Joy D. Cogan, F. Sessions Cole, Heather A. Colley, Cynthia M. Cooper, Heidi Cope, William J. Craigen, Precilla D'Souza, Surendra Dasari, Mariska Davids, Jean M. Davidson, Jyoti G. Dayal, Esteban C. Dell'Angelica, Shweta U. Dhar, Naghmeh Dorrani, Daniel C. Dorset, Emilie D. Douine, David D. Draper, Annika M. Dries, Laura Duncan, David J. Eckstein, Lisa T. Emrick, Christine M. Eng, Gregory M. Enns, Cecilia Esteves, Tyra Estwick, Liliana Fernandez, Carlos Ferreira, Elizabeth L. Fieg, Paul G. Fisher, Brent L. Fogel, Irman Forghani, Noah D. Friedman, William A. Gahl, Rena A. Godfrey, Alica M. Goldman, David B. Goldstein, Jean-Philippe F. Gourdine, Alana Grajewski, Catherine A. Groden, Andrea L. Gropman, Melissa Haendel, Rizwan Hamid, Neil A. Hanchard, Frances High, Ingrid A. Holm, Jason Hom, Alden Huang, Yong Huang, Rosario Isasi, Fariha Jamal, Yong-hui Jiang, Jean M. Johnston, Angela L. Jones, Lefkothea Karaviti, Emily G. Kelley, David M. Koeller, Isaac S. Kohane, Jennefer N. Kohler, Deborah Krakow, Donna M. Krasnewich, Susan Korrick, Mary Koziura, Joel B. Krier, Jennifer E. Kyle, Seema R. Lalani, Byron Lam, Brendan C. Lanpher, Ian R. Lanza, C. Christopher Lau, Jozef Lazar, Kimberly LeBlanc, Brendan H. Lee, Hane Lee, Roy Levitt, Shawn E. Levy, Richard A. Lewis, Sharyn A. Lincoln, Pengfei Liu, Xue Zhong Liu, Sandra K. Loo, Joseph Loscalzo, Richard L. Maas, Ellen F. Macnamara, Calum A. MacRae, Valerie V. Maduro, Marta M. Majcherska, May Christine V. Malicdan, Laura A. Mamounas, Teri A. Manolio, Thomas C. Markello, Ronit Marom, Martin G. Martin, Julian A. Martínez-Agosto, Shruti Marwaha, Thomas May, Jacob McCauley, Allyn McConkie-Rosell, Colleen E. McCormack, Alexa T. McCray, Jason D. Merker, Thomas O. Metz, Matthew Might, Eva Morava-Kozicz, Paolo M. Moretti, Marie Morimoto, John J. Mulvihill, David R. Murdock, Avi Nath, Stan F. Nelson, J. Scott Newberry, John H. Newman, Sarah K. Nicholas, Donna Novacic, Devin Oglesbee, James P. Orengo, Stephen Pak, J. Carl Pallais, Christina GS. Palmer, Jeanette C. Papp, Neil H. Parker, John A. Phillips III, Jennifer E. Posey, John H. Postlethwait, Lorraine Potocki, Barbara N. Pusey, Genecee Renteri, Chloe M. Reuter, Lynette Rives, Amy K. Robertson, Lance H. Rodan, Jill A. Rosenfeld, Robb K. Rowley, Ralph Sacco, Jacinda B. Sampson, Susan L. Samson, Mario Saporta, Judy Schaechter, Timothy Schedl, Daryl A. Scott, Lisa Shakachite, Prashant Sharma, Kathleen Shields, Jimann Shin, Rebecca Signer, Catherine H. Sillari, Edwin K. Silverman, Janet S. Sinsheimer, Kevin S. Smith, Lilianna Solnica-Krezel, Rebecca C. Spillmann, Joan M. Stoler, Nicholas Stong, David A. Sweetser, Cecelia P. Tamburro, Queenie K.-G. Tan, Mustafa Tekin, Fred Telischi, Willa Thorson, Cynthia J. Tifft, Camilo Toro, Alyssa A. Tran, Tiina K. Urv, Tiphanie P. Vogel, Daryl M. Waggott, Colleen E. Wahl, Nicole M. Walley, Chris A. Walsh, Melissa Walker, Jennifer Wambach, Jijun Wan, Lee-kai Wang, Michael F. Wangler, Patricia A. Ward, Katrina M. Waters, Bobbie-Jo M. Webb-Robertson, Daniel Wegner, Monte Westerfield, Matthew T. Wheeler, Anastasia L. Wise, Lynne A. Wolfe, Jeremy D. Woods, Elizabeth A. Worthey, Shinya Yamamoto, John Yang, Amanda J. Yoon, Guoyun Yu, Diane B. Zastrow, Chunli Zhao and Stephan Zuchner. The principal investigator of the Undiagnosed Disease Network is William Gahl ( [email protected] ).

      Identification

      DOI: https://doi.org/10.1016/j.biopsych.2019.05.028

      Copyright

      © 2019 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

      ScienceDirect

      Access this article on ScienceDirect
      We use cookies to help provide and enhance our service and tailor content. To update your cookie settings, please visit the for this site.
      Copyright © 2022 Elsevier Inc. except certain content provided by third parties. The content on this site is intended for healthcare professionals.


      RELX