Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

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  • Dong Li
  • Qin Wang
  • Allan Bayat
  • Mark R. Battig
  • Yijing Zhou
  • Daniëlle G.M. Bosch
  • Gijs van Haaften
  • Leslie Granger
  • Andrea K. Petersen
  • Luis A. Pérez-Jurado
  • Gemma Aznar-Laín
  • Anushree Aneja
  • Miroslava Hancarova
  • Sarka Bendova
  • Martin Schwarz
  • Radka Kremlikova Pourova
  • Zdenek Sedlacek
  • Beth A. Keena
  • Michael E. March
  • Cuiping Hou
  • Nora O’Connor
  • Elizabeth J. Bhoj
  • Margaret H. Harr
  • Gabrielle Lemire
  • Kym M. Boycott
  • Meghan Towne
  • Megan Li
  • Mark Tarnopolsky
  • Lauren Brady
  • Michael J. Parker
  • Hanna Faghfoury
  • Lea Kristin Parsley
  • Emanuele Agolini
  • Maria Lisa Dentici
  • Antonio Novelli
  • Meredith Wright
  • Rachel Palmquist
  • Khanh Lai
  • Marcello Scala
  • Pasquale Striano
  • Michele Iacomino
  • Federico Zara
  • Annina Cooper
  • Timothy J. Maarup
  • Melissa Byler
  • Robert Roger Lebel
  • Tugce B. Balci
  • Raymond Louie
  • Michael Lyons
  • Jessica Douglas
  • Catherine Nowak
  • Alexandra Afenjar
  • Juliane Hoyer
  • Boris Keren
  • Saskia M. Maas
  • Mahdi M. Motazacker
  • Julian A. Martinez-Agosto
  • Ahna M. Rabani
  • Elizabeth M. McCormick
  • Marni J. Falk
  • Sarah M. Ruggiero
  • Ingo Helbig
  • Rikke S. Møller
  • Lino Tessarollo
  • Francesco Tomassoni Ardori
  • Mary Ellen Palko
  • Tzung Chien Hsieh
  • Peter M. Krawitz
  • Mythily Ganapathi
  • Bruce D. Gelb
  • Vaidehi Jobanputra
  • Ashley Wilson
  • John Greally
  • Sébastien Jacquemont
  • Khadijé Jizi
  • Ange Line Bruel
  • Chloé Quelin
  • Vinod K. Misra
  • Erika Chick
  • Corrado Romano
  • Donatella Greco
  • Alessia Arena
  • Manuela Morleo
  • Vincenzo Nigro
  • Rie Seyama
  • Yuri Uchiyama
  • Naomichi Matsumoto
  • Ryoji Taira
  • Katsuya Tashiro
  • Yasunari Sakai
  • Gökhan Yigit
  • Bernd Wollnik
  • Michael Wagner
  • Barbara Kutsche
  • Anna C.E. Hurst
  • Michelle L. Thompson
  • Ryan Schmidt
  • Linda Randolph
  • Rebecca C. Spillmann
  • Vandana Shashi
  • Edward J. Higginbotham
  • Dawn Cordeiro
  • Amanda Carnevale
  • Gregory Costain
  • Tayyaba Khan
  • Benoît Funalot
  • Frederic Tran Mau-Them
  • Luis Fernandez Garcia Moya
  • Sixto García-Miñaúr
  • Matthew Osmond
  • Lauren Chad
  • Nada Quercia
  • Diana Carrasco
  • Chumei Li
  • Amarilis Sanchez-Valle
  • Meghan Kelley
  • Mathilde Nizon
  • Brynjar O. Jensson
  • Patrick Sulem
  • Kari Stefansson
  • Svetlana Gorokhova
  • Tiffany Busa
  • Marlène Rio
  • Hamza Hadj Habdallah
  • Marion Lesieur-Sebellin
  • Jeanne Amiel
  • Véronique Pingault
  • Sandra Mercier
  • Marie Vincent
  • Christophe Philippe
  • Clemence Fatus-Fauconnier
  • Kathryn Friend
  • Rebecca K. Halligan
  • Sunita Biswas
  • Jane Rosser
  • Cheryl Shoubridge
  • Mark Corbett
  • Christopher Barnett
  • Jozef Gecz
  • Kathleen Leppig
  • Anne Slavotinek
  • Carlo Marcelis
  • Rolph Pfundt
  • Bert B.A. de Vries
  • Marjon A. van Slegtenhorst
  • Alice S. Brooks
  • Benjamin Cogne
  • Thomas Rambaud
  • Elaine H. Zackai
  • Naiara Akizu
  • Yuanquan Song
  • Hakon Hakonarson
Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.
OriginalsprogEngelsk
Artikelnummere171235
TidsskriftJournal of Clinical Investigation
Vol/bind134
Udgave nummer1
Antal sider17
ISSN0021-9738
DOI
StatusUdgivet - 2024

Bibliografisk note

Funding Information:
We thank the patients and their families for participating in this research. We acknowledge Clara L. Kielkopf (University of Rochester, Rochester, New York, USA) for providing the pyPY minigene construct. This study was supported in part by a CHOP Roberts Collaborative Functional Genomics Rapid grant (to DL, MB, and YS); Institutional Development Funds (to HH); an Eagles Autism Foundation grant (to DL); NIH grant R01NS107392 (to YS); and a Pennsylvania Department of Health grant 4100088540 (to YS). Work for U2AF2 individual 30 was supported by the NIH Common Fund, through the Office of Strategic Coordination/Office of the NIH Director under Award U01HG007672 (to Duke University). Work for U2AF2 individual 27 was conducted as part of the Clinical Sequencing Evidence-Generating Research (CSER) consortium, which is funded by the National Human Genome Research Institute (NHGRI) (U01HG007301) with co-funding from the National Institute on Minority Health and Health Disparities (NIMHD) and the NCI, NIH. Work for U2AF2 individual 28 was conducted at the University of Alabama at Birmingham and the HudsonAlpha Institute for Biotechnology, and funded by the state of Alabama. Work for U2AF2 individual 45 was supported in part by the Telethon Undiagnosed Diseases Program (TUDP) (GSP15001). Work for PRPF19 individual P2 was supported by NIH U01 award HG009610 (to BDG). Additional support includes grant NU22-07-00165 from the Czech Ministry of Health (to ZS); the German Research Foundation (DFG, Deutsche Forschungsgemeinschaft) under Germany’s Excellence Strategy (EXC 2067/1-390729940); and the DZHK (German Centre for Cardiovascular Research; partner site Göttingen) (to BW); the Dutch Organization for Health Research and Development ZON-MW grant 912-12-109 (to BBADV); the Novo Nordisk Foundation grant NNF20SA0064340 (to AB); the Japan Agency for Medical Research and Development (AMED) under grant numbers JP22ek0109486, JP22ek0109549, and JP22ek0109493 (to NM); JSPS KAKENHI under grant number JP21K15907 (to YU); and the Takeda Science Foundation (to NM). The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant HICF-1009-003). This study makes use of DECIPHER (https://www.deciphergenomics.org), which is funded by Wellcome (grant 223718/Z/21/Z) and hosted by EMBL-EBI. See Nature PMID: 25533962 or www.ddduk.org/access.html for full acknowledgment. The illustration in the Graphical Abstract was generated in part using Biorender.com.

Publisher Copyright:
Copyright: © 2023, Li et al. This is an open access article published under the terms of the Creative Commons Attribution 4.0 International License.

ID: 379878060