Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease
Daniel G. Calame, Tianyu Guo, Chen Wang, Lillian Garrett, Angad Jolly, Moez Dawood, Alina Kurolap, Noa Zunz Henig, Jawid M. Fatih, Isabella Herman, Haowei Du, Tadahiro Mitani, Lore Becker, Birgit Rathkolb, Raffaele Gerlini, Claudia Seisenberger, Susan Marschall, Jill V. Hunter, Amanda Gerard, Alexis R. Heidlebaugh, Thomas D. Challman, Rebecca C. Spillmann, Shalini N. Jhangiani, Zeynep Coban‐Akdemir, Seema R. Lalani, Lingxiao Liu, Anya Revah‐Politi, Alejandro Iglesias, Edwin R. Guzman, Evan H. Baugh, Nathalie Boddaert, Sophie Rondeau, Clothide Ormieres, Giulia Barcia, Queenie K.‐G. Tan, Isabelle Thiffault, Tomi Pastinen, Kazim A. Sheikh, Suur Biliciler, Davide Mei, Federico Melani, Vandana Shashi, Yuval Yaron, Mary Steele, Emma Wakeling, Elsebet Østergaard, Lusine Nazaryan‐Petersen, Francisca Millan, Teresa Santiago‐Sim, Julien Thévenon, Ange‐Line Bruel, Christel Thauvin‐Robinet, Denny Popp, Konrad Platzer, Paweł Gawliński, Wojciech Wiszniewski, Dana Marafi, Davut Pehli̇van, Jennifer E. Posey, Richard A. Gibbs, Valérie Gailus‐Durner, Renzo Guerrini, Helmut Fuchs, Martin Hrabě de Angelis, Sabine M. Hölter, Hoi‐Hung Cheung, Shen Gu, James R. Lupski
Abstract
DExD/H-box RNA helicases (DDX/DHX) are encoded by a large paralogous gene family; in a subset of these human helicase genes, pathogenic variation causes neurodevelopmental disorder (NDD) traits and cancer. DHX9 encodes a BRCA1-interacting nuclear helicase regulating transcription, R-loops, and homologous recombination and exhibits the highest mutational constraint of all DDX / DHX paralogs but remains unassociated with disease traits in OMIM. Using exome sequencing and family-based rare-variant analyses, we identified 20 individuals with de novo , ultra-rare, heterozygous missense or loss-of-function (LoF) DHX9 variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative Human Phenotype Ontology (HPO) analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigated DHX9 variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 was restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from an individual with an NLS variant also showed abnormal cytoplasmic DHX9 accumulation. CMT2-associated missense variants caused aberrant nucleolar DHX9 accumulation, a phenomenon previously associated with cellular stress. Two NDD-associated variants, p.Gly411Glu and p.Arg761Gln, altered DHX9 ATPase activity. The severe NDD-associated variant p.Arg141Gln did not affect DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks. Dhx9 −/− mice exhibited hypoactivity in novel environments, tremor, and sensorineural hearing loss. All together, these results establish DHX9 as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.