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.

Original languageEnglish
Pages (from-to)1394-1413
Number of pages20
JournalAmerican Journal of Human Genetics
Volume110
Issue number8
DOIs
StatePublished - 3 Aug 2023

Funding

FundersFunder number
Baylor College of Medicine Human Genome Sequencing CenterU54HG003273
General Research Fund of the Research Grants Council of Hong Kong14104321, 24101921
NHBLI
National Institutes of HealthT32 GM007526-42
National Institutes of Health
National Heart, Lung, and Blood Institute
National Human Genome Research Institute
National Institute of Neurological Disorders and StrokeR35NS105078
National Institute of Neurological Disorders and Stroke
International Rett Syndrome FoundationT32 NS043124, K08 HG008986, T32 GM007526, 3701-1, 873841
International Rett Syndrome Foundation
Muscular Dystrophy Association512848
Muscular Dystrophy Association
Uehara Memorial Foundation1K23 NS125126-01A1
Uehara Memorial Foundation
Rett Syndrome Research Trust
Baylor-Hopkins Center for Mendelian GenomicsUM1 HG006542, U01 HG011758
Baylor-Hopkins Center for Mendelian Genomics
Spastic Paraplegia Foundation
National Natural Science Foundation of China82202045
National Natural Science Foundation of China

    Keywords

    • Charcot-Marie-Tooth disease
    • DExD/H-box RNA helicases
    • DHX9
    • DNA damage repair
    • R-loops
    • allelic series
    • epilepsy
    • homologous recombination
    • neurodevelopmental disorders
    • neuropathy

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