Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease

Am J Hum Genet. 2023 Aug 3;110(8):1394-1413. doi: 10.1016/j.ajhg.2023.06.013. Epub 2023 Jul 18.

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.

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

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Line
  • Charcot-Marie-Tooth Disease* / genetics
  • DEAD-box RNA Helicases / genetics
  • DNA Helicases
  • Dichlorodiphenyl Dichloroethylene
  • Humans
  • Mammals
  • Mice
  • Neoplasm Proteins / genetics
  • Neurodevelopmental Disorders*

Substances

  • DEAD-box RNA Helicases
  • DHX9 protein, human
  • Dichlorodiphenyl Dichloroethylene
  • DNA Helicases
  • Neoplasm Proteins
  • Dhx9 protein, mouse