Monoallelic variation inDHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease

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.DHX9encodes 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 without disease trait associations. Using exome sequencing and family-based rare variant analysis, we identified 20 individuals withde novo, ultra-rare, heterozygous missense or loss-of-function (LoF)DHX9variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative HPO analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigatedDHX9variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from a patient 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 impact DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks.Dhx9-/-mice exhibit hypoactivity in novel environments, tremor, and sensorineural hearing loss. Taken together, these results establishDHX9as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.

Complete genomic assembly of Mauritian cynomolgus macaque killer immunoglobulin-like receptor and natural killer group 2 haplotypes

“…Isolated DNA was analyzed for purity and molecular weight using PicoGreen and gel imaging. After DNA quality control tests, Illumina sequencing libraries with incorporated barcodes were produced following standard procedures (48) using human genome sequencing center custom exome design (HG38_HGSC_Twist_Comprehensive_Exome) and Rhesus Spike-In probes following manufacturer’s protocol (https://www.twistbioscience.com/). This new design is a modification of our previous Rhexome design using NimbleGen Human whole exome probes plus rhesus-specific probes (49).…”