Pathogenic variation in R-loop helicase gene DHX9 causes axonal neuropathy and neurodevelopmental disorders


Pre-Clinical Research

Poster Number: T398


Daniel Calame, MD, PhD, Baylor College of Medicine, Tianyu Guo, PhD, Chinese University of Hong Kong, Chen Wang, PhD, Chinese University of Hong Kong, Lingxiao Liu, MD, Chinese University of Hong Kong, Hoi-Hung Cheung, PhD, Chinese University of Hong Kong, Shen Gu, PhD, Chinese University of Hong Kong, James lupski, MD, PhD, DSc (hon), Baylor College of Medicine

DHX9 is a nuclear RNA helicase involved in R-loop regulation and DNA damage repair through homologous recombination. It is part of a large paralogous gene family encoding over 50 DDX-DHX RNA helicases. The gene DHX9 exhibits the highest mutational constraint to loss-of-function (LoF) and missense variation of all DDX-DHX helicases; it is also robustly expressed in the central and peripheral nervous system through development and into adulthood. While several DDX-DHX genes are linked to neurodevelopmental disorders (NDD), few have been connected to neuromuscular diseases. We have identified 24 individuals to date with de novo, ultra-rare, heterozygous missense or LoF DHX9 variants. Disease phenotypes range from adult-onset axonal neuropathy (CMT2) without history of NDDs to severe NDDs with associated microcephaly and seizures. One individual had both severe NDD and severe axonal sensorimotor polyneuropathy detected on nerve conduction study and electromyography. 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. The cellular consequences of pathogenic DHX9 variation were examined in human cell lines. While wild-type DHX9 localizes to the nucleus, NLS missense variants abnormally accumulate in the cytoplasm. CMT2-associated missense variants caused abnormal nucleolar DHX9 localization. As DHX9 localizes to the nucleolus during cellular stress, this may indicate a gain-of-function diseases mechanism whereby CMT2-associated variants either cause or mimic stress states. The severe NDD-associated DHX9 variant p.Arg141Gln did not affect DHX9 localization but increased R-loop levels and double-stranded DNA breaks. Finally, two NDD-associated DHX9 variants, p.Gly411Glu and p.Arg761Gln, altered DHX9 ATPase activity. Taken together, these results suggests pathogenic DHX9 variation underlies a broad neurologic disease spectrum ranging from adult-onset neuromuscular disease to childhood-onset NDDs. The disease mechanisms involved in DHX9¬-related disease are highly complex and range from haploinsufficiency to gain-of-function.