Neurodevelopmental Disorders Linked to Small Nuclear RNA Variants

Genetic variants of a specific small nuclear RNA (snRNA), a family of non-coding RNAs that play a vital role in the spliceosome, account for nearly one in every twenty cases of neurodevelopmental disorders. According to early-access research published in Nature, these variants in the U4 snRNA RNU4-2 account for approximately 0.4% of individuals with neurodevelopmental disorders.

This research is important because approximately 60% of individuals with neurodevelopmental disorders are not diagnosed even after undergoing thorough genetic testing, mainly focusing on protein-coding genes. Currently, the overwhelming majority of disease-causing variations are found in about 1.5% of the genome responsible for producing proteins. In contrast, the non-coding genome, which makes up the remaining 98.5%, has been minimally studied, especially in regions far from protein-coding genes. Non-coding RNAs, accounting for 37.4% of processed exonic RNA sequences in humans, play crucial roles as regulators of biological processes in various cells and tissues.

This isn’t the first time snRNAs have been shown to play a part in human disorders. Two of these are snRNA components of the minor spliceosome: RNU12 variants cause autosomal recessive early-onset cerebellar ataxia, and RNU4ATAC variants cause an autosomal recessive multisystem congenital disorder known as Taybi-Linder, Lowry-Wood, or Roifman syndromes, which is marked by microcephaly, growth retardation, and developmental delay. By integrating RNU4-2 and other snRNAs into standard clinical protocols, numerous patients suffering from neurodevelopmental disorders will be spared from undergoing a challenging diagnostic procedure. Additionally, detecting the disease-causing gene will expedite research on potential treatments for these patients.

This large-scale international collaboration was spearheaded in the lab of Nicola (Nicky) Whiffin, PhD, an associate professor and group leader at the Wellcome Centre for Human Genetics and the Big Data Institute. Whiffin is also a visiting scientist at the Broad Institute of MIT and Harvard.

De novo variants in RNU4-2 cause neurodevelopmental syndrome

Yuyang Chen, a PhD student at the University of Oxford, and his colleagues utilized a group of 8,841 individuals with neurodevelopmental disorders of unknown genetic origin in the Genomics England 100,000 genomes project (GEL) to discover related genetic variations. This method zeroed in on a crucial 18-base-pair (bp) area central to RNU4-2 that is linked to a substantial neurodevelopmental phenotype. Compared to all other probands with neurodevelopmental disorders in GEL, individuals with the variant are more likely to have global developmental delay, microcephaly, gross motor development, hypotonia, short stature, drooling, and absent speech.

This variant was first identified as occurring de novo in 38 probands recruited for genome sequencing alongside their unaffected parents. By expanding the search to encompass probands in the full GEL cohort who did not have data for both parents, the researchers found eight more individuals with the n.64_65insT variant. The detectable inheritance in all eight cases is consistent with the variant arising de novo; the variant was not detected in cases where only one parent sample was available. Of the 8,841 probands in GEL with undiagnosed neurodevelopmental disorders, 0.52% have this variant; all 46 carriers have an unidentified neurodevelopmental disorder (such as intellectual disability, autism spectrum disorder, or global developmental delay). None of the 3,408 probands with a preexisting genetic diagnosis of neurodevelopmental disorders, 21,817 probands with phenotypes other than neurodevelopmental disorders, or 33,122 unaffected individuals have the n.64_65insT variant. 

These differences concern critical structural parts of the U4/U6 complex that help start the spliceosome and are needed to receive the 5′ splice site. The researchers demonstrate that RNU4-2 exhibits a significantly elevated expression level in the developing human brain, in contrast to RNU4-1 and other U4 homologs. Using RNA-sequencing, the researchers demonstrate the systematic disruption of 5′ splice site usage in individuals with RNU4-2 variants. This disruption aligns with the established function of this region in activating the spliceosome.

This study highlights the significance of non-coding genes in rare disorders and will offer a diagnosis to numerous individuals globally with neurodevelopmental disorders.