Bi-allelic loss-of-function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental syndrome

Spliceosome complex and neurodevelopmental disorders

Neurodevelopment requires complex spatiotemporal expression, which heavily relies on proper RNA splicing. The spliceosome is a ribonucleoprotein complex that removes introns from pre-mRNA, joins exons, and produces mature mRNA. Pathogenic variants in genes that code for spliceosome RNAs and proteins cause RNA mis-splicing and spliceosomopathies. Splicing defects during nervous system development upend the tightly controlled neurodevelopmental process, leading to neurodevelopmental disorders (NDDs). Despite the fact that the spliceosome is expressed in every cell, not all spliceosomopathies present as NDDs; spliceosomopathies are often tissue-specific in that a variant has a greater impact on certain cell lineages or cell types. Here we discuss spliceosomopathies whose presentations include NDDs and focus on spliceosome-coding genes.

Exploring the connection between RNA splicing and intellectual disability

Intellectual disability (ID) is a broad diagnostic category that encompasses individuals with impaired cognitive ability. While these disorders have heterogeneous causes, recent developments in next-generation sequencing (NGS) are revealing the prevalence of genetic etiologies. In particular, germline mutations in genes that affect RNA splicing are increasingly common causes of ID disorders. Research to elucidate the functional relationship between splicing and neurodevelopment is critical since molecular therapeutics require a nuanced understanding of the pathological mechanism. In this review, we first summarize the trends that have led to the discovery of the RNA splicing-ID relationship, then discuss recent progress and future directions for research surrounding RNA splicing in neurodevelopment. Finally, we speak on how these results may serve as the foundation for burgeoning therapies.

Deep phenotyping of 11 individuals with pathogenic variants in RNU4-2 reveals a clinically recognizable syndrome

PURPOSE

Despite ever-increasing knowledge of the genetic etiologies of neurodevelopmental disorders, approximately half remain undiagnosed after exome or genome sequencing. Here, we provide a deep clinical characterization of 11 previously unreported patients with a recently described neurodevelopmental disorder (NDD) due to pathogenic variants in RNU4-2.

METHODS

The 11 patients were identified in a pool of 70 patients selected for targeted RNU4-2 sequencing on the basis of their clinical phenotypes from a cohort of 1032 individuals with a NDD and without a prior genetic diagnosis.

RESULTS

The 11 patients were aged between 13 months and 36 years. All patients showed moderate to severe developmental delay and/or intellectual disability. Height and weight were below 10th percentile and most showed microcephaly. In almost 50% of the patients, intrauterine growth retardation was detected. All patients showed a distinctive pattern of dysmorphic features, including hooded upper eyelid and epicanthus, full cheeks, tented philtrum, mouth constantly slightly open with an everted lower lip vermilion, high palate, and profuse drooling. Of 11 patients, 64% also presented with ophthalmological problems (mainly strabismus, nystagmus, and refraction errors) and 64% had musculoskeletal features (joint hypermobility, mild scoliosis, and easy fractures).

CONCLUSION

This work provides an improved characterization of the phenotypic spectrum of RNU4-2 syndrome across different age groups and demonstrates that thorough clinical assessment of patients with an NDD can be enhanced significantly for this novel syndrome.

Transcriptional analysis of cancer cachexia: conserved and unique features across preclinical models and biological sex

Studies suggest heterogeneity in cancer cachexia (CC) among models and biological sexes, yet examinations comparing models and sexes are scarce. We compared the transcriptional landscape of skeletal muscle across murine CC models and biological sexes during early and late CC. Global gene expression analyses were performed on gastrocnemius [Lewis lung carcinoma (LLC)], quadriceps (KPC-pancreatic), and tibialis anterior [Colon-26 (C26)-colorectal and ApcMin/+] muscles across biological sexes. Differentially expressed genes (DEGs) were identified using an adj-P value of <0.05, followed by pathway and computational cistrome analyses. Integrating all controls, early and late stages of all models and sexes revealed up to 68% of DEGs and pathways were enriched at early and late CC, indicating a conserved transcriptional profile during CC development. Comparing DEGs and pathways within sexes and across models, in early CC, the transcriptional response was highly heterogeneous. At late stage, 11.5% of upregulated and 10% of downregulated genes were shared between models in males, whereas 18.9% of upregulated and 7% of downregulated DEGs were shared in females. Shared DEGs were enriched in proteasome and mitophagy/autophagy pathways (upregulated), and downregulation of energy metabolism pathways in males only. Between sexes, though the proportion of shared DEGs was low (<16%), similar pathway enrichment was observed, including proteasome and mitophagy at late-stage CC. In early CC, oncostatin M receptor (Osmr) upregulation was the only commonality across all models and sexes, whereas CLOCK and ARNTL/BMAL1 were predicted transcriptional factors associated with dysregulations in all three male models. This study highlights sex and model differences in CC progression and suggests conserved transcriptional changes as potential therapeutic targets.NEW & NOTEWORTHY This study is among the first to integrate and compare the skeletal muscle transcriptional landscape across multiple preclinical models and biological sexes. We highlight that 1) early CC transcriptional changes are two-thirds conserved at late stages, 2) DEGs are largely model and sex specific, and 3) transcriptional factors including CLOCK and ARNTL/BMAL1, which influence early CC gene expression, might represent a global therapeutic target with a chance of efficacy across various cancer types.

Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders

Most people with intellectual disability (ID) do not receive a molecular diagnosis following genetic testing. To identify new etiologies of ID, we performed a genetic association analysis comparing the burden of rare variants in 41,132 noncoding genes between 5,529 unrelated cases and 46,401 unrelated controls. RNU4-2, which encodes U4 small nuclear RNA, a critical component of the spliceosome, was the most strongly associated gene. We implicated de novo variants among 47 cases in two regions of RNU4-2 in the etiology of a syndrome characterized by ID, microcephaly, short stature, hypotonia, seizures and motor delay. We replicated this finding in three collections, bringing the number of unrelated cases to 73. Analysis of national genomic diagnostic data showed RNU4-2 to be a more common etiological gene for neurodevelopmental abnormality than any previously reported autosomal gene. Our findings add to the growing evidence of spliceosome dysfunction in the etiologies of neurological disorders.

The spectrum of pre-mRNA splicing in autism

Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre-mRNA splicing. Abnormal splicing patterns have been identified in the brains of individuals with ASD, and mutations in splicing factors have been found to contribute to neurodevelopmental delays associated with ASD. Here we review studies that shed light on the importance of splicing observed in ASD and that explored the intricate relationship between splicing factors and ASD, revealing how disruptions in pre-mRNA splicing may underlie ASD pathogenesis. We provide an overview of the research regarding all splicing factors associated with ASD and place a special emphasis on five specific splicing factors-HNRNPH2, NOVA2, WBP4, SRRM2, and RBFOX1-known to impact the splicing of ASD-related genes. In the discussion of the molecular mechanisms influenced by these splicing factors, we lay the groundwork for a deeper understanding of ASD's complex etiology. Finally, we discuss the potential benefit of unraveling the connection between splicing and ASD for the development of more precise diagnostic tools and targeted therapeutic interventions. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.

Neurodevelopmental disorders: 2024 update

Neurodevelopmental disorders encompass a range of conditions such as intellectual disability, autism spectrum disorder, rare genetic disorders and developmental and epileptic encephalopathies, all manifesting during childhood. Over 1,500 genes involved in various signaling pathways, including numerous transcriptional regulators, spliceosome elements, chromatin-modifying complexes and de novo variants have been recognized for their substantial role in these disorders. Along with new machine learning tools applied to neuroimaging, these discoveries facilitate genetic diagnoses, providing critical insights into neuropathological mechanisms and aiding in prognosis, and precision medicine. Also, new findings underscore the importance of understanding genetic contributions beyond protein-coding genes and emphasize the role of RNA and non-coding DNA molecules but also new players, such as transposable elements, whose dysregulation generates gene function disruption, epigenetic alteration, and genomic instability. Finally, recent developments in analyzing neuroimaging now offer the possibility of characterizing neuronal cytoarchitecture in vivo, presenting a viable alternative to traditional post-mortem studies. With a recently launched digital atlas of human fetal brain development, these new approaches will allow answering complex biological questions about fetal origins of cognitive function in childhood. In this review, we present ten fascinating topics where major progress has been made in the last year.