Summary: An international team led by researchers at the Children’s Hospital of Philadelphia (CHOP) has identified how three previously uncharacterized genes contribute to neurodevelopmental disorders by disrupting the spliceosome, the cellular machinery that processes pre-mRNA. This discovery clarifies molecular pathways underlying developmental delay, intellectual disability and autism, and highlights potential targets for future therapies.
Using a combination of genomic sequencing, detailed clinical phenotyping, and functional modeling in human stem cells and fruit flies, the study mapped how variants in these genes impair pre-mRNA splicing and neuronal development. The work links specific missense variants in U2AF2, PRPF19 and RBFOX1 to altered splicing, defective neurite formation and behavioral changes in model organisms, establishing a hierarchical genetic network essential for brain development and function.
Key Facts:
- Researchers identified pathogenic variants in three splicing-factor genes—U2AF2, PRPF19 and RBFOX1—that are associated with neurodevelopmental disorders.
- Functional tests in human pluripotent stem cell–derived neurons and Drosophila models showed disrupted splicing, impaired neuritogenesis and developmental and behavioral abnormalities.
- The findings demonstrate that spliceosome malfunction can be a direct cause of overlapping neurodevelopmental phenotypes and suggest new avenues for diagnostic and therapeutic development.
Source: CHOP
An international collaboration led by investigators at the Children’s Hospital of Philadelphia has clarified how three novel genes cause neurodevelopmental disorders by disrupting pre-mRNA splicing.
The full report appears in the Journal of Clinical Investigation.
Over recent decades, large-scale sequencing efforts have linked more than 1,500 genes across diverse signaling pathways to neurodevelopmental disorders (NDDs). Despite these advances, only about one-third of affected individuals currently receive a definitive genetic diagnosis, and the relationships among many implicated genes remain poorly understood.
This study addressed that gap by focusing on pre-mRNA splicing, the process that removes noncoding introns and joins coding exons to produce mature mRNA. Splicing is orchestrated by the spliceosome, a dynamic protein–RNA complex. Although splicing defects have been implicated in several neurological conditions, variants that directly impair spliceosome components have seldom been associated with NDDs—until now.
The investigators combined clinical sequencing data from unrelated patients with experimental assays. They identified 46 individuals carrying de novo U2AF2 missense variants, including several recurrent changes seen in many patients, and six individuals with de novo PRPF19 variants. Functional assays showed that multiple U2AF2 variants altered splicing of model substrates. Human neurons derived from pluripotent stem cells bearing two recurrent U2AF2 variants exhibited reduced neuritogenesis, indicating disrupted neuronal morphogenesis.
In parallel, loss-of-function studies in Drosophila orthologs—U2af50 and Prp19—caused lethality, abnormal mushroom body architecture (a brain structure linked to learning and memory) and social behavior deficits. Rescue experiments demonstrated that wild-type but not mutant forms of U2AF2 or PRPF19 could restore certain functions, supporting the pathogenicity of the human variants.
Transcriptome profiling of affected samples revealed downstream splicing substrates and regulators, including RBFOX1, a third splicing factor uncovered by the analyses. Re-examination of previously negative clinical exomes and subsequent data-sharing identified six patients with RBFOX1 missense variants. In vitro testing showed that these RBFOX1 variants impaired function, consistent with a role in the same splicing network.
“By integrating genomic data with cross-species functional modeling and cellular phenotyping, we mapped how variants in three splicing factors disrupt the machinery that shapes neuronal development,” said Dong Li, Ph.D., lead author and research faculty member in CHOP’s Center for Applied Genomics and Division of Human Genetics. “These results illuminate molecular mechanisms behind overlapping neurodevelopmental phenotypes and identify splicing as a critical vulnerability in brain development.”
Co-author Yuanquan Song, Ph.D., noted that fly and human genetic approaches were complementary: “Loss of each gene produced distinct structural and functional brain abnormalities in Drosophila, demonstrating their essential roles in development and validating their clinical relevance.”
Senior author Hakon Hakonarson, M.D., Ph.D., director of the Center for Applied Genomics at CHOP, emphasized the broader implications: “This study not only identifies three causative genes for neurodevelopmental disorders, but also highlights the central importance of pre-mRNA splicing to central nervous system development.”
Funding: The research received support from multiple sources, including CHOP internal grants, philanthropic foundations, the National Institutes of Health, national research agencies across several countries, and other institutional and international funding programs.
About this genetics and neurodevelopment research news
Author: Ben Leach
Source: CHOP
Contact: Ben Leach – CHOP
Image: The image is credited to Neuroscience News
Original Research: Open access. “Spliceosome malfunction causes neurodevelopmental disorders with overlapping features” by Dong Li et al., Journal of Clinical Investigation.
Abstract
Spliceosome malfunction causes neurodevelopmental disorders with overlapping features
Pre-mRNA splicing is a tightly regulated process essential for accurate gene expression. While splicing dysregulation has been associated with various neurological deficits, the underlying molecular and cellular mechanisms remain incompletely defined. In this study, pathogenic missense variants in U2AF2 and PRPF19—genes encoding spliceosome components—were implicated in NDDs through the identification of 46 individuals with de novo U2AF2 variants and six individuals with de novo PRPF19 variants. Functional experiments showed that several U2AF2 variants dysregulated splicing, and stem cell–derived human neurons carrying recurrent U2AF2 variants displayed impaired neuritogenesis. Drosophila loss-of-function of orthologous genes resulted in lethality, abnormal mushroom body patterning and social deficits, with differential rescue by wild-type versus mutant alleles. Transcriptome profiling uncovered affected splicing substrates and effectors, including RBFOX1, for which damaging missense variants were subsequently identified in additional patients and shown to produce loss of function in vitro. Together, these results implicate three splicing factors as causative genes for NDDs and establish a hierarchical genetic network essential for human brain development and function.