The findings implicate DCLK1 in a previously unrecognized progressive neurodevelopmental disorder and demonstrate the power of integrative cross-species functional genomics in resolving ultra-rare disease variants.
Abstract
Neurodevelopmental disorders are genetically heterogeneous and often remain unresolved despite extensive clinical evaluation and genomic testing. Here, we report a proband with a progressive neurodevelopmental disorder evaluated through the Undiagnosed Diseases Network who harbored heterozygous de novo missense variants in two genes, DCLK1 (p.(S228L)) and SFPQ (p.(P623R)). To determine the clinical significance of these candidate variants, we employed an integrative pipeline combining structural modeling, cross-species functional genomics, and patient-derived neuronal analyses. While the SFPQ variant yielded no detectable phenotype in Drosophila melanogaster, modeling the DCLK1 p.S228L variant in Caenorhabditis elegans induced severe locomotor deficits and aberrant neuronal morphology, including neurite blebbing. Parallel analyses of directly reprogrammed patient-derived neurons recapitulated these neurite defects, characterized by neurite beading, swelling and fragmentation, and elevated apoptosis. Transcriptomic profiling revealed dysregulation of neurodevelopmental and axon-guidance pathways alongside molecular signatures of neurodegeneration. Crucially, exogenous expression of wild-type DCLK1 or pharmacological targeting of a downstream dysregulated pathway partially rescued the neurite defects. Collectively, our findings implicate DCLK1 in a previously unrecognized progressive neurodevelopmental disorder and demonstrate the power of integrative cross-species functional genomics in resolving ultra-rare disease variants.
Rare variants in SETD1A, encoding a histone H3K4 methyltransferase, are among the strongest genetic risk factors for schizophrenia. Exome sequencing (n=3,736) revealed a population-enriched SETD1A missense variant (P596L) in the Lancaster Old Order Amish founder population, presenting a unique opportunity to elucidate variant-specific, multi-scale mechanisms. Psychiatric and cognitive phenotyping revealed nearly two-fold increased risk for bipolar disorder, accompanied by allele dose-dependent cognitive deficits in adulthood. Induced pluripotent stem cells (iPSCs) from homozygous carriers exhibited signatures of SETD1A hypofunction, including reduced proliferation and heightened susceptibility to replication stress and DNA double-strand breaks. During forebrain-directed differentiation, homozygous mutant cells displayed premature activation of neurodevelopmental transcriptional programs but impaired neural rosette formation, reduced neurite complexity, and early progenitor senescence. Multi-omic profiling revealed dysregulation of gene modules converging on replication stress pathways and neuronal regulatory networks enriched for autism and psychiatric risk genes. Pharmacologic inhibition of the H3K4 demethylase KDM5 partially rescued replication stress and neurite deficits, supporting an epigenetic mechanism and suggesting therapeutic tractability. Together, these findings link a population-enriched missense variant to disrupted chromatin regulation, genome stability, and neurodevelopmental timing, bridging human genetic risk with cellular pathophysiology.
R. Lease, Rediet T. Oshone, Yumna Ahmed et al.· Research Square· 0 citations
Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by impaired ciliary motility that leads to respiratory symptoms, laterality defects, and other systemic abnormalities. Despite significant advancements in genetic research identifying over 50 causative genes and enabling genetic diagnosis in approximately 90% of cases, comprehensive phenotypic characterization remains underexplored. We investigated two respiratory asymptomatic individuals (sisters) who exhibited laterality defects in a three-generation family, both of whom harbored novel compound heterozygous mutations (NM_001372.4:c.308del and NM_001372.4:c.11845G > A) in the
dynein axonemal heavy chain 9
(
DNAH9
) gene associated with primary ciliary dyskinesia-40 (CILD40). Structural modeling and western blotting analysis of HEK-293T cells demonstrated that the frameshift mutation abolished DNAH9 stability, whereas the missense mutation disrupted hydrogen bonds, leading to partial protein destabilization. Peripheral blood RNA sequencing revealed extensive dysregulation of axonemal and intraflagellar transport genes, implicating defects in microtubule-based motility in the two affected siblings with biallelic DNAH9 mutations, but not in their heterozygous family members or one unaffected relative. Plasma proteomic analysis of patients with CILD40 identified significant enrichment of pathways related to platelet activation, complement and coagulation cascades. Further comparative analysis with a patient with PCD caused by a CCDC40 mutation (CILD15 subtype) revealed differential signatures in CILD40, highlighting the potential of plasma proteomics for understanding distinct pathogenic mechanisms across PCD subtypes. These findings underscore the critical role of
DNAH9
compound heterozygous mutations in CILD40 and provide new insights into the genetic, transcriptional, and proteomic phenotypic heterogeneity of PCD.
Siming Kong, Mingshuo Wang, Xuedong Wang et al.· Phenomics· 0 citations
This study provides substantial evidence for the vital role of trip12 in the early stages of development, as homozygous individuals exhibited early mortality by Day 23 post-fertilization, while a substantial mortality rate was observed by Day 35 in ‘heterozygous’ mutants.
Maider Roibás-Santos, P. Suarez‐Bregua, J. Rotllant et al.· Brain Communications· 0 citations
Neurodevelopmental disorders (NDDs) are a group of developmental brain disorders caused by various genetic or acquired factors. OMIM has only recently associated the KCNK3 gene with developmental delay associated with sleep apnea (DDSA). Most prior studies on the KCNK3 gene have focused on PAH and cardiovascular diseases. In a 2-year-old girl presenting with generalized hypotonia and delayed language development, we identified a de novo missense variant in KCNK3 through the reanalysis of trio-whole exome sequencing (trio-WES) data. To further explore the relationship between KCNK3 and neurodevelopmental phenotypes, we conducted bidirectional expression regulation of the homologous gene Task7 based on the Drosophila model. Both overexpression and knockdown of the Task7 gene induced anxiety-like behaviors and impaired learning and memory. Notably, Task7 overexpression also led to reduced climbing ability and abnormal sleep patterns; collectively, these four phenotypes recapitulate the characteristic hallmarks of human neurodevelopmental disorders. This study represents the first application of a Drosophila model to demonstrate that KCNK3 functions as a dosage-sensitive regulator of neurodevelopment. While the underlying mechanisms remain to be fully elucidated, these findings position KCNK3 as a candidate gene for molecular screening and pave the way for future functional studies and therapeutic exploration in NDDs.
The biological plausibility of LNX2 as a candidate gene for neurodevelopmental disorders is supported, highlighting its preferential association with neuronal projection-cell networks, synaptic vesicle trafficking pathways, and neuron-specific regulatory programs.
M. Vinci, M. Figura, A. Musumeci et al.· Genes· 0 citations
Combined transcriptomics profiling in cyp2u1-/- zebrafish and SPG56 patient iPSC-derived cortical neurons supports impaired neural network development as a key disease mechanism.
D. Galatolo, Devid Damiani, V. Naef et al.· Human Molecular Genetics· 0 citations