132 research outputs found
Neurodevelopmental disorders in 3D : interpreting the impact of non-coding structural variation on gene regulation and 3D chromatin structure
No full textCRISPR-ing the gap between discovery and validation of candidate genes for neurodevelopmental disorders
No full textGenomic structural variation in patients with intellectual disability and congenital anomalies
No full textInterpreting the impact of noncoding structural variation in neurodevelopmental disorders
No full textThe emergence of novel sequencing technologies has greatly improved the identification of structural variation, revealing that a human genome harbors tens of thousands of structural variants (SVs). Since these SVs primarily impact noncoding DNA sequences, the next challenge is one of interpretation, not least to improve our understanding of human disease etiology. However, this task is severely complicated by the intricacy of the gene regulatory landscapes embedded within these noncoding regions, their incomplete annotation, as well as their dependence on the three-dimensional (3D) conformation of the genome. Also in the context of neurodevelopmental disorders (NDDs), reports of putatively causal, noncoding SVs are accumulating and understanding their impact on transcriptional regulation is presenting itself as the next step toward improved genetic diagnosis
HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations
No full textStructural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within the HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3 '-HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7(Delta/Delta)) or CTCF site (CTCF-5(Delta/Delta)) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior/posterior limb expression patterns of SHH pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1(+/-) mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a CTCF site, and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9(INV/+)) in mice that does not disrupt Hdac9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidates essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence. It suggests that SVs encompassing protein-coding sequences could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene
Report of an apparently balanced translocation disrupting the AUTS2 gene in a patient with developmental delay
No full textFamilial cases of a submicroscopic Xp22.2 deletion : genotype-phenotype correlation in microphthalmia with linear skin defects syndrome
No full textPurpose: Microphthalmia with linear skin defects syndrome (MLS or MIDAS, OMIM #309801) is a rare X-linked male-lethal disorder characterized by microphthalmia or other ocular anomalies and skin lesions limited to the face and neck. However, inter-and intrafamilial variability is high. Here we report a familial case of MLS.
Methods: A mother and daughter with MLS underwent a complete ophthalmological examination, and extensive imaging, including anterior segment pictures, corneal topography and keratometry, autofluorescence, infrared reflectance and red free images, as well as spectral-domain optical coherence tomography. The mother also underwent full-field flash electroretinography. In addition, high-resolution array comparative genomic hybridization analysis was performed in both as well as in the maternal grandparents of the proband.
Results: Microphthalmia and retinal abnormalities were noted in the proband and the mother, whereas only the mother presented with scars of the typical neonatal linear skin defects. Array comparative genomic hybridization analysis revealed a 185-220 kb deletion on chromosome band Xp22.2 including the entire HCCS gene.
Conclusions: The identification of a deletion including HCCS led to the diagnosis of MLS in these patients. Retinal abnormalities can be part of the ocular manifestations of MLS
A comprehensive comparison of different seeding densities and the use of microscaffolds to establish a reproducible protocol for unguided neural organoid differentiation
No full textOver the last decade, neural organoids evolved as a highly promising state-of-the-art tissue model, which can recapitulate early human brain development. While guided organoid differentiation protocols to specific brain regions are more reproducible, the use of patterning factors may reduce cell diversity and mask important developmental processes. Unguided protocols on the other hand produce organoids reminiscent of the whole brain, which contain diverse but heterogeneous cell types/brain regions. To compare disease-specific neural organoids to wild-type organoids as a model system to study NDDs, reproducibility is a prerequisite.
Stem Cell Technologies offers a commercial kit to differentiate iPSCs into whole-brain organoids based on the formulation published by Lancaster et al. The optimized protocol of the kit suggests a seeding density of 9000 cells for Embryoid body (EB) formation. However, the best performance of the kit is reported with small EBs from 3000 cells. Other papers use microscaffolds during EB formation to enhance neuroectoderm formation and obtain more reproducible formation of the forebrain.
We performed a comprehensive comparison of the different seeding densities with and without microscaffolds . To assess their within-& between-batch reproducibility, various parameters during organoid development were monitored, such as size, oxygenation, cell type composition and transcriptome profile. Preliminary result show that smaller organoids are less variable in size and more oxygenated. Microscaffolds increase variability in size in early stages of organoid development, but seem to improve oxygenation of larger organoids. To conclude, with this comprehensive comparison, we hope to establish a reproducible protocol for unguided neural organoid differentiation
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