Biology subjects

Steyaert, W.

Publications and source records attributed to Steyaert, W..

5 recordsLinked to original sources

bioRxiv2026

Sequence architecture shapes human allele frequencies through ectopic gene conversion

Population-genetic interpretations of allele frequency commonly begin from a single-origin assumption: that a variant arose once and was subsequently shaped by selection, drift and demographic history. Here we show that for a substantial fraction of human variation this assumption fails, and fails predictably: ectopic gene conversion reintroduces the same nucleotide change generation after generation, at rates strongly structured by two fixed properties of genome architecture, homologous template length and donor-acceptor distance. Across 534 million gnomAD v4.1 variants, this recurrent input accounts for an estimated 4% of the rarest variants and more than 15% of common ones. De novo mutations in 11,963 trios show the process directly: the mutation rate is elevated up to 28-fold precisely where the same variant is already common, with the newly arising allele matching the paralogous donor in 94% of such cases at long templates. The effect is strongest within segmental duplications but extends along every chromosome. Affected positions show reduced linkage disequilibrium and, at common frequencies, are depleted by 30-40% among reported GWAS associations. For this fraction of human variation, allele frequency is encoded in genome sequence architecture rather than set by population-genetic processes alone.

genetics↗

bioRxiv2025

Systematic disruption of zebrafish fibrillin genes identifies a translational zebrafish model for Marfan syndrome

BackgroundFibrillins are essential components of the extracellular matrix. Marfan syndrome (MFS), the most common fibrillinopathy, is characterized by severe cardiovascular complications, including cardiac valve abnormalities, myocardial dysfunction, arrhythmias, and, most commonly, thoracic aortic disease. Unfortunately, no definitive medical cure is available. ObjectivesTo establish a zebrafish model of MFS, to enhance understanding of the cardiovascular consequences of fibrillin impairment and identify novel therapeutic targets. MethodsCRISPR/Cas9 technology was used to systematically target all zebrafish fibrillin genes. The cardiovascular phenotype was investigated using fluorescent microscopy at embryonic stages and cardiac ultrasound, histology, and synchrotron X-ray imaging in adults. RNA sequencing and drug testing were performed during early development. ResultsFibrillin-2b mutant (fbn2b-/-) zebrafish had a reproducible phenotype, with a subset of embryos showing endocardial detachment leading to early mortality. Interestingly, the remaining fbn2b-/- zebrafish developed dilation of the bulbus arteriosus, a structure analogous to the aortic root in humans, and survived normally to adulthood. Adult fbn2b-/- zebrafish displayed cardiac valve abnormalities. Transcriptomic analysis of fbn2b-/-embryos suggested the involvement of extracellular matrix remodeling and immune-related pathways. Administration of nebivolol and losartan did not improve the phenotype of fbn2b-/- larvae. Zebrafish lacking fibrillin-1 and/or fibrillin-2a did not show any phenotype. ConclusionOur fbn2b-/- zebrafish model recapitulates key aspects of human cardiovascular manifestations of MFS and can therefore be considered a novel relevant animal model for MFS. Studying this model allows us to broaden the knowledge of the underlying mechanisms of the disease and discover much-needed disease-specific treatment options. CONDENSED ABSTRACTFibrillin defects lead to severe cardiovascular complications in Marfan syndrome (MFS), including aortic dilation, dissection, and rupture. To model MFS, we generated zebrafish mutants lacking various fibrillin genes. Among these mutant lines, only fibrillin-2b-deficient zebrafish exhibited cardiovascular phenotypes mimicking human disease. Multimodal imaging revealed early cardiac defects, bulbus arteriosus dilation, and valve abnormalities. Transcriptomic analysis identified altered regulation of pathways related to extracellular matrix homeostasis and immune system activation. Compound testing demonstrated the models potential for drug discovery. This zebrafish model, recapitulating key cardiovascular features of MFS, provides a valuable platform to investigate disease mechanisms and identify novel treatment strategies.

genetics↗

bioRxiv2025

Decoding Phenotypic Variability in Osteogenesis Imperfecta: Zebrafish as a Model for Molecular and Ultrastructural Insights.

Phenotypic variability is common in human diseases, even when the same genes are affected. In this study, three zebrafish models of Osteogenesis Imperfecta (OI) with dominant glycine substitutions in type I collagen genes (col1a1amh13/+, col1a1adc124/+, and col1a2mh15/+) were characterized for phenotypic severity and variability, using a newly developed standardized scoring system. Comprehensive analyses of the vertebral columns in these models revealed histological and ultrastructural differences that corresponded with phenotypic severity. Increasing skeletal severity correlated with a higher incidence of skeletal deformities and abnormalities. This, in turn, was associated with thinner bones and increased disorganization of collagen fibrils, fiber accumulation and mineralization, elastin deposits, and increased cell proliferation in the notochord and intervertebral ligament (IVL). Additionally, osteoblast function and bone regenerative capacity were increasingly compromised. These characteristics, combined with genetic information, have the potential to predict the severity of phenotypic outcomes in dominant forms of OI, caused by mutations in type I collagen. A remarkable intra-familial phenotypic variability in the col1a2mh15/+mutant holds potential for future approaches that could help in understanding the underlying mechanisms of this variability and the identification of modifier genes. Finally, through proteomics analysis three potential protein biomarkers (HSP47, Col8a1, and Bcan) were identified, that could serve as indicators of disease severity. These biomarkers not only have diagnostic value, but will allow stratification by OI type, have predictive value towards progression of the clinical presentation and will play a role in treatment guidance. Validation in human tissue samples will further reveal their clinical relevance. Significance StatementPhenotypic variability in human diseases, such as Osteogenesis Imperfecta (OI), remains poorly understood. Using zebrafish models with dominant glycine substitutions in type I collagen, this study links genetic mutations to phenotypic severity through standardized scoring and detailed ultrastructural and molecular analyses. Key findings include skeletal abnormalities, compromised osteoblast function, and intra-familial phenotypic variability, suggesting the role of modifier genes. Proteomics identified three potential biomarkers (HSP47, Col8a1, and Bcan) with diagnostic and prognostic value. These results provide critical insights into genotype-phenotype correlations, offering a foundation for personalized approaches to diagnosis, stratification, and treatment of OI and related disorders.

molecular biology↗

bioRxiv2021

DeNovoCNN: A deep learning approach to de novo variant calling in next generation sequencing data

De novo mutations (DNMs) are an important cause of genetic disorders. The accurate identification of DNMs from sequencing data is therefore fundamental to rare disease research and diagnostics. Unfortunately, identifying reliable DNMs remains a major challenge due to sequence errors, uneven coverage, and mapping artifacts. Here, we developed a deep convolutional neural network (CNN) DNM caller (DeNovoCNN), that encodes the alignment of sequence reads for a trio as 160x164 resolution images. DeNovoCNN was trained on DNMs of 5,616 whole exome sequencing (WES) trios achieving total 96.74% recall and 96.55% precision on the test dataset. We find that DeNovoCNN has increased recall/sensitivity and precision compared to existing DNM calling approaches (GATK, DeNovoGear, DeepTrio, Samtools) based on the Genome in a Bottle reference dataset and independent WES and WGS trios. Validations of DNMs based on Sanger and PacBio HiFi sequencing confirm that DeNovoCNN outperforms existing methods. Most importantly, our results suggest that DeNovoCNN is likely robust against different exome sequencing and analyses approaches, thereby allowing the application on other datasets. DeNovoCNN is freely available as a Docker container and can be run on existing alignment (BAM/CRAM) and variant calling (VCF) files from WES and WGS without a need for variant recalling.

bioinformatics↗

bioRxiv2018

Loss-of-function in IRF2BPL is associated with neurological phenotypes

The Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) gene encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals affected with neurological symptoms who carry damaging heterozygous variants in IRF2BPL. Five cases carrying nonsense variants in IRF2BPL resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The bioinformatics signature for IRF2BPL based on population genomics is consistent with a gene that is intolerant to variation. We show that the IRF2BPL ortholog in the fruit fly, called pits (protein interacting with Ttk69 and Sin3A), is broadly expressed including the nervous system. Complete loss of pits is lethal early in development, whereas partial knock-down with RNA interference in neurons leads to neurodegeneration, revealing requirement for this gene in proper neuronal function and maintenance. The nonsense variants in IRF2BPL identified in patients behave as severe loss-of-function alleles in this model organism, while ectopic expression of the missense variants leads to a range of phenotypes. Taken together, IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.

genetics↗