Biology subjects

De Baere, E.

Publications and source records attributed to De Baere, E..

9 recordsLinked to original sources

bioRxiv2026

The Lipidome of iPSC-Derived Retinal Organoids and RPE Partially Resembles that of the Human Retina

New approach methodologies (NAMs), including induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) and retinal pigment epithelium (iRPE), are increasingly applied to study retinal disease mechanisms and therapeutic strategies. However, these models often remain relatively immature. Given the high lipid content and complex metabolism of the retina, it is unclear to what extent iPSC-derived systems recapitulate the human retinal lipidome. Here, we compared the lipidomic profiles of ROs and iRPE, collected at several differentiation stages, with those of post-mortem adult human macular, non-macular and RPE plus choroid (pmRPE). The lipidome of iRPE differed markedly from pmRPE, whereas prolonged differentiation of ROs resulted in a lipidomic profile increasingly resembling that of the post-mortem retina. Moreover, ROs showed similarities to both macular and non-macular lipidome. These findings show that iPSC-derived models can become valuable NAMs to study lipid-related retinal disorders and provide a framework to optimize differentiation protocols.

molecular biology↗

bioRxiv2025

TurboID proximity interactome mapping reveals NR2E3 association with AP-1 and retinal developmental complexes

The photoreceptor-specific nuclear receptor NR2E3 is a key transcription factor in the retinal transcriptional network, essential in photoreceptor cell fate and maintenance. Various biallelic loss-of-function variants lead to autosomal recessive inherited retinal disease (IRD), while a single missense variant G56R has been identified to cause autosomal dominant retinitis pigmentosa (adRP). However, a comprehensive understanding of the interactome of NR2E3 remains elusive. Here, we aimed to map the interactome of this nuclear receptor and the G56R pathogenic variant through proximity labelling followed by mass spectrometry. We used the TurboID "T2A split/link design" to identify the proximity interactome of wild-type NR2E3 and mutant G56R-NR2E3 in ARPE-19 cells. Several protein complexes involved in retinal development, including the AP-1 complex, were enriched. The results suggest similar interactomes for NR2E3 and G56R-NR2E3 in ARPE-19. However, BCOR was exclusively enriched in the G56R-NR2E3 network, strengthening the connection with the IRD phenotype. In conclusion, our approach has mapped the proximity interactome of NR2E3 and G56R-NR2E3, revealing interaction with protein complexes involved in (retinal) development.

systems biology↗

bioRxiv2025

omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data.

The unprecedented speed and sensitivity of mass spectrometry (MS) unlocked large-scale applications of proteomics and even enabled proteome profiling of single cells. However, this fast-evolving field is hindered by a lack of scalable dimensionality reduction tools that can compensate for substantial batch effects and missingness across MS runs. Therefore, we present omicsGMF, a fast, scalable, and interpretable matrix factorization method, tailored for bulk and single-cell proteomics data. Unlike current workflows that sequentially apply imputation, batch correction, and principal component analysis, omicsGMF integrates these steps into a unified framework, dramatically enhancing data processing and dimensionality reduction. Additionally, omicsGMF provides robust imputation of missing values, outperforming bespoke state-of-the-art imputation tools. We further demonstrate how this integrated approach increases statistical power to detect differentially abundant proteins in the downstream data analysis. Hence, omicsGMF is a highly scalable approach to dimensionality reduction in proteomics, that dramatically improves many important steps in proteomics data analysis.

bioinformatics↗

bioRxiv2024

A proteogenomic atlas of the human neural retina

The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific splicing but have limitations in detailing transcript isoforms. To address this, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass spectrometry and whole genome sequencing data of three healthy human neural retina samples. We identified nearly 60,000 transcript isoforms, of which approximately one-third are novel. Additionally, ten novel peptides confirmed novel transcript isoforms. For instance, we identified a novel IMPDH1 isoform with a novel combination of known exons that is supported by peptide evidence. Our research underscores the potential of in-depth tissue-specific transcriptomic analysis to enhance our grasp of tissue-specific alternative splicing. The data underlying the proteogenomic atlas are available via EGA with identifier EGAD50000000101, via ProteomeXchange with identifier PXD045187, and accessible through the UCSC genome browser. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/595273v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e0810org.highwire.dtl.DTLVardef@1a382b6org.highwire.dtl.DTLVardef@1da7d9eorg.highwire.dtl.DTLVardef@16d29a3_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2023

Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses.

RNA-seq data analysis relies on many different tools, each tailored to specific applications and coming with unique assumptions and limitations. Indeed, tools for differential transcript usage or rare disease diagnosis through splicing and expression outliers, either lack performance, discard information, or do not scale to large datasets. We show that replacing normalization offsets unlocks bulk RNA-seq tools for differential usage and aberrant splicing, providing a single framework for various short- and long-read applications. We then introduce saseR, a tool for prioritizing expression and usage outliers that is much faster than state-of-the-art methods, and significantly outperforms these for aberrant splicing detection.

bioinformatics↗

bioRxiv2023

Comparative 3D genome analysis between neural retina and RPE reveals differential cis-regulatory interactions at retinal disease loci

Vision depends on the functional interplay between the photoreceptor cells of the neural retina and the supporting cells of the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases (IRD) display highly specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space. To understand the role of differential chromatin architecture in establishing tissue-specific expression patterns at IRD loci in the human neural retina and the RPE, we mapped genome-wide chromatin interactions by applying in situ Hi-C and H3K4me3 HiChIP to human adult post-mortem donor retinas. A comparative 3D genome analysis between neural retina and RPE/choroid revealed that almost 60% of 290 known IRD genes were marked by differential 3D genome structure and/or cis-regulatory interactions. One of these genes was ABCA4, which is implicated in the most common autosomal recessive IRD. We zoomed in on tissue-specific chromatin interactions at the ABCA4 locus using high-resolution UMI-4C assays. Upon integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish, we revealed tissue-specific CREs interacting with ABCA4. In summary, through extensive comparative 3D genome mapping, based on genome-wide (Hi-C), promoter-centric (HiChIP) and locus-specific (UMI-4C) assays of human neural retina and RPE, we have shown that gene regulation at key IRD loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes of IRD genes, but also delineate the search space for non-coding genomic variation underlying unsolved IRD. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/543842v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@fd0d7dorg.highwire.dtl.DTLVardef@180a5bforg.highwire.dtl.DTLVardef@101aec1org.highwire.dtl.DTLVardef@1781d1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2022

Multi-omics profiling, in vitro and in vivo enhancer assays dissect the cis -regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy

North Carolina macular dystrophy (NCMD) is a rare autosomal dominant disease affecting macular development. The disease is caused by non-coding single nucleotide variants (SNVs) in two hotspot regions near PRDM13 and by duplications in two distinct chromosomal loci, overlapping DNase I hypersensitive sites near either PRDM13 or IRX1. To unravel the mechanisms by which these variants cause disease, we first established a genome-wide multi-omics retinal database, RegRet. Integration of UMI-4C profiles we generated on adult human retina then allowed fine-mapping of the interactions of the PRDM13 and IRX1 gene promoters, and the identification of eighteen candidate cis-regulatory elements (cCREs), the activity of which was investigated by luciferase and Xenopus enhancer assays. Next, luciferase assays showed that the non-coding SNVs located in the two hotspot regions of PRDM13 affect cCRE activity, including two novel NCMD-associated non-coding SNVs that we identified. Interestingly, the cCRE containing one of these SNVs was shown to interact with the PRDM13 promoter, demonstrated in vivo activity in Xenopus, and is active at the developmental stage when progenitor cells of the central retina exit mitosis, putting forward this region as a PRDM13 enhancer. Finally, mining of single-cell transcriptional data of embryonic and adult retina revealed the highest expression of PRDM13 and IRX1 when amacrine cells start to synapse with retinal ganglion cells, supporting the hypothesis that altered PRDM13 or IRX1 expression impairs interactions between these cells during retinogenesis. Overall, this study gained insight into the cis-regulatory mechanisms of NCMD and supports that this condition is a retinal enhanceropathy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/481329v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@4a85e3org.highwire.dtl.DTLVardef@9bfe55org.highwire.dtl.DTLVardef@156a9d8org.highwire.dtl.DTLVardef@a8cb92_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2021

Loss of CEP162 function at the primary cilium delays ciliogenesis and causes retinal ciliopathy in humans

Defects in primary or motile cilia result in a variety of human pathologies, and retinal degeneration is frequently associated with these so-called ciliopathies. We show that homozygosity for a truncating variant in CEP162, a centrosome and microtubule-associated protein required for transition zone (TZ) assembly during ciliogenesis and neuronal differentiation in the retina, causes late-onset retinitis pigmentosa in 2 unrelated families. The mutant CEP162-E646R*5 protein is expressed and properly localized to the mitotic spindle but missing from the basal body in primary and photoreceptor cilia. This impairs recruitment of TZ components to the basal body and corresponds to complete loss of CEP162 function at the ciliary compartment, reflected by delayed formation of dysmorphic cilia. In contrast, rescue of increased cell death in the developing mouse retina after shRNA knockdown of Cep162 by expression of CEP162-E646R*5 indicates that the mutant retains its role for retinal neurogenesis. Human retinal degeneration thus results from specific loss of ciliary CEP162 function. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=134 HEIGHT=200 SRC="FIGDIR/small/469779v3_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@593dccorg.highwire.dtl.DTLVardef@e84d7forg.highwire.dtl.DTLVardef@137ce56org.highwire.dtl.DTLVardef@cba1f7_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2020

New pathogenic variants and insights into pathogenic mechanisms in GRK1-related Oguchi disease.

PurposeBiallelic mutations in G-Protein coupled receptor kinase 1 (GRK1) cause Oguchi disease, a rare subtype of congenital stationary night blindness (CSNB). The purpose of this study was to identify pathogenic GRK1 variants and use in-depth bioinformatic analyses to evaluate how their impact on protein structure could lead to pathogenicity. MethodsPatients genomic DNA was sequenced by whole genome, whole exome or focused exome sequencing. Pathogenic variants, published and novel, were compared to nondisease associated missense variants. The impact of GRK1 missense variants at the protein level were then predicted using a series of computational tools. ResultsWe identified eleven previously unpublished cases with biallelic pathogenic GRK1 variants, including seven novel variants, and reviewed all GRK1 pathogenic variants. Further structure-based scoring revealed a hotspot for missense variants in the kinase domain. Additionally, to aid future clinical interpretation, we identified the bioinformatics tools best able to differentiate pathogenic from non-pathogenic variants. ConclusionWe identified new GRK1 pathogenic variants in Oguchi disease patients and investigated how disease-causing variants may impede protein function, giving new insights into the mechanisms of pathogenicity. All pathogenic GRK1 variants described to date have been collated into a Leiden Open Variation Database (http://dna2.leeds.ac.uk/GRK1_LOVD/genes/GRK1).

genetics↗