Biology subjects

Gorissen, B.

Publications and source records attributed to Gorissen, B..

4 recordsLinked to original sources

bioRxiv2026

Mapping active cis-regulatory elements from transcription initiation events

Determining the activity of cis-regulatory elements (CREs) is essential for modeling gene regulation and interpreting genetic variation. Yet, current methods often lack the specificity to distinguish active regulation from permissive chromatin, the sensitivity to detect unstable enhancer RNAs, or the scalability required to profile limited input material and primary cells. Here, we introduce nucCAGE, a transcription start site (TSS) assay for profiling nuclear, capped RNAs, and PRIME, a computational framework for identifying active CREs from TSS data. Together, these methods increase sensitivity to low-abundance RNAs and enable robust detection of active regulatory elements across diverse contexts. Across multiple orthogonal functional and genetic benchmarks, including fine-mapped eQTLs, ClinVar variants, GWAS loci, and CRISPRi-tested elements, nucCAGE-derived PRIME predictions achieve superior recall compared to state-of-the-art methods while maintaining strong enrichment for phenotype-associated variation. Applying PRIME to the FANTOM5 dataset yields a comprehensive, cell-type-resolved atlas of active CREs that recapitulates known tissue-trait relationships. We demonstrate how this atlas can be used to nominate causal noncoding variants, linking immune-cell enhancer regulation of SMAD3 to asthma and NCOR2 to premature separation of placenta. Together, nucCAGE and PRIME provide a framework for high-sensitivity genome-wide discovery of active CREs and a resource for variant-to-function studies.

genomics↗

bioRxiv2025

Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes

High-throughput, human-relevant approaches for predicting chemical toxicity are urgently needed for better decision-making in human health. Here, we apply image-based profiling (the Cell Painting assay) and two cytotoxicity assays (metabolic and membrane damage readouts) to primary human hepatocytes after exposure to eight concentrations of 1085 compounds that include pharmaceuticals, pesticides, and industrial chemicals with known liver toxicity-related outcomes. Three computational methods (CellProfiler, a Cell Painting-specific convolutional neural network, and a pretrained vision transformer) were compared to extract morphology features from single cells or entire images. We used these morphology features to predict activity in the measured cytotoxicity assays, as well as in 412 curated ToxCast assays that span cytotoxicity, cell-based, and cell-free categories. We found that the morphological profiles detect compound bioactivity at lower concentrations than standard cytotoxicity assays. In supervised analyses, they predict cytotoxicity and targeted cell-based assay readouts, but not cell-free assay readouts. We also found that the various feature extraction methods performed relatively similarly and that filtering out non-bioactive or cytotoxic concentrations did not boost supervised assay prediction performance for any assay endpoint category, although it did have a large influence on unsupervised cluster analysis. We envision that image-based profiling could serve as a key component of modern safety assessment.

pharmacology and toxicology↗

bioRxiv2024

Widespread naturally variable human exons aid genetic interpretation

Most mammalian genes undergo alternative splicing. The splicing of some exons has been acquired or lost in specific mammalian lineages, but differences in splicing within the human population are poorly characterized. Using GTEx tissue transcriptomes from 838 individuals, we identified 56,415 exons which are included in mRNAs in some individuals but entirely excluded from others, which we term "naturally variable exons" (NVEs). NVEs impact three quarters of protein-coding genes, occur at all population frequencies, and are often absent from reference annotations. NVEs are more abundant in genes depleted of genetic loss-of-function mutations and aid in the interpretation of causal genetic variants. Genetic variants modulate the splicing of many NVEs, and 5UTR and coding-region NVEs are often associated with increased and decreased gene expression, respectively. Together, our findings characterize abundant splicing variation in the human population, with implications for a range of human genetic analyses.

genetics↗

bioRxiv2020

Actuation Enhances Patterning in Human Neural Tube Organoids

Tissues achieve their complex spatial organization through an interplay between gene regulatory networks, cell-cell communication, and physical interactions mediated by mechanical forces. Current strategies to generate in-vitro tissues have largely failed to implement such active, dynamically coordinated mechanical manipulations, relying instead on extracellular matrices which respond to, rather than impose mechanical forces. Here we develop devices that enable the actuation of organoids. We show that active mechanical forces increase growth and lead to enhanced patterning in an organoid model of the neural tube derived from single human pluripotent stem cells (hPSC). Using a combination of single-cell transcriptomics and immunohistochemistry, we demonstrate that organoid mechanoregulation due to actuation operates in a temporally restricted competence window, and that organoid response to stretch is mediated extracellularly by matrix stiffness and intracellularly by cytoskeleton contractility and planar cell polarity. Exerting active mechanical forces on organoids using the approaches developed here is widely applicable and should enable the generation of more reproducible, programmable organoid shape, identity and patterns, opening avenues for the use of these tools in regenerative medicine and disease modelling applications.

bioengineering↗