Biology subjects

Vermeulen, F.

Publications and source records attributed to Vermeulen, F..

3 recordsLinked to original sources

bioRxiv2026

A functional comparison of readthrough agent ELX-02 across a wide range of nonsense CFTR variants

BackgroundNonsense variants in CFTR account for ~10% of cystic fibrosis (CF) variants and cannot be treated with approved CFTR modulators. Translational readthrough agents such as ELX-02 offer a potential therapeutic strategy, but clinical trials evaluated mainly in G542X CFTR nonsense variant and underlined limited efficacy. This study aimed to evaluate ELX-02-mediated CFTR rescue across a broad range of nonsense variants using patient-derived intestinal organoids (PDIOs) to define variant-specific determinants of readthrough efficacy and assess its potential across a genetically diverse CF population. MethodThe ex vivo response to ELX-02 was assessed in 206 PDIOs carrying heterogeneous nonsense variants. CFTR function was quantified using forskolin-induced swelling (FIS) assay after 48-hour exposure to ELX-02. Responses were analysed by genotype and stop codon identity, with secondary validation performed in a selected subset of PDIOs (n = 60). ResultsELX-02-mediated CFTR rescue varied markedly, ranging from responses approaching those observed with approved CFTR modulators (LUM/IVA) to responses at or below detection limit. Overall, maximal responses were modest and at the lower end of the functional range for CFTR modulators. Rescue was dose-dependent and higher in PDIOs carrying two nonsense variants when compared with PDIOs carrying a single nonsense variant combined with a residual or minimal function variant. Nonsense variants in nucleotide-binding domain 1, including G542X, S466X, G550X and R553X, showed relatively higher responsiveness. ConclusionELX-02 induces limited and highly heterogeneous CFTR rescue across nonsense variants. PDIO-based functional screening provides a framework to guide patient selection and stratification for future readthrough therapy trials.

molecular biology↗

bioRxiv2024

EVE is an open modular data analysis software for event-based localization microscopy

Event-based sensors (EBS), or neuromorphic vision sensors, offer a novel approach to imaging by recording light intensity changes asynchronously, unlike conventional cameras that capture light over fixed exposure times. This capability results in high temporal resolution, reduced data redundancy, and a wide dynamic range. This makes EBS ideal for Single-Molecule Localization Microscopy (SMLM) as SMLM relies on the sequential imaging of sparse, blinking fluorescent emitters to achieve super-resolution. Recent studies have shown that EBS can effectively capture these emitters, achieving spatial resolution comparable to traditional cameras. However, existing analyses of event-based SMLM (eveSMLM) data have relied on converting event lists into image frames for conventional analysis, limiting the full potential of the technology. To overcome this limitation, we developed EVE, a specialized software for analyzing eveSMLM data. EVE offers an integrated platform for detection, localization, and post-processing, with various algorithmic options tailored for the unique structure of eveSMLM data. EVE is user-friendly and features an open, modular infrastructure that supports ongoing development and optimization. EVE is the first dedicated tool for event-based SMLM, transforming the analysis process to fully utilize the spatiotemporal data generated by EBS. This allows researchers to explore the full potential of eveSMLM and encourages the development of new analytical methods and experimental improvements.

biophysics↗

bioRxiv2022

Nanoblades allow high-level genome editing in organoids

Genome engineering has become more accessible thanks to the RNA programmable endonucleases such as the CRISPR/Cas9 system. However, using this editing technology in synthetic organs called organoids is still very inefficient. This is due to the delivery methods used for the CRISPR-Cas9 machinery, which include electroporation of CRISPR/Cas9 DNA, mRNA or ribonucleoproteins (RNPs) containing the CAS9-gRNA complex. However, these procedures are toxic to some extent for the organoids. Here we describe the use of the Nanoblade technology, which outperformed by far knock-out (KO) levels achieved to date by gene editing in murine and human tissue derived organoids. We reached up to 80% of gene KO in organoids after treatment with nanoblades. Indeed, high-level nanoblade-mediated KO for the androgen receptor (AR) encoding gene and the cystic fibrosis transmembrane conductance regulator (CFTR) gene was achieved with single gRNA or dual gRNA containing nanoblades in murine prostate and colon organoids. Likewise, nanoblades achieved high levels of gene editing in human organoids ranging between 20% and 50%. Most importantly, in contrast to other gene editing methods, this was obtained without toxicity for the organoids. Only four weeks are required to obtain stable gene KO in organoids and nanoblades simplify and allow rapid genome editing in organoids with little to no side-effects such as possible unwanted INDELS in off-target sites.

bioengineering↗