Biology subjects

Mulder, F.

Publications and source records attributed to Mulder, F..

4 recordsLinked to original sources

bioRxiv2026

Consensus native-like hepatitis C virus E1E2 engages broadly neutralizing antibody precursors

A major goal for hepatitis C virus (HCV) vaccine development is to elicit broadly neutralizing antibodies (bNAbs) against the E1E2 glycoprotein complex located on the viral surface. Inducing HCV bNAbs requires engagement of their germline B cell precursors. HCV glycoproteins usually do not bind and activate inferred germline precursors of bNAbs (igl-bNAbs), possibly because most circulating strains contain non-conserved isolate-specific residues, even in bNAb epitopes. Here, we generated stabilized native-like soluble E1E2 (sE1E2) antigens based on a consensus sequence of HCV (HepCon) to limit the exposure of antigenically rare residues. The antigenicity and glycosylation profiles show that HepCon sE1E2 resembles a native-like E1E2 heterodimer. HepCon sE1E2 induced cross-reactive neutralizing antibody responses as a soluble protein immunogen and as membrane-anchored mRNA-delivered immunogen in animals. Importantly, HepCon sE1E2 engages multiple igl-bNAbs against two major epitopes: antigenic region 3 (AR3), which is targeted by igl-bNAbs derived from the widely expressed human VH1-69 B cell gene, and antigenic region 4 (AR4), which is only present on native-like E1E2. Nanoparticles with HepCon sE1E2 efficiently activated B cell lines expressing AR3 and AR4 igl-bNAb B cell receptors in vitro. Finally, using HepCon sE1E2 we elucidated the atomic contacts of an AR3 igl-bNAb by cryo-electron microscopy. Thus, HepCon sE1E2 is a promising candidate for germline-targeting vaccination strategies.

immunology↗

bioRxiv2025

The Lettuce Expression Browser: from lab to LEB

Lettuce (Lactuca sativa L.) is an economically important leafy vegetable within the Asteraceae family, cultivated worldwide across diverse agricultural systems. Recent advances in genomic and transcriptomic resources have positioned lettuce as a promising model system for functional genomics in the Asteraceae. However, currently available gene expression datasets lack comprehensive tissue-specific resolution, primarily focus on a single cultivar and are not visualised in an interpretable manner, limiting their utility for broader genetic and physiological studies. To bridge this gap, we developed the Lettuce Expression Browser (LEB), a publicly available platform providing high-resolution gene expression maps across various organs, tissues and developmental stages in both cultivated and wild lettuce species. The LEB integrates transcriptomic data from finely dissected seedlings, shoot tissues at various developmental stages and seedlings subjected to abiotic stresses (salt and far-red), visualised using the ggPlantmap R package. This platform offers an intuitive interface for exploring gene expression patterns and serves as a valuable resource for those studying lettuce development, stress responses, and evolutionary genomics. The LEB is hosted on the LettuceKnow Web Portal (https://lettuce.bioinformatics.nl) and can be expanded to include additional datasets, enhancing its role as a key tool for lettuce research and crop improvement. Significance statementThe Lettuce Expression Browser (LEB) provides the first high-resolution gene expression atlas for both cultivated and wild lettuce species. This open-access resource enables detailed exploration of gene activity across development stages and stress conditions, advancing functional genomics in the Asteraceae family.

plant biology↗

bioRxiv2024

Bispecific antibodies against the hepatitis C virus E1E2 envelope glycoprotein

Hepatitis C virus (HCV) currently causes about one million infections and 240,000 deaths worldwide each year. To reach the goal set by the World Health Organization (WHO) of global HCV elimination by 2030, it is critical to develop a prophylactic vaccine. Broadly neutralizing antibodies (bNAbs) target the E1E2 envelope glycoproteins on the viral surface, can neutralize a broad range of the highly diverse circulating HCV strains and are essential tools to inform vaccine design. However, bNAbs targeting a single E1E2 epitope might be limited in neutralization breadth, which can be enhanced by using combinations of bNAbs that target different envelope epitopes. We have generated 60 IgG-like bispecific antibodies (bsAbs) that can simultaneously target two distinct epitopes on E1E2. We combine non-overlapping E1E2 specificities into three types of bsAbs, each containing a different hinge length. The bsAbs show retained or increased potency and breadth against a diverse panel of HCV pseudoparticles (HCVpp) and HCV produced in cell culture (HCVcc) compared to monospecific and cocktail controls. Additionally, we demonstrate that changes in the hinge length of bsAbs can alter the binding stoichiometry to E1E2. These results provide insights into the binding modes and the role of avidity in bivalent targeting of diverse E1E2 epitopes, and suggest structural differences between HCVpp and HCVcc. This study illustrates how potential cooperative effects of HCV bNAbs can be utilized by strategically designing bispecific constructs. These new HCV bsAbs can guide vaccine development and unlock novel therapeutic and prophylactic strategies against HCV and other (flavi)viruses.

microbiology↗

bioRxiv2018

EXtrACtor, a tool for multiple queries and data extractions from the EXAC and gnomAD database

IntroductionEXtrACtor provides an easy and flexible way to perform multiple queries of the ExAC and gnomAD databases (Lek M, al. e, 2016) and process the results. The ExAC browser is an often-used tool to gather information from a large number of exomes while the gnomAD database expands on this by increasing the number of exomes but also adding genomes. However the websites only allow the users to query a single gene, transcript or location at a time. On the other hand downloading the entire database results in other challenges for the average user, especially with the download size for the gnomAD database approaching 100GB. EXtrACtor allows the user to supply a list of genes, transcripts or regions to be queried against either the ExAC or the gnomAD database. At the same time it gives the user a flexible user interface in order to quickly filter on various properties such as cohort, variant type and more.\n\nAvailability and implementationEXtrACtor source code is freely available from https://github.com/dagrim1/extractor and is written in platform independent software Java for use on windows, UNIX and mac.\n\nContactf.mulder@umcutrecht.nl

bioinformatics↗