Biology subjects

Wilbers, R. H. P.

Publications and source records attributed to Wilbers, R. H. P..

4 recordsLinked to original sources

bioRxiv2025

Precision Glycoform Engineering: Combining plant and in vitro systems for tailored biopharmaceutical production

Protein biopharmaceuticals play a key role in providing effective, targeted, and personalized therapies for diverse diseases, while also preventing and mitigating a broad range of infections. N-glycosylation is a key post-translational modification influencing the biological activity of many protein-based therapeutics, yet structure-function relationships of N-glycans remain poorly understood due to challenges in producing homogeneous glycoforms. Current go-to production hosts, mammalian and yeast cells, often yield heterogeneous glycan profiles and require extensive genetic manipulation. Alternative production hosts such as the plant Nicotiana benthamiana, provide more homogeneous glycosylation and flexibility through transient expression, but are limited in the generation of certain glycoforms. In vitro glycoengineering can overcome these limitations but is time consuming and requires expensive resources. In this study, we show that by combining in planta and in vitro glycoengineering strategies, we can quickly produce a wide range of homogeneous glycoforms of pharmaceutical proteins with high mannose, paucimannose, hybrid and complex N-glycan structures. Using N. benthamiana as a transient expression host, we produced two pharmaceutical glycoproteins -- the monoclonal antibody rituximab and the helminth vaccine candidate OoASP-1 -- and modified them in vitro using Escherichia coli produced glycoenzymes. The combination of these two glycoengineering systems minimizes the amount of time and resources required, while maintaining high glycan homogeneity. This scalable, flexible, and cost-effective platform opens the door to glycan structure-function relationship studies and can support rational design of next-generation biopharmaceuticals.

bioengineering↗

bioRxiv2020

Conserved codon adaptation in highly expressed genes is associated with higher regularity in mRNA secondary structures

The redundancy of the genetic code allows for a regulatory layer to optimize protein synthesis by modulating translation and degradation of mRNAs. Patterns in synonymous codon usage in highly expressed genes have been studied in many species, but scarcely in conjunction with mRNA secondary structure. Here, we analyzed over 2,000 expression profiles covering a range of strains, treatments, and developmental stages of five model species (Escherichia coli, Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, and Mus musculus). By comparative analyses of genes constitutively expressed at high and low levels, we revealed a conserved shift in codon usage and predicted mRNA secondary structures. Highly abundant transcripts and proteins, as well as high protein per transcript ratios, were consistently associated with less variable and shorter stretches of weak mRNA secondary structures (loops). Genome-wide recoding showed that codons with the highest relative increase in highly expressed genes, often C-ending and not necessarily the most frequent, enhanced formation of uniform loop sizes. Our results point at a general selective force contributing to the optimal expression of abundant proteins as less variable secondary structures promote regular ribosome trafficking with less detrimental collisions, thereby leading to an increase in mRNA stability and a higher translation efficiency.

bioinformatics↗

bioRxiv2020

Tumor Necrosis Factor and Schistosoma mansoni egg antigen Omega-1 shape distinct aspects of the early egg-induced granulomatous response

Infections by schistosomes result in granulomatous lesions around parasite eggs entrapped within the host tissues. The host and parasite determinants of the Schistosoma mansoni egg-induced granulomatous response are areas of active investigation. Some studies in mice implicate Tumor Necrosis Factor (TNF) produced in response to the infection whereas others fail to find a role for it. In addition, in the mouse model, the S. mansoni secreted egg antigen omega-1 is found to induce granulomas but the underlying mechanism remains unknown. We have recently developed the zebrafish larva as a model to study macrophage recruitment and granuloma formation in response to Schistosoma mansoni eggs. Here we use this model to investigate the mechanisms by which TNF and omega-1 shape the early granulomatous response. We find that TNF, specifically signaling through TNF receptor 1, is not required for macrophage recruitment to the egg and granuloma initiation but does mediate granuloma enlargement. In contrast, omega-1 mediates initial macrophage recruitment, with this chemotactic activity being dependent on its RNase activity. Our findings further the understanding of the role of these host- and parasite-derived factors and show that they impact distinct facets of the granulomatous response to the schistosome egg.

microbiology↗

bioRxiv2017

GM-CSF negatively regulates early IL-10 mediated responses

Inflammatory disorders are becoming more prevalent in the Western world. Treatment of these diseases relies on the intervention in inflammatory responses thereby restoring immune homeostasis. One cytokine that has the potential to restore immune homeostasis is the anti-inflammatory cytokine interleukin-10 (IL-10). But until now IL-10 treatment has not been as successful as anticipated. A reason for this may be that IL-10 responsiveness depends on the environment of the inflamed tissue. In this study we describe that granulocyte-macrophage colony-stimulating factor (GM-CSF) is a key cytokine that negatively regulates IL-10-mediated responses. Dendritic cells differentiated from bone marrow with GM-CSF have a reduced ability to respond to IL-10. Dendritic cells are impaired in their up-regulation of IL-10-induced SOCS3 expression and are unable to suppress LPS-induced TNF- expression at an early time point. Furthermore, GM-CSF treatment partially replicates this phenotype in macrophages. Surprisingly, GM-CSF seems to regulate IL-10 activity in macrophages without affecting STAT3 activation. Still, GM-CSF induces constitutive phosphorylation of glycogen synthase kinase 3{beta}, a signalling component downstream of the PI3K/Akt pathway. Knowledge on the exact mechanism by which GM-CSF negatively regulates IL-10 activity could give novel insights on the integration of signal transduction pathways elicited by different cytokines. Ultimately this knowledge could provide us with new therapeutic strategies to treat inflammatory disorders.

immunology↗