Biology subjects

Verbeke, R.

Publications and source records attributed to Verbeke, R..

4 recordsLinked to original sources

bioRxiv2025

Lipid-stabilized ICG nanoaggregates for the photodisruption of vitreous opacities

Collagen aggregation in the vitreous is a major cause of vision impairment. Current treatments such as vitrectomy or YAG laser vitreolysis remain limited by invasiveness and safety concerns. In previous work, we introduced a novel approach combining indocyanine green (ICG) with nanosecond laser pulses to achieve photodisruption of collagen aggregates via vapor nanobubbles (VNBs), while using a significantly lower total light dose than that applied in clinical laser vitreolysis. However, despite its clinical approval, free ICG poses a risk of retinal toxicity. In this work, we report the development of ICG nanoaggregates (ICG AGG NPs) stabilized with a minimal amount of a hyaluronic acid (HA)-lipid (DOPE) conjugate designed to limit retinal penetration of ICG while preserving efficient VNB generation and collagen aggregate disruption. We demonstrate that supramolecular aggregation is a key requirement for efficient VNB generation, whereas encapsulation of ICG in conventional liposomes impairs this process. Using a newly established in vitro model for quantifying collagen disruption, we show that ICG AGG NPs significantly enhance photodisruption compared to free ICG. Furthermore, cell toxicity assays on retinal pigment epithelium (RPE) and Muller cells indicate that ICG AGG NPs maintain an acceptable safety profile at therapeutic concentrations. These findings represent the first successful demonstration of dye-loaded nanoparticles enabling efficient VNB-mediated photodisruption of vitreous opacities and highlight the promise of ICG AGG NPs as a safer and more effective alternative to free ICG for floater treatment.

biophysics↗

bioRxiv2025

Development of a General Purpose Targeted LC-MS Method for Accurate Quantification of the SARS-CoV-2 Spike Protein Expression

The COVID-19 pandemic has catalyzed interest in immuno-multiple reaction monitoring (immuno-MRM) methods, with the detection of peptides unique to the nucleocapsid protein in nasopharyngeal swabs. While current applications predominantly focus on disease biomarkers, the pandemic has unveiled new opportunities, namely for the quantification of antigen expression following mRNA vaccination. Here, we present an optimized immuno-MRM method for quantifying SARS-CoV-2 spike protein fusion peptide, SFIEDLLFNK, for several practical applications. The method is versatile, applicable to multiple biological matrices, including plasma, and can be extended to nasopharyngeal swabs. It also offers a high-precision tool for assessing protein expression following plasmid and mRNA transfection. Moreover, in parallel to enabling accurate antigen quantification, the flow-through can be used to determine the proteome profile of the infected cells, providing insights into the intracellular immune response. This dual capability supports the rapid optimization of mRNA vaccines, thereby driving advancements in vaccine development strategies.

immunology↗

bioRxiv2024

TCR transgenic clone selection guided by immune receptor analysis and single cell RNA expression of polyclonal responders

Since the precursor frequency of naive T cells is extremely low, investigating the early steps of antigen-specific T cell activation is challenging. To overcome this detection problem, adoptive transfer of a cohort of T cells purified from T cell receptor (TCR) transgenic donors has been extensively used but is not readily available for emerging pathogens. Constructing TCR transgenic mice from T cell hybridomas is a labor-intensive and sometimes erratic process, since the best clones are selected based on antigen-induced CD69 upregulation or IL-2 production in vitro, and TCR chains are PCR-cloned into expression vectors. Here, we exploited the rapid advances in single cell sequencing and TCR repertoire analysis to select the best clones without hybridoma selection, and generated CORSET8 mice (CORona Spike Epitope specific CD8 T cell), carrying a TCR specific for the Spike protein of SARS-CoV-2. Implementing newly created DALI software for TCR repertoire analysis in single cell analysis enabled the rapid selection of the ideal responder CD8 T cell clone, based on antigen reactivity, proliferation and immunophenotype in vivo. Identified TCR sequences were inserted as synthetic DNA into an expression vector and transgenic CORSET8 donor mice were created. After immunization with Spike/CpG-motifs, mRNA vaccination or SARS-CoV2 infection, CORSET8 T cells strongly proliferated and showed signs of T cell activation. Thus, a combination of TCR repertoire analysis and scRNA immunophenotyping allowed rapid selection of antigen-specific TCR sequences that can be used to generate TCR transgenic mice.

immunology↗

bioRxiv2022

Immunopeptidomics-based design of highly effective mRNA vaccine formulations against Listeria monocytogenes

Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and increasing antibiotic resistance no clinically approved vaccine against Listeria is available. Attenuated Listeria strains offer protection and are tested as antitumor vaccine vectors, but would benefit from a better knowledge on immunodominant vector antigens. To identify novel antigens, we screened for Listeria epitopes presented on the surface of infected human cell lines by mass spectrometry-based immunopeptidomics. In between more than 15,000 human self-peptides, we detected 68 Listeria epitopes from 42 different bacterial proteins, including several known antigens. Peptide epitopes presented on different cell lines were often derived from the same bacterial surface proteins, classifying these antigens as potential vaccine candidates. Encoding these highly presented antigens in lipid nanoparticle mRNA vaccine formulations resulted in specific CD8+ T-cell responses and high levels of protection in vaccination challenge experiments in mice. Our results pave the way for the development of a clinical mRNA vaccine against Listeria and aid to improve attenuated Listeria vaccines and vectors, demonstrating the power of immunopeptidomics for next-generation bacterial vaccine development.

immunology↗