Biology subjects

De Muynck, L.

Publications and source records attributed to De Muynck, L..

3 recordsLinked to original sources

bioRxiv2025

Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

Targeted protein degradation (TPD) has emerged as a highly promising therapeutic strategy for a wide range of diseases, including cancer and neurodegenerative disorders. The ubiquitin-proteasome system, which is responsible for protein degradation, plays a critical role in this process. Gaining comprehensive insights into the ubiquitylation landscape is essential for the development of selective and efficient targeted protein degradation approaches. Recently, data-independent acquisition (DIA) has gained significant popularity as a robust and unbiased approach for quantitative proteomics. Here, we report a cutting-edge workflow that utilizes diGly antibody-based enrichment followed by an optimized Orbitrap-based DIA method for the identification of ubiquitylated peptides. We identify over 40,000 diGly precursors corresponding to more than 7,000 proteins in a single measurement from cells exposed to a proteasome inhibitor, highlighting an exceptional throughput. By applying our optimized workflow, we successfully identify ubiquitylation sites on substrate proteins with various TPD approaches. Therefore, our workflow holds tremendous potential for rapidly establishing mode of action for various TPD modalities, including PROTACs and molecular glues.

cell biology↗

bioRxiv2025

In vivo validation of novel non-invasive PHP.eB AAVs as a potential therapeutic approach for alpha-Synucleinopathies

Parkinsons disease (PD) is characterized by the accumulation of alpha-synuclein (aSyn) aggregates in specific brain regions, which are likely to be the disease-causing entities. Herein, we employed novel, systemically administered, brain-penetrating viral vectors (PHP.eB AAVs) in order to evaluate the potential therapeutic utility of lowering the endogenous aSyn protein burden in the aSyn pre-formed fibril (PFF)-mouse model. Such vectors expressing short hairpin RNAs or micro RNAs targeting the mouse Snca transcript (or respective scrambled control sequences) were intravenously administered in adult wild-type mice and two weeks later human aSyn PFFs were injected into the dorsal striatum. Following the administration of the Snca-targeting PHP.eB AAVs, a successful widespread viral transduction was achieved throughout the brain, accompanied by an efficient reduction of endogenous aSyn protein levels within transduced dopaminergic neurons. Intrastriatal injection of human aSyn PFFs led to the formation of pSer129-aSyn-rich cytoplasmic inclusions in brain regions connected to the PFF-injection site, nigrostriatal degeneration and relevant behavioral motor deficits, at 2.5 months post PFF-injection. Importantly, PHP.eB AAV-mediated down-regulation of endogenous aSyn reduced the accumulation of pSer129-aSyn+ inclusions, mitigated nigrostriatal degeneration and alleviated motor impairments. Spread of pathology to other brain regions was also attenuated. Overall, such data highlight further the contribution of the intracellular aSyn protein load to the spread of pathology and suggest that this non-invasive delivery strategy holds promise in the research avenues for treating neurodegenerative diseases with widespread pathology, such as Synucleinopathies.

neuroscience↗

bioRxiv2025

Targeted degradation of α-synuclein prevents PFF-induced aggregation

Accumulation of misfolded -synuclein protein in intracellular inclusion bodies of dopaminergic neurons underlies the pathogenesis of Synucleinopathies, which include Parkinsons Disease (PD), Dementia with Lewy Bodies (DLB) and Multiple System Atrophy (MSA). Therefore, clearance of misfolded -synuclein from dopaminergic neurons could in principle offer a therapeutic window for Synucleinopathies, which currently remain untreatable. In this study, we employ the Affinity-directed PROtein Missile (AdPROM) system consisting of the substrate receptor of the CUL2-E3 ligase complex VHL and a nanobody selectively recognising the human -synuclein protein and demonstrate targeted degradation of endogenous -synuclein from human cell lines with remarkable selectivity. We further demonstrate that targeted degradation of -synuclein prevents the pre-formed fibril (PFF)-induced aggregation of -synuclein in primary neurons derived from rats expressing human -synuclein. This approach represents the first demonstration of nanobody-guided proteasomal degradation of all clinically relevant -synuclein variants, highlighting its potential as a therapeutic strategy against Synucleinopathies.

neuroscience↗