Title of the project: Exploring the interactome and composition of variants of proteasome complexes involved in NeuroDevelopmental Disorders using proteomics and MS approaches

Supervision: Marie-Pierre Bousquet (MCF UPS) / marie-pierre.bousquet@ipbs.fr & Julien Marcoux (CR CNRS) / julien.marcoux@ipbs.fr & Angelique Dafun (PhD student) / angelique.dafun@ipbs.fr Team: «Proteomics and Biological Mass Spectrometry», IPBS CNRS UMR 5089, 205 route de Narbonne, Toulouse.

Background Neurodevelopmental disorders (NDDs) are a major public health concern affecting 3-10% of children worldwide [1]. 10-15% of the genes involved in NDDs encode components of the ubiquitin-proteasome system (UPS) [2]. This pathway is essential for the proteostatic equilibrium of eukaryotic cells. It ensures the specific degradation of denatured proteins that have become non-functional or even toxic. The UPS has been shown essential to neuronal development and function. The recognition of UPS-related NDDs (UPS-NDDs) is fairly recent, and, although about 1,200 genes contribute to the UPS pathway, amongst which many are highly expressed in the brain, only a limited number of UPS-related NDDs (UPS-NDDs) have been identified to date. 150 pathogenic or likely pathogenic variants are associated with NDD in 17 UPS genes and of which 8 genes are proteasomal subunits. Biological samples from 67 families from child and unaffected parents, have been collected by our collaborators at the CHU of Nantes, resulting in a biobank of 140 individuals. Preliminary functional studies from affected individuals T cells showed impaired proteolytic activity and/or assembly of proteasome 26S caused by PSMD12, PSMC3, PSMC5, PSMB3 or PSMB5 variants.

The main objective of this project is to study the consequences of the mutations in NDD-UPS genes on proteasome complexes composition (20S core subunits as well as 20S-associated regulators), proteasome assembly, but also on the proteasome interactome, as these three levels of regulation are known to affect proteasome cellular activity both in physiological and pathological situations [3]. The experiments will involve:  The biochemical purification of endogenous 20S proteasome [4],  The functional characterization of purified proteasome from mutant T cells and their controls,  Their analysis using bottom-up proteomics and top-down proteomics using already established methods [4].

References [1] Ebstein et al. MedRxiv. (2021). [2] Alvarez-Castelao et al. (2015). [3] Coux O. et al. (2020) Adv. Exp. Med. Biol. [4] Fabre et al. (2015) Mol. Sys. Biol. ; Zivkovic D. et al (2022) PNAS.

Techniques used during the internship:

• Protein analysis (SDS-PAGE, Western Blot), Protein complexes purification (immunopurification) and biochemical enrichment (Size Exclusion Chromatography),
• Proteasomal enzymatic activity measurement (Fluorescence-based kinetic assay),
• Bottom-up and top-down mass spectrometry analysis (nanoHPLC ESI-MS/MS on different types of Orbitrap mass spectrometers),
• Mass spectrometry-based differential quantification and statistical analysis.